Publications by authors named "Jordi García-Fernández"

73 Publications

Analysis of Fox genes in Schmidtea mediterranea reveals new families and a conserved role of Smed-foxO in controlling cell death.

Sci Rep 2021 Feb 3;11(1):2947. Epub 2021 Feb 3.

Department of Genetics, Microbiology and Statistics and Institute of Biomedicine, Universitat de Barcelona, Barcelona, Catalunya, Spain.

The forkhead box (Fox) genes encode transcription factors that control several key aspects of development. Present in the ancestor of all eukaryotes, Fox genes underwent several duplications followed by loss and diversification events that gave rise to the current 25 families. However, few Fox members have been identified from the Lophotrochozoa clade, and specifically from planarians, which are a unique model for understanding development, due to the striking plasticity of the adult. The aim of this study was to identify and perform evolutionary and functional studies of the Fox genes of lophotrochozoan species and, specifically, of the planarian Schmidtea mediterranea. Generating a pipeline for identifying Forkhead domains and using phylogenetics allowed us the phylogenetic reconstruction of Fox genes. We corrected the annotation for misannotated genes and uncovered a new family, the QD, present in all metazoans. According to the new phylogeny, the 27 Fox genes found in Schmidtea mediterranea were classified into 12 families. In Platyhelminthes, family losses were accompanied by extensive gene diversification and the appearance of specific families, the A(P) and N(P). Among the newly identified planarian Fox genes, we found a single copy of foxO, which shows an evolutionary conserved role in controlling cell death.
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http://dx.doi.org/10.1038/s41598-020-80627-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859237PMC
February 2021

The ADAR Family in Amphioxus: RNA Editing and Conserved Orthologous Site Predictions.

Genes (Basel) 2020 Nov 30;11(12). Epub 2020 Nov 30.

Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08007 Barcelona, Spain.

RNA editing is a relatively unexplored process in which transcribed RNA is modified at specific nucleotides before translation, adding another level of regulation of gene expression. Cephalopods use it extensively to increase the regulatory complexity of their nervous systems, and mammals use it too, but less prominently. Nevertheless, little is known about the specifics of RNA editing in most of the other clades and the relevance of RNA editing from an evolutionary perspective remains unknown. Here we analyze a key element of the editing machinery, the ADAR (adenosine deaminase acting on RNA) gene family, in an animal with a key phylogenetic position at the root of chordates: the cephalochordate amphioxus. We show, that as in cephalopods, ADAR genes in amphioxus are predominantly expressed in the nervous system; we identify a number of RNA editing events in amphioxus; and we provide a newly developed method to identify RNA editing events in highly polymorphic genomes using orthology as a guide. Overall, our work lays the foundations for future comparative analysis of RNA-editing events across the metazoan tree.
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http://dx.doi.org/10.3390/genes11121440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761149PMC
November 2020

Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions.

Genome Biol 2020 10 26;21(1):267. Epub 2020 Oct 26.

Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.

Background: One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes at the core of key macroevolutionary changes, their origin and organismal function are generally poorly understood.

Results: Here, we identify several previously unreported transposable element domestication events in the human and mouse genomes. Among them, we find a remarkable molecular domestication that gave rise to a multigenic family in placental mammals, the Bex/Tceal gene cluster. These genes, which act as hub proteins within diverse signaling pathways, have been associated with neurological features of human patients carrying genomic microdeletions in chromosome X. The Bex/Tceal genes display neural-enriched patterns and are differentially expressed in human neurological disorders, such as autism and schizophrenia. Two different murine alleles of the cluster member Bex3 display morphological and physiopathological brain modifications, such as reduced interneuron number and hippocampal electrophysiological imbalance, alterations that translate into distinct behavioral phenotypes.

Conclusions: We provide an in-depth understanding of the emergence of a gene cluster that originated by transposon domestication and gene duplication at the origin of placental mammals, an evolutionary process that transformed a non-functional transposon sequence into novel components of the eutherian genome. These genes were integrated into existing signaling pathways involved in the development, maintenance, and function of the CNS in eutherians. At least one of its members, Bex3, is relevant for higher brain functions in placental mammals and may be involved in human neurological disorders.
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http://dx.doi.org/10.1186/s13059-020-02172-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7586669PMC
October 2020

Mutation of amphioxus Pdx and Cdx demonstrates conserved roles for ParaHox genes in gut, anus and tail patterning.

BMC Biol 2020 06 16;18(1):68. Epub 2020 Jun 16.

Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.

Background: The homeobox genes Pdx and Cdx are widespread across the animal kingdom and part of the small ParaHox gene cluster. Gene expression patterns suggest ancient roles for Pdx and Cdx in patterning the through-gut of bilaterian animals although functional data are available for few lineages. To examine evolutionary conservation of Pdx and Cdx gene functions, we focus on amphioxus, small marine animals that occupy a pivotal position in chordate evolution and in which ParaHox gene clustering was first reported.

Results: Using transcription activator-like effector nucleases (TALENs), we engineer frameshift mutations in the Pdx and Cdx genes of the amphioxus Branchiostoma floridae and establish mutant lines. Homozygous Pdx mutants have a defect in amphioxus endoderm, manifest as loss of a midgut region expressing endogenous GFP. The anus fails to open in homozygous Cdx mutants, which also have defects in posterior body extension and epidermal tail fin development. Treatment with an inverse agonist of retinoic acid (RA) signalling partially rescues the axial and tail fin phenotypes indicating they are caused by increased RA signalling. Gene expression analyses and luciferase assays suggest that posterior RA levels are kept low in wild type animals by a likely direct transcriptional regulation of a Cyp26 gene by Cdx. Transcriptome analysis reveals extensive gene expression changes in mutants, with a disproportionate effect of Pdx and Cdx on gut-enriched genes and a colinear-like effect of Cdx on Hox genes.

