Publications by authors named "René Dréos"

23 Publications

  • Page 1 of 1

Low expression of the PPARγ-regulated gene thioredoxin-interacting protein accompanies human melanoma progression and promotes experimental lung metastases.

Sci Rep 2021 Apr 12;11(1):7847. Epub 2021 Apr 12.

Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland.

The thioredoxin system plays key roles in regulating cancer cell malignancy. Here we identify the Thioredoxin-interacting protein (TXNIP) as a gene, which expression is regulated by PPARγ in melanoma cells. We show that high TXNIP expression levels associate with benign melanocytic lesions, with tumor regression in patients on MAP kinase targeted therapy, with decreased proliferation in patients' melanoma biopsies, and with cell cycle arrest in human melanoma cell lines. In contrast, reduced TXNIP expression associates with advanced melanoma and with disease progression in patients. TXNIP depletion in human melanoma cells altered the expression of integrin beta-3 and the localization of the integrin alpha-v/beta-3 dimer at their surface. Moreover, TXNIP depletion affected human melanoma cell motility and improved their capacity to colonize mouse lungs in an in vivo assay. This study establishes TXNIP as a PPARγ-regulated gene in melanoma cells, thereby suggesting a link between these two proteins both involved in the regulation of cancer and of energy metabolism. It also reveals that the decrease in TXNIP expression, which is observed in advanced patient tumors, likely favors lung metastatic seeding of malignant cells.
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http://dx.doi.org/10.1038/s41598-021-86329-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042115PMC
April 2021

Jasmonate biosynthesis arising from altered cell walls is prompted by turgor-driven mechanical compression.

Sci Adv 2021 Feb 10;7(7). Epub 2021 Feb 10.

Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany.

Despite the vital roles of jasmonoyl-isoleucine (JA-Ile) in governing plant growth and environmental acclimation, it remains unclear what intracellular processes lead to its induction. Here, we provide compelling genetic evidence that mechanical and osmotic regulation of turgor pressure represents a key elicitor of JA-Ile biosynthesis. After identifying cell wall mutant alleles in () with elevated JA-Ile in seedling roots, we found that ectopic JA-Ile resulted from cell nonautonomous signals deriving from enlarged cortex cells compressing inner tissues and stimulating JA-Ile production. Restoring cortex cell size by cell type-specific KOR1 complementation, by isolating a genetic suppressor, and by lowering turgor pressure with hyperosmotic treatments abolished JA-Ile signaling. Conversely, hypoosmotic treatment activated JA-Ile signaling in wild-type plants. Furthermore, constitutive JA-Ile levels guided mutant roots toward greater water availability. Collectively, these findings enhance our understanding on JA-Ile biosynthesis initiation and reveal a previously undescribed role of JA-Ile in orchestrating environmental resilience.
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http://dx.doi.org/10.1126/sciadv.abf0356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875531PMC
February 2021

Translation is required for miRNA-dependent decay of endogenous transcripts.

EMBO J 2021 Feb 10;40(3):e104569. Epub 2020 Dec 10.

Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.

Post-transcriptional repression of gene expression by miRNAs occurs through transcript destabilization or translation inhibition. mRNA decay is known to account for most miRNA-dependent repression. However, because transcript decay occurs co-translationally, whether target translation is a requirement for miRNA-dependent transcript destabilization remains unknown. To decouple these two molecular processes, we used cytosolic long noncoding RNAs (lncRNAs) as models for endogenous transcripts that are not translated. We show that, despite interacting with the miRNA-loaded RNA-induced silencing complex, the steady-state abundance and decay rates of these transcripts are minimally affected by miRNA loss. To further validate the apparent requirement of translation for miRNA-dependent decay, we fused two lncRNA candidates to the 3'-end of a protein-coding gene reporter and found this results in their miRNA-dependent destabilization. Further analysis revealed that the few natural lncRNAs whose levels are regulated by miRNAs in mESCs tend to associate with translating ribosomes, and possibly represent misannotated micropeptides, further substantiating the necessity of target translation for miRNA-dependent transcript decay. In summary, our analyses suggest that translation is required for miRNA-dependent transcript destabilization, and demonstrate that the levels of coding and noncoding transcripts are differently affected by miRNAs.
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http://dx.doi.org/10.15252/embj.2020104569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7849302PMC
February 2021

Readthrough of stop codons under limiting ABCE1 concentration involves frameshifting and inhibits nonsense-mediated mRNA decay.