Conclusions: These data reveal that amphioxus Pdx and Cdx have roles in specifying middle and posterior cell fates in the endoderm of the gut, roles that likely date to the origin of Bilateria. This conclusion is consistent with these two ParaHox genes playing a role in the origin of the bilaterian through-gut with a distinct anus, morphological innovations that contributed to ecological change in the Cambrian. In addition, we find that amphioxus Cdx promotes body axis extension through a molecular mechanism conserved with vertebrates. The axial extension role for Cdx dates back at least to the origin of Chordata and may have facilitated the evolution of the post-anal tail and active locomotion in chordates.
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http://dx.doi.org/10.1186/s12915-020-00796-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296684PMC
June 2020

Planarian cell number depends on , a novel gene family that balances cell proliferation and cell death.

Development 2020 04 8;147(7). Epub 2020 Apr 8.

Department of Genetics, Microbiology and Statistics and Institute of Biomedicine, Universitat de Barcelona, Barcelona 08028, Catalunya, Spain

Control of cell number is crucial to define body size during animal development and to restrict tumoral transformation. The cell number is determined by the balance between cell proliferation and cell death. Although many genes are known to regulate those processes, the molecular mechanisms underlying the relationship between cell number and body size remain poorly understood. This relationship can be better understood by studying planarians, flatworms that continuously change their body size according to nutrient availability. We identified a novel gene family, (), that consists of and taxonomically restricted genes that control cell proliferation:cell death ratio. Their silencing promotes faster regeneration and increases cell number during homeostasis. Importantly, this increase in cell number leads to an increase in body size only in a nutrient-rich environment; in starved planarians, silencing results in a decrease in cell size and cell accumulation that ultimately produces overgrowths. expression is downregulated after feeding and is related to activity of the insulin/Akt/mTOR network, suggesting that the family evolved in planarians as an additional mechanism for restricting cell number in nutrient-fluctuating environments.
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http://dx.doi.org/10.1242/dev.184044DOI Listing
April 2020

Under pressure: Cerebrospinal fluid contribution to the physiological homeostasis of the eye.

Semin Cell Dev Biol 2020 06 21;102:40-47. Epub 2019 Nov 21.

Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, Barcelona, Spain. Electronic address:

The cerebrospinal fluid (CSF) is a waterly, colorless fluid contained within the brain ventricles and the cranial and spinal subarachnoid spaces. CSF physiological functions range from hydromechanical protection of the central nervous system (CNS) to CNS modulation of developmental processes and regulation of interstitial fluid homeostasis. Optic nerve (ON) is surrounded by CSF circulating in the subarachnoid spaces and is exposed to both CSF (CSFP) and intra ocular (IOP) pressures, which converge at the lamina cribrosa (LC) as two opposite forces. The trans-lamina cribrosa pressure gradient (TLPG) is defined as IOP - CSFP and its alterations (due either to an elevation in IOP or a reduction in ICP) could result in structural damaging of the ON, including glaucomatous changes. The purpose of this review is to update the readers on the CSF contribution in controlling the functions/dysfunctions of ON by regulating homeostasis at LC. We also highlight emerging parallelisms regarding the expression of cilia-related genes in the regulation of common functions of body fluids in both brain and eye structures.
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http://dx.doi.org/10.1016/j.semcdb.2019.11.003DOI Listing
June 2020

Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation.

Biology (Basel) 2019 Aug 24;8(3). Epub 2019 Aug 24.

Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.

Homologous long non-coding RNAs (lncRNAs) are elusive to identify by sequence similarity due to their fast-evolutionary rate. Here we develop LincOFinder, a pipeline that finds conserved intergenic lncRNAs (lincRNAs) between distant related species by means of microsynteny analyses. Using this tool, we have identified 16 bona fide homologous lincRNAs between the amphioxus and human genomes. We characterized and compared in amphioxus and the expression domain of one of them, , located in the anterior part of the Hox cluster. In addition, we analyzed the function of this lincRNA in , showing that its disruption produces a severe headless phenotype, most probably by interfering with the regulation of the Hox cluster. Our results strongly suggest that this lincRNA has probably been regulating the Hox cluster since the early origin of chordates. Our work pioneers the use of syntenic searches to identify non-coding genes over long evolutionary distances and helps to further understand lncRNA evolution.
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http://dx.doi.org/10.3390/biology8030061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6784235PMC
August 2019

Metazoan evolution of glutamate receptors reveals unreported phylogenetic groups and divergent lineage-specific events.

Elife 2018 11 22;7. Epub 2018 Nov 22.

Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain.