Nucleic Acids Res 2020 10;48(18):10259-10279

Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.

To gain insight into the mechanistic link between translation termination and nonsense-mediated mRNA decay (NMD), we depleted the ribosome recycling factor ABCE1 in human cells, resulting in an upregulation of NMD-sensitive mRNAs. Suppression of NMD on these mRNAs occurs prior to their SMG6-mediated endonucleolytic cleavage. ABCE1 depletion caused ribosome stalling at termination codons (TCs) and increased ribosome occupancy in 3' UTRs, implying enhanced TC readthrough. ABCE1 knockdown indeed increased the rate of readthrough and continuation of translation in different reading frames, providing a possible explanation for the observed NMD inhibition, since enhanced readthrough displaces NMD activating proteins from the 3' UTR. Our results indicate that stalling at TCs triggers ribosome collisions and activates ribosome quality control. Collectively, we show that improper translation termination can lead to readthrough of the TC, presumably due to ribosome collisions pushing the stalled ribosomes into the 3' UTR, where it can resume translation in-frame as well as out-of-frame.
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http://dx.doi.org/10.1093/nar/gkaa758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544199PMC
October 2020

Human NMD ensues independently of stable ribosome stalling.

Nat Commun 2020 08 17;11(1):4134. Epub 2020 Aug 17.

Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland.

Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway that is important for the elimination of faulty, and the regulation of normal, mRNAs. The molecular details of the early steps in NMD are not fully understood but previous work suggests that NMD activation occurs as a consequence of ribosome stalling at the termination codon (TC). To test this hypothesis, we established an in vitro translation-coupled toeprinting assay based on lysates from human cells that allows monitoring of ribosome occupancy at the TC of reporter mRNAs. In contrast to the prevailing NMD model, our in vitro system reveals similar ribosomal occupancy at the stop codons of NMD-sensitive and NMD-insensitive reporter mRNAs. Moreover, ribosome profiling reveals a similar density of ribosomes at the TC of endogenous NMD-sensitive and NMD-insensitive mRNAs in vivo. Together, these data show that NMD activation is not accompanied by stable stalling of ribosomes at TCs.
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http://dx.doi.org/10.1038/s41467-020-17974-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431590PMC
August 2020

Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing.

Genome Res 2020 07 23;30(7):985-999. Epub 2020 Jul 23.

Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.

Translation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of nonuniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ∼10% of translating ribosomes in the disome state. A distinct class of pause sites is indicative of deterministic pausing signals. Pause site association with specific amino acids, peptide motifs, and nascent polypeptide structure is suggestive of programmed pausing as a widespread mechanism associated with protein folding. Evolutionary conservation at disome sites indicates functional relevance of translational pausing. Collectively, our disome profiling approach allows unique insights into gene regulation occurring at the step of translation elongation.
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http://dx.doi.org/10.1101/gr.257741.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397865PMC
July 2020

CDK7 Mediates the Beta-Adrenergic Signaling in Thermogenic Brown and White Adipose Tissues.

iScience 2020 Jun 15;23(6):101163. Epub 2020 May 15.

Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Institut National de la Santé et de la Recherche Médicale (Inserm), Languedoc Roussillon, France. Electronic address:

Cyclin-dependent kinases (CDKs) are emerging regulators of adipose tissue metabolism. Here we aimed to explore the role of CDK7 in thermogenic fat. We found that CDK7 brown adipose tissue (BAT)-specific knockout mice (Cdk7) have decreased BAT mass and impaired β3-adrenergic signaling and develop hypothermia upon cold exposure. We found that loss of CDK7 in BAT disrupts the induction of thermogenic genes in response to cold. However, Cdk7 mice do not show systemic metabolic dysfunction. Increased expression of genes of the creatine metabolism compensates for the heat generation in the BAT of Cdk7 mice in response to cold. Finally, we show that CDK7 is required for beta 3-adrenergic agonist-induced browning of white adipose tissue (WAT). Indeed, Cdk7 ablation in all adipose tissues (Cdk7) has impaired browning in WAT. Together, our results demonstrate that CDK7 is an important mediator of beta-adrenergic signaling in thermogenic brown and beige fat.
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http://dx.doi.org/10.1016/j.isci.2020.101163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7256631PMC
June 2020

A Reservoir of Pluripotent Phloem Cells Safeguards the Linear Developmental Trajectory of Protophloem Sieve Elements.

Curr Biol 2020 03 6;30(5):755-766.e4. Epub 2020 Feb 6.

Group of Plant Vascular Development, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland. Electronic address:

Plant cells can change their identity based on positional information, a mechanism that confers developmental plasticity to plants. This ability, common to distinct multicellular organisms, is particularly relevant for plant phloem cells. Protophloem sieve elements (PSEs), one type of phloem conductive cells, act as the main organizers of the phloem pole, which comprises four distinct cell files organized in a conserved pattern. Here, we report how Arabidopsis roots generate a reservoir of meristematic phloem cells competent to swap their cell identities. Although PSE misspecification induces cell identity hybridism, the activity of RECEPTOR LIKE PROTEIN KINASE 2 (RPK2) by perceiving CLE45 peptide contributes to restrict PSE identity to the PSE position. By maintaining a spatiotemporal window when PSE and PSE-adjacent cells' identities are interchangeable, CLE45 signaling endows phloem cells with the competence to re-pattern a functional phloem pole when protophloem fails to form.
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http://dx.doi.org/10.1016/j.cub.2019.12.043DOI Listing
March 2020

EPD in 2020: enhanced data visualization and extension to ncRNA promoters.

Nucleic Acids Res 2020 01;48(D1):D65-D69

Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats (FASTA, BED, CSV) for subsequent analysis with other tools. Recent work has focused on the improvement of the EPD promoter viewers, which use the UCSC Genome Browser as visualization platform. Thousands of high-resolution tracks for CAGE, ChIP-seq and similar data have been generated and organized into public track hubs. Customized, reproducible promoter views, combining EPD-supplied tracks with native UCSC Genome Browser tracks, can be accessed from the organism summary pages or from individual promoter entries. Moreover, thanks to recent improvements and stabilization of ncRNA gene catalogs, we were able to release promoter collections for certain classes of ncRNAs from human and mouse. Furthermore, we developed automatic computational protocols to assign orphan TSS peaks to downstream genes based on paired-end (RAMPAGE) TSS mapping data, which enabled us to add nearly 9000 new entries to the human promoter collection. Since our last article in this journal, EPD was extended to five more model organisms: rhesus monkey, rat, dog, chicken and Plasmodium falciparum.
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http://dx.doi.org/10.1093/nar/gkz1014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145694PMC
January 2020

Opposing chromatin remodelers control transcription initiation frequency and start site selection.

Nat Struct Mol Biol 2019 08 5;26(8):744-754. Epub 2019 Aug 5.

Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland.

Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome occupancy following rapid remodeler depletion, we investigated the interplay between these enzymes and their impact on transcription in yeast. We show that many promoters are affected by multiple CRs that operate in concert or in opposition to position the key transcription start site (TSS)-associated +1 nucleosome. We also show that nucleosome movement after CR inactivation usually results from the activity of another CR and that in the absence of any remodeling activity, +1 nucleosomes largely maintain their positions. Finally, we present functional assays suggesting that +1 nucleosome positioning often reflects a trade-off between maximizing RNA polymerase recruitment and minimizing transcription initiation at incorrect sites. Our results provide a detailed picture of fundamental mechanisms linking promoter nucleosome architecture to transcription initiation.
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http://dx.doi.org/10.1038/s41594-019-0273-3DOI Listing
August 2019

MGA repository: a curated data resource for ChIP-seq and other genome annotated data.