Glutamate receptors are divided in two unrelated families: ionotropic (iGluR), driving synaptic transmission, and metabotropic (mGluR), which modulate synaptic strength. The present classification of GluRs is based on vertebrate proteins and has remained unchanged for over two decades. Here we report an exhaustive phylogenetic study of GluRs in metazoans. Importantly, we demonstrate that GluRs have followed different evolutionary histories in separated animal lineages. Our analysis reveals that the present organization of iGluRs into six classes does not capture the full complexity of their evolution. Instead, we propose an organization into four subfamilies and ten classes, four of which have never been previously described. Furthermore, we report a sister class to mGluR classes I-III, class IV. We show that many unreported proteins are expressed in the nervous system, and that new Epsilon receptors form functional ligand-gated ion channels. We propose an updated classification of glutamate receptors that includes our findings.
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http://dx.doi.org/10.7554/eLife.35774DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307864PMC
November 2018

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Nature 2018 12 21;564(7734):64-70. Epub 2018 Nov 21.

Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that-in vertebrates-over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations.
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http://dx.doi.org/10.1038/s41586-018-0734-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6292497PMC
December 2018

Characterization of the TLR Family in and Discovery of a Novel TLR22-Like Involved in dsRNA Recognition in Amphioxus.

Front Immunol 2018 2;9:2525. Epub 2018 Nov 2.

Department of Cell Biology, Animal Physiology and Immunology, Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, Bellaterra, Spain.

Toll-like receptors (TLRs) are important for raising innate immune responses in both invertebrates and vertebrates. Amphioxus belongs to an ancient chordate lineage which shares key features with vertebrates. The genomic research on TLR genes in and reveals the expansion of TLRs in amphioxus. However, the repertoire of TLRs in has not been studied and the functionality of amphioxus TLRs has not been reported. We have identified from transcriptomic data 30 new putative TLRs in and all of them are transcribed in adult amphioxus. Phylogenetic analysis showed that the repertoire of TLRs consists of both non-vertebrate and vertebrate-like TLRs. It also indicated a lineage-specific expansion in orthologous clusters of the vertebrate TLR11 family. We did not detect any representatives of the vertebrate TLR1, TLR3, TLR4, TLR5 and TLR7 families. To gain insight into these TLRs, we studied in depth a particular TLR highly similar to a gene annotated as bbtTLR1. The phylogenetic analysis of this novel BlTLR showed that it clusters with the vertebrate TLR11 family and it might be more related to TLR13 subfamily according to similar domain architecture. Transient and stable expression in HEK293 cells showed that the BlTLR localizes on the plasma membrane, but it did not respond to the most common mammalian TLR ligands. However, when the ectodomain of BlTLR is fused to the TIR domain of human TLR2, the chimeric protein could indeed induce NF-κB transactivation in response to the viral ligand Poly I:C, also indicating that in amphioxus, specific accessory proteins are needed for downstream activation. Based on the phylogenetic, subcellular localization and functional analysis, we propose that the novel BlTLR might be classified as an antiviral receptor sharing at least partly the functions performed by vertebrate TLR22. TLR22 is thought to be viral teleost-specific TLR but here we demonstrate that teleosts and amphioxus TLR22-like probably shared a common ancestor. Additional functional studies with other lancelet TLR genes will enrich our understanding of the immune response in amphioxus and will provide a unique perspective on the evolution of the immune system.
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http://dx.doi.org/10.3389/fimmu.2018.02525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6224433PMC
October 2019

Origin and evolution of the chordate central nervous system: insights from amphioxus genoarchitecture.

Int J Dev Biol 2017 ;61(10-11-12):655-664

Dept. Genetics, Microbiology and Statistics and Institute of Biomedicine (IBUB), Faculty of Biology, University of Barcelona, Barcelona, Spain.

The vertebrate brain is arguably the most complex anatomical and functional structure in nature. During embryonic development, the central nervous system (CNS) undergoes a series of morphogenetic processes that eventually obscure the major axes of the early neural plate to our perception. Notwithstanding this complexity, the "genoarchitecture" of the developing neural tube brings into light homologous regions between brains of different vertebrate species, acting as a molecular barcode of each particular domain. Those homologous regions and their topological inter-relations constitute the ancestral, deeply conserved, bauplan of the vertebrate brain. Remarkably, although simpler, the cephalochordate amphioxus shares multiple features of this bauplan, serving as a privileged reference point to understand the origins of the vertebrate brain. Here, we review the development of the chordate CNS in view of the latest morphological and genoarchitectonic data from amphioxus. This comparison reveals that the amphioxus CNS is far from simple and provides unique insights into the structure of the vertebrate CNS and its evolutionary origins. In particular, we summarize recent research in amphioxus and vertebrates that has challenged views on the major partitions of the vertebrate brain, proposing a novel organization of the chordate CNS bauplan that better reflects developmental and evolutionary data.
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http://dx.doi.org/10.1387/ijdb.170258jgDOI Listing
January 2019

Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes.

Nat Commun 2017 11 27;8(1):1799. Epub 2017 Nov 27.

Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, Barcelona, 08003, Spain.

Epithelial-mesenchymal interactions are crucial for the development of numerous animal structures. Thus, unraveling how molecular tools are recruited in different lineages to control interplays between these tissues is key to understanding morphogenetic evolution. Here, we study Esrp genes, which regulate extensive splicing programs and are essential for mammalian organogenesis. We find that Esrp homologs have been independently recruited for the development of multiple structures across deuterostomes. Although Esrp is involved in a wide variety of ontogenetic processes, our results suggest ancient roles in non-neural ectoderm and regulating specific mesenchymal-to-epithelial transitions in deuterostome ancestors. However, consistent with the extensive rewiring of Esrp-dependent splicing programs between phyla, most developmental defects observed in vertebrate mutants are related to other types of morphogenetic processes. This is likely connected to the origin of an event in Fgfr, which was recruited as an Esrp target in stem chordates and subsequently co-opted into the development of many novel traits in vertebrates.
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http://dx.doi.org/10.1038/s41467-017-01961-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703972PMC
November 2017

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain.

PLoS Biol 2017 04 19;15(4):e2001573. Epub 2017 Apr 19.

Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, Murcia, Spain.

All vertebrate brains develop following a common Bauplan defined by anteroposterior (AP) and dorsoventral (DV) subdivisions, characterized by largely conserved differential expression of gene markers. However, it is still unclear how this Bauplan originated during evolution. We studied the relative expression of 48 genes with key roles in vertebrate neural patterning in a representative amphioxus embryonic stage. Unlike nonchordates, amphioxus develops its central nervous system (CNS) from a neural plate that is homologous to that of vertebrates, allowing direct topological comparisons. The resulting genoarchitectonic model revealed that the amphioxus incipient neural tube is unexpectedly complex, consisting of several AP and DV molecular partitions. Strikingly, comparison with vertebrates indicates that the vertebrate thalamus, pretectum, and midbrain domains jointly correspond to a single amphioxus region, which we termed Di-Mesencephalic primordium (DiMes). This suggests that these domains have a common developmental and evolutionary origin, as supported by functional experiments manipulating secondary organizers in zebrafish and mice.
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http://dx.doi.org/10.1371/journal.pbio.2001573DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5396861PMC
April 2017

Evolutionary development of embryonic cerebrospinal fluid composition and regulation: an open research field with implications for brain development and function.

Fluids Barriers CNS 2016 Mar 15;13. Epub 2016 Mar 15.

Department of Genetics, Microbiology and Statistics, Unit of Biomedical, Evolutionary and Developmental Genetics, Faculty of Biological Sciences, University of Barcelona, Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain.

Within the consolidated field of evolutionary development, there is emerging research on evolutionary aspects of central nervous system development and its implications for adult brain structure and function, including behaviour. The central nervous system is one of the most intriguing systems in complex metazoans, as it controls all body and mind functions. Its failure is responsible for a number of severe and largely incurable diseases, including neurological and neurodegenerative ones. Moreover, the evolution of the nervous system is thought to be a critical step in the adaptive radiation of vertebrates. Brain formation is initiated early during development. Most embryological, genetic and evolutionary studies have focused on brain neurogenesis and regionalisation, including the formation and function of organising centres, and the comparison of homolog gene expression and function among model organisms from different taxa. The architecture of the vertebrate brain primordium also reveals the existence of connected internal cavities, the cephalic vesicles, which in fetuses and adults become the ventricular system of the brain. During embryonic and fetal development, brain cavities and ventricles are filled with a complex, protein-rich fluid called cerebrospinal fluid (CSF). However, CSF has not been widely analysed from either an embryological or evolutionary perspective. Recently, it has been demonstrated in higher vertebrates that embryonic cerebrospinal fluid has key functions in delivering diffusible signals and nutrients to the developing brain, thus contributing to the proliferation, differentiation and survival of neural progenitor cells, and to the expansion and patterning of the brain. Moreover, it has been shown that the composition and homeostasis of CSF are tightly controlled in a time-dependent manner from the closure of the anterior neuropore, just before the initiation of primary neurogenesis, up to the formation of functional choroid plexuses. In this review, we draw together existing literature about the formation, function and homeostatic regulation of embryonic cerebrospinal fluid, from the closure of the anterior neuropore to the formation of functional fetal choroid plexuses, from an evolutionary perspective. The relevance of these processes to the normal functions and diseases of adult brain will also be discussed.
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http://dx.doi.org/10.1186/s12987-016-0029-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793645PMC
March 2016

Embryonic blood-cerebrospinal fluid barrier formation and function.

Front Neurosci 2014 28;8:343. Epub 2014 Oct 28.

Department of Genetics, Faculty of Biological Sciences, University of Barcelona Barcelona, Spain.

During embryonic development and adult life, brain cavities and ventricles are filled with cerebrospinal fluid (CSF). CSF has attracted interest as an active signaling medium that regulates brain development, homeostasis and disease. CSF is a complex protein-rich fluid containing growth factors and signaling molecules that regulate multiple cell functions in the central nervous system (CNS). The composition and substance concentrations of CSF are tightly controlled. In recent years, it has been demonstrated that embryonic CSF (eCSF) has a key function as a fluid pathway for delivering diffusible signals to the developing brain, thus contributing to the proliferation, differentiation and survival of neural progenitor cells, and to the expansion and patterning of the brain. From fetal stages through to adult life, CSF is primarily produced by the choroid plexus. The development and functional activities of the choroid plexus and other blood-brain barrier (BBB) systems in adults and fetuses have been extensively analyzed. However, eCSF production and control of its homeostasis in embryos, from the closure of the anterior neuropore when the brain cavities become physiologically sealed, to the formation of the functional fetal choroid plexus, has not been studied in as much depth and remains open to debate. This review brings together the existing literature, some of which is based on experiments conducted by our research group, concerning the formation and function of a temporary embryonic blood-CSF barrier in the context of the crucial roles played by the molecules in eCSF.
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http://dx.doi.org/10.3389/fnins.2014.00343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211391PMC
November 2014

The embryonic blood-cerebrospinal fluid barrier function before the formation of the fetal choroid plexus: role in cerebrospinal fluid formation and homeostasis.