Nucleic Acids Res 2018 01;46(D1):D175-D180

Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.

The Mass Genome Annotation (MGA) repository is a resource designed to store published next generation sequencing data and other genome annotation data (such as gene start sites, SNPs, etc.) in a completely standardised format. Each sample has undergone local processing in order the meet the strict MGA format requirements. The original data source, the reformatting procedure and the biological characteristics of the samples are described in an accompanying documentation file manually edited by data curators. 10 model organisms are currently represented: Homo sapiens, Mus musculus, Danio rerio, Drosophila melanogaster, Apis mellifera, Caenorhabditis elegans, Arabidopsis thaliana, Zea mays, Saccharomyces cerevisiae and Schizosaccharomyces pombe. As of today, the resource contains over 24 000 samples. In conjunction with other tools developed by our group (the ChIP-Seq and SSA servers), it allows users to carry out a great variety of analysis task with MGA samples, such as making aggregation plots and heat maps for selected genomic regions, finding peak regions, generating custom tracks for visualizing genomic features in a UCSC genome browser window, or downloading chromatin data in a table format suitable for local processing with more advanced statistical analysis software such as R. Home page: http://ccg.vital-it.ch/mga/.
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http://dx.doi.org/10.1093/nar/gkx995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753388PMC
January 2018

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms.

Nucleic Acids Res 2017 01 28;45(D1):D51-D55. Epub 2016 Nov 28.

Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.

We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next generation sequencing (NGS) data. Thanks to the abundant release of new high-throughput transcript mapping data (CAGE, TSS-seq, GRO-cap) the database could be extended to plant and fungal species. We further report on the expansion of the mass genome annotation (MGA) repository containing promoter-relevant chromatin profiling data and on improvements for the EPD entry viewers. Finally, we present a new data access tool, ChIP-Extract, which enables computational biologists to extract diverse types of promoter-associated data in numerical table formats that are readily imported into statistical analysis platforms such as R.
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http://dx.doi.org/10.1093/nar/gkw1069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210552PMC
January 2017

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

BMC Genomics 2016 11 18;17(1):938. Epub 2016 Nov 18.

School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.

Background: ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data.

Results: Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade.

Conclusions: The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .
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http://dx.doi.org/10.1186/s12864-016-3288-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5116162PMC
November 2016

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters.

PLoS Comput Biol 2016 Oct 7;12(10):e1005144. Epub 2016 Oct 7.

Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.

The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription factors (TFs). However, only a minority of animal promoters contains CPEs. It is still unknown how Pol-II selects the TSS in their absence. Here we present a comparative analysis of promoters' sequence composition and chromatin architecture in five eukaryotic model organisms, which shows the presence of common and unique DNA-encoded features used to organize chromatin. Analysis of Pol-II initiation patterns uncovers that, in the absence of certain CPEs, there is a strong correlation between the spread of initiation and the intensity of the 10 bp periodic signal in the nearest downstream nucleosome. Moreover, promoters' primary and secondary initiation sites show a characteristic 10 bp periodicity in the absence of CPEs. We also show that DNA natural variants in the region immediately downstream the TSS are able to affect both the nucleosome-DNA affinity and Pol-II initiation pattern. These findings support the notion that, in addition to CPEs mediated selection, sequence-induced nucleosome positioning could be a common and conserved mechanism of TSS selection in animals.
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http://dx.doi.org/10.1371/journal.pcbi.1005144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055345PMC
October 2016

Multilayered Organization of Jasmonate Signalling in the Regulation of Root Growth.

PLoS Genet 2015 Jun 12;11(6):e1005300. Epub 2015 Jun 12.

Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland.

Physical damage can strongly affect plant growth, reducing the biomass of developing organs situated at a distance from wounds. These effects, previously studied in leaves, require the activation of jasmonate (JA) signalling. Using a novel assay involving repetitive cotyledon wounding in Arabidopsis seedlings, we uncovered a function of JA in suppressing cell division and elongation in roots. Regulatory JA signalling