Croat Med J 2014 Aug;55(4):306-16

David Bueno, Departament de Genética, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Catalonia (Spain),

Cerebrospinal fluid (CSF) has attracted interest as an active signaling milieu that regulates brain development, homeostasis, and course disease. CSF is a nutrient-rich fluid, which also contains growth factors and signaling molecules that regulate multiple cell functions in the central nervous system (CNS). CSF constitution is controlled tightly and constituent concentrations are maintained narrow, depending on developmental stage. From fetal stages to adult life, CSF is produced mainly by the choroid plexus. The development and functional activities of the choroid plexus, and other blood-brain barrier systems in adults, have been extensively analyzed. However, the study of CSF production and homeostasis in embryos from the closure of the anterior neuropore, when the brain cavities become physiologically sealed, to the formation of the functional fetal choroid plexus has been largely neglected. This developmental stage is characterized by tightly controlled morphological and cellular events in the anterior part of the CNS, such as rapid brain anlagen growth and initiation of primary neurogenesis in the neural progenitor cells lining the cavities, events which are driven by specific molecules contained within the embryonic CSF. In this article, we review the existing literature on formation and function of the temporary embryonic blood-CSF barrier, from closure of the anterior neuropore to the formation of functional fetal choroid plexuses, with regard to crucial roles that embryonic CSF plays in neural development.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157384PMC
http://dx.doi.org/10.3325/cmj.2014.55.306DOI Listing
August 2014

The non-canonical Wnt/PKC pathway regulates mitochondrial dynamics through degradation of the arm-like domain-containing protein Alex3.

PLoS One 2013 2;8(7):e67773. Epub 2013 Jul 2.

Department of Cell Biology, University of Barcelona, Barcelona, Spain.

The regulation of mitochondrial dynamics is vital in complex cell types, such as neurons, that transport and localize mitochondria in high energy-demanding cell domains. The Armcx3 gene encodes a mitochondrial-targeted protein (Alex3) that contains several arm-like domains. In a previous study we showed that Alex3 protein regulates mitochondrial aggregation and trafficking. Here we studied the contribution of Wnt proteins to the mitochondrial aggregation and dynamics regulated by Alex3. Overexpression of Alex3 in HEK293 cells caused a marked aggregation of mitochondria, which was attenuated by treatment with several Wnts. We also found that this decrease was caused by Alex3 degradation induced by Wnts. While the Wnt canonical pathway did not alter the pattern of mitochondrial aggregation induced by Alex3, we observed that the Wnt/PKC non-canonical pathway regulated both mitochondrial aggregation and Alex3 protein levels, thereby rendering a mitochondrial phenotype and distribution similar to control patterns. Our data suggest that the Wnt pathway regulates mitochondrial distribution and dynamics through Alex3 protein degradation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067773PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699457PMC
January 2014

Evolution of Hox gene clusters in deuterostomes.

BMC Dev Biol 2013 Jul 2;13:26. Epub 2013 Jul 2.

Hox genes, with their similar roles in animals as evolutionarily distant as humans and flies, have fascinated biologists since their discovery nearly 30 years ago. During the last two decades, reports on Hox genes from a still growing number of eumetazoan species have increased our knowledge on the Hox gene contents of a wide range of animal groups. In this review, we summarize the current Hox inventory among deuterostomes, not only in the well-known teleosts and tetrapods, but also in the earlier vertebrate and invertebrate groups. We draw an updated picture of the ancestral repertoires of the different lineages, a sort of "genome Hox bar-code" for most clades. This scenario allows us to infer differential gene or cluster losses and gains that occurred during deuterostome evolution, which might be causally linked to the morphological changes that led to these widely diverse animal taxa. Finally, we focus on the challenging family of posterior Hox genes, which probably originated through independent tandem duplication events at the origin of each of the ambulacrarian, cephalochordate and vertebrate/urochordate lineages.
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http://dx.doi.org/10.1186/1471-213X-13-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707753PMC
July 2013

Amphioxus makes the cut-Again.

Commun Integr Biol 2012 Sep;5(5):499-502

Centre for Organismal Studies; University of Heidelberg; Heidelberg, Germany ; CNRS; UMR7232; Universite Pierre et Marie Curie Paris 06; Observatoire Oceanologique; Banyuls-sur-Mer; Paris, France ; Department de Genètica; Facultat de Biologia; Universitat de Barcelona; Barcelona, Spain.

The cephalochordate amphioxus is now established as an important model system for understanding the evolution of vertebrate novelties from an invertebrate chordate ancestor. It is also emerging as a serious candidate for studies of organ regeneration. We extend here our previous observations on the European amphioxus´ extensive adult regenerative capacity. The expression of Wnt5 and the presence of β-catenin protein in the early bud-stage blastema support a role for Wnt signaling during tail regeneration in amphioxus. We also present data showing that Branchiostoma lanceolatum continues to regenerate well after repeated amputation of the post-anal tail. These results are discussed in relation to vertebrate regeneration and other stem cell systems, and in the context of regeneration decline with aging.
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http://dx.doi.org/10.4161/cib.21075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502216PMC
September 2012

CERKL knockdown causes retinal degeneration in zebrafish.

PLoS One 2013 9;8(5):e64048. Epub 2013 May 9.

Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.

The human CERKL gene is responsible for common and severe forms of retinal dystrophies. Despite intense in vitro studies at the molecular and cellular level and in vivo analyses of the retina of murine knockout models, CERKL function remains unknown. In this study, we aimed to approach the developmental and functional features of cerkl in Danio rerio within an Evo-Devo framework. We show that gene expression increases from early developmental stages until the formation of the retina in the optic cup. Unlike the high mRNA-CERKL isoform multiplicity shown in mammals, the moderate transcriptional complexity in fish facilitates phenotypic studies derived from gene silencing. Moreover, of relevance to pathogenicity, teleost CERKL shares the two main human protein isoforms. Morpholino injection has been used to generate a cerkl knockdown zebrafish model. The morphant phenotype results in abnormal eye development with lamination defects, failure to develop photoreceptor outer segments, increased apoptosis of retinal cells and small eyes. Our data support that zebrafish Cerkl does not interfere with proliferation and neural differentiation during early developmental stages but is relevant for survival and protection of the retinal tissue. Overall, we propose that this zebrafish model is a powerful tool to unveil CERKL contribution to human retinal degeneration.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064048PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650063PMC
December 2013

Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates.

Semin Cell Dev Biol 2013 Feb 3;24(2):83-94. Epub 2013 Jan 3.

Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain.

The study of the evolutionary origin of vertebrates has been linked to the study of genome duplications since Susumo Ohno suggested that the successful diversification of vertebrate innovations was facilitated by two rounds of whole-genome duplication (2R-WGD) in the stem vertebrate. Since then, studies on the functional evolution of many genes duplicated in the vertebrate lineage have provided the grounds to support experimentally this link. This article reviews cases of gene duplications derived either from the 2R-WGD or from local gene duplication events in vertebrates, analyzing their impact on the evolution of developmental innovations. We analyze how gene regulatory networks can be rewired by the activity of transposable elements after genome duplications, discuss how different mechanisms of duplication might affect the fate of duplicated genes, and how the loss of gene duplicates might influence the fate of surviving paralogs. We also discuss the evolutionary relationships between gene duplication and alternative splicing, in particular in the vertebrate lineage. Finally, we discuss the role that the 2R-WGD might have played in the evolution of vertebrate developmental gene networks, paying special attention to those related to vertebrate key features such as neural crest cells, placodes, and the complex tripartite brain. In this context, we argue that current evidences points that the 2R-WGD may not be linked to the origin of vertebrate innovations, but to their subsequent diversification in a broad variety of complex structures and functions that facilitated the successful transition from peaceful filter-feeding non-vertebrate ancestors to voracious vertebrate predators.
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http://dx.doi.org/10.1016/j.semcdb.2012.12.008DOI Listing
February 2013

The evolutionary origins of chordate hematopoiesis and vertebrate endothelia.

Dev Biol 2013 Mar 27;375(2):182-92. Epub 2012 Nov 27.

Departament de Genètica and Institut de Biomedicina (IBUB), University of Barcelona, Av. Diagonal, 643, 08028 Barcelona, Spain.

The vertebrate circulatory system is the most complex vascular system among those of metazoans, with key innovations including a multi-chambered heart and highly specialized blood cells. Invertebrate vessels, on the other hand, consist of hemal spaces between the basal laminae of epithelia. How the evolutionary transition from an invertebrate-type system to the complex vertebrate one occurred is, however, poorly understood. We investigate here the development of the cardiovascular system of the cephalochordate amphioxus Branchiostoma lanceolatum in order to gain insight into the origin of the vertebrate cardiovascular system. The cardiac markers Hand, Csx (Nkx2-5) and Tbx4/5 reveal a broad cardiac-like domain in amphioxus; such a decentralized organization during development parallels that seen in the adult anatomy. Our data therefore support the hypothesis that amphioxus never possessed a proper heart, even transiently during development. We also define a putative hematopoietic domain, supported by the expression of the hematopoietic markers Scl and Pdvegfr. We show that this area is closed to the dorsal aorta anlages, partially linked to excretory tissues, and that its development is regulated by retinoic acid, thus recalling the aorta-gonads-mesonephros (AGM) area of vertebrates. This region probably produces Pdvegfr+ hemal cells, with an important role in amphioxus vessel formation, since treatments with an inhibitor of PDGFR/VEGFR lead to a decrease of Laminin in the basal laminae of developing vessels. Our results point to a chordate origin of hematopoiesis in an AGM-like area from where hemal Pdvegfr+ cells are produced. These Pdvegfr+ cells probably resemble the ancestral chordate blood cells from which the vertebrate endothelium later originated.
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http://dx.doi.org/10.1016/j.ydbio.2012.11.015DOI Listing
March 2013

Broken colinearity of the amphioxus Hox cluster.

Evodevo 2012 Dec 3;3(1):28. Epub 2012 Dec 3.

Departament de Genètica and Institut de Biomedicina (IBUB), University of Barcelona, Av, Diagonal, 643, Barcelona, 08028, Spain.

Unlabelled:

Background: In most eumetazoans studied so far, Hox genes determine the identity of structures along the main body axis. They are usually linked in genomic clusters and, in the case of the vertebrate embryo, are expressed with spatial and temporal colinearity. Outside vertebrates, temporal colinearity has been reported in the cephalochordate amphioxus (the least derived living relative of the chordate ancestor) but only for anterior and central genes, namely Hox1 to Hox4 and Hox6. However, most of the Hox gene expression patterns in amphioxus have not been reported. To gain global insights into the evolution of Hox clusters in chordates, we investigated a more extended expression profile of amphioxus Hox genes.

Results: Here we report an extended expression profile of the European amphioxus Branchiostoma lanceolatum Hox genes and describe that all Hox genes, except Hox13, are expressed during development. Interestingly, we report the breaking of both spatial and temporal colinearity for at least Hox6 and Hox14, which thus have escaped from the classical Hox code concept. We show a previously unidentified Hox6 expression pattern and a faint expression for posterior Hox genes in structures such as the posterior mesoderm, notochord, and hindgut. Unexpectedly, we found that amphioxus Hox14 had the most divergent expression pattern. This gene is expressed in the anterior cerebral vesicle and pharyngeal endoderm. Amphioxus Hox14 expression represents the first report of Hox gene expression in the most anterior part of the central nervous system. Nevertheless, despite these divergent expression patterns, amphioxus Hox6 and Hox14 seem to be still regulated by retinoic acid.

Conclusions: Escape from colinearity by Hox genes is not unusual in either vertebrates or amphioxus and we suggest that those genes escaping from it are probably associated with the patterning of lineage-specific morphological traits, requiring the loss of those developmental constraints that kept them colinear.
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http://dx.doi.org/10.1186/2041-9139-3-28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3534614PMC
December 2012

Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties.

Sci Rep 2012 31;2:433. Epub 2012 May 31.

Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.

The origin and evolution of the complex regulatory landscapes of some vertebrate developmental genes, often spanning hundreds of Kbp and including neighboring genes, remain poorly understood. The Sonic Hedgehog (Shh) genomic regulatory block (GRB) is one of the best functionally characterized examples, with several discrete enhancers reported within its introns, vast upstream gene-free region and neighboring genes (Lmbr1 and Rnf32). To investigate the origin and evolution of this GRB, we sequenced and characterized the Hedgehog (Hh) loci from three invertebrate chordate amphioxus species, which share several early expression domains with Shh. Using phylogenetic footprinting within and between chordate lineages, and reporter assays in zebrafish probing >30 Kbp of amphioxus Hh, we report large sequence and functional divergence between both groups. In addition, we show that the linkage of Shh to Lmbr1 and Rnf32, necessary for the unique gnatostomate-specific Shh limb expression, is a vertebrate novelty occurred between the two whole-genome duplications.
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http://dx.doi.org/10.1038/srep00433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3364491PMC
February 2013

The Eutherian Armcx genes regulate mitochondrial trafficking in neurons and interact with Miro and Trak2.

Nat Commun 2012 May 8;3:814. Epub 2012 May 8.

Developmental Neurobiology and Regeneration Lab, IRB Barcelona, Parc Cientific de Barcelona, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED, ISCIII), Department of Cell Biology, University of Barcelona, Barcelona E-08028, Spain.

Brain function requires neuronal activity-dependent energy consumption. Neuronal energy supply is controlled by molecular mechanisms that regulate mitochondrial dynamics, including Kinesin motors and Mitofusins, Miro1-2 and Trak2 proteins. Here we show a new protein family that localizes to the mitochondria and controls mitochondrial dynamics. This family of proteins is encoded by an array of armadillo (Arm) repeat-containing genes located on the X chromosome. The Armcx cluster is unique to Eutherian mammals and evolved from a single ancestor gene (Armc10). We show that these genes are highly expressed in the developing and adult nervous system. Furthermore, we demonstrate that Armcx3 expression levels regulate mitochondrial dynamics and trafficking in neurons, and that Alex3 interacts with the Kinesin/Miro/Trak2 complex in a Ca(2+)-dependent manner. Our data provide evidence of a new Eutherian-specific family of mitochondrial proteins that controls mitochondrial dynamics and indicate that this key process is differentially regulated in the brain of higher vertebrates.
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http://dx.doi.org/10.1038/ncomms1829DOI Listing
May 2012

Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1.

RNA Biol 2012 Jan 1;9(1):12-21. Epub 2012 Jan 1.

Departament de Genètica, Facultat de Biología, Universitat de Barcelona, Barcelona, Spain.

The structural complexity of the vertebrate brain is mirrored by its unparalleled transcriptome complexity. In particular, two post-transcriptional processes, alternative splicing and RNA editing, greatly diversify brain transcriptomes. Here we report a close connection between these two processes: we show A-to-I RNA editing in Nova1, a key brain-specific regulator of alternative splicing. Nova1 editing levels increase during embryonic development in mouse and chicken brains and show significant variation across postnatal brain regions. Evolutionary conservation of both editing and editing-associated RNA secondary structure of the Nova1 mRNA for 300 million years attests to the functional importance of Nova1 editing. Using a combination of different assays in human HEK293T cell lines, we report a novel post-translational role for this RNA editing. Whereas functional assays showed no effect of RNA editing on the regulatory splicing activity of the encoded proteins, we found evidence that edited forms exhibit reduced proteasome targeting and increased protein half-life. In addition, we found evidence for similar regulation of protein half-life by an evolutionarily conserved alternative splicing event in Nova1. These results open new venues of research on the multi-level integration of gene expression by: (1) revealing the novel role of RNA editing in regulating protein stability, and (2) establishing protein stability as a new target of multifaceted regulation.
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http://dx.doi.org/10.4161/rna.9.1.18387DOI Listing
January 2012

An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement.

Genome Res 2012 Apr 10;22(4):642-55. Epub 2012 Jan 10.

Departament de Genètica, Facultat de Biologia, Universitat de Barcelona 08028, Barcelona, Spain.

Developmental genes are regulated by complex, distantly located cis-regulatory modules (CRMs), often forming genomic regulatory blocks (GRBs) that are conserved among vertebrates and among insects. We have investigated GRBs associated with Iroquois homeobox genes in 39 metazoans. Despite 600 million years of independent evolution, Iroquois genes are linked to ankyrin-repeat-containing Sowah genes in nearly all studied bilaterians. We show that Iroquois-specific CRMs populate the Sowah locus, suggesting that regulatory constraints underlie the maintenance of the Iroquois-Sowah syntenic block. Surprisingly, tetrapod Sowah orthologs are intronless and not associated with Iroquois; however, teleost and elephant shark data demonstrate that this is a derived feature, and that many Iroquois-CRMs were ancestrally located within Sowah introns. Retroposition, gene, and genome duplication have allowed selective elimination of Sowah exons from the Iroquois regulatory landscape while keeping associated CRMs, resulting in large associated gene deserts. These results highlight the importance of CRMs in imposing constraints to genome architecture, even across large phylogenetic distances, and of gene duplication-mediated genetic redundancy to disentangle these constraints, increasing genomic plasticity.
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http://dx.doi.org/10.1101/gr.132233.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317147PMC
April 2012

Vertebrate-like regeneration in the invertebrate chordate amphioxus.

Proc Natl Acad Sci U S A 2012 Jan 27;109(2):517-22. Epub 2011 Dec 27.

Observatoire Océanologique de Banyuls-sur-Mer, Centre National de la Recherche Scientifique and Université Pierre et Marie Curie Paris VI, F-66650 Banyus-sur-Mer, France.

An important question in biology is why some animals are able to regenerate, whereas others are not. The basal chordate amphioxus is uniquely positioned to address the evolution of regeneration. We report here the high regeneration potential of the European amphioxus Branchiostoma lanceolatum. Adults regenerate both anterior and posterior structures, including neural tube, notochord, fin, and muscle. Development of a classifier based on tail regeneration profiles predicts the assignment of young and old adults to their own class with >94% accuracy. The process involves loss of differentiated characteristics, formation of an msx-expressing blastema, and neurogenesis. Moreover, regeneration is linked to the activation of satellite-like Pax3/7 progenitor cells, the extent of which declines with size and age. Our results provide a framework for understanding the evolution and diversity of regeneration mechanisms in vertebrates.
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http://dx.doi.org/10.1073/pnas.1100045109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258630PMC
January 2012

Transphyletic conservation of developmental regulatory state in animal evolution.

Proc Natl Acad Sci U S A 2011 Aug 15;108(34):14186-91. Epub 2011 Aug 15.

Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Cientificas - Universidad Pablo de Olavide, E-41013 Sevilla, Spain.

Specific regulatory states, i.e., sets of expressed transcription factors, define the gene expression capabilities of cells in animal development. Here we explore the functional significance of an unprecedented example of regulatory state conservation from the cnidarian Nematostella to Drosophila, sea urchin, fish, and mammals. Our probe is a deeply conserved cis-regulatory DNA module of the SRY-box B2 (soxB2), recognizable at the sequence level across many phyla. Transphyletic cis-regulatory DNA transfer experiments reveal that the plesiomorphic control function of this module may have been to respond to a regulatory state associated with neuronal differentiation. By introducing expression constructs driven by this module from any phyletic source into the genomes of diverse developing animals, we discover that the regulatory state to which it responds is used at different levels of the neurogenic developmental process, including patterning and development of the vertebrate forebrain and neurogenesis in the Drosophila optic lobe and brain. The regulatory state recognized by the conserved DNA sequence may have been redeployed to different levels of the developmental regulatory program during evolution of complex central nervous systems.
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http://dx.doi.org/10.1073/pnas.1109037108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161536PMC
August 2011

Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures.

Genome Biol Evol 2011 16;3:551-64. Epub 2011 Jun 16.

Department of Genetics, School of Biology, University of Barcelona, Barcelona, Spain.

Organisms show striking differences in genome structure; however, the functional implications and fundamental forces that govern these differences remain obscure. The intron-exon organization of nuclear genes is involved in a particularly large variety of structures and functional roles. We performed a 22-species study of Meis/hth genes, intron-rich homeodomain-containing transcription factors involved in a wide range of developmental processes. Our study revealed three surprising results that suggest important and very different functions for Meis intron-exon structures. First, we find unexpected conservation across species of intron positions and lengths along most of the Meis locus. This contrasts with the high degree of structural divergence found in genome-wide studies and may attest to conserved regulatory elements residing within these conserved introns. Second, we find very different evolutionary histories for the 5' and 3' regions of the gene. The 5'-most 10 exons, which encode the highly conserved Meis domain and homeodomain, show striking conservation. By contrast, the 3' of the gene, which encodes several domains implicated in transcriptional activation and response to cell signaling, shows a remarkably active evolutionary history, with diverse isoforms and frequent creation and loss of new exons and splice sites. This region-specific diversity suggests evolutionary "tinkering," with alternative splicing allowing for more subtle regulation of protein function. Third, we find a large number of cases of convergent evolution in the 3' region, including 1) parallel losses of ancestral coding sequence, 2) parallel gains of external and internal splice sites, and 3) recurrent truncation of C-terminal coding regions. These results attest to the importance of locus-specific splicing functions in differences in structural evolution across genes, as well as to commonalities of forces shaping the evolution of individual genes along different lineages.
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http://dx.doi.org/10.1093/gbe/evr056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140891PMC
October 2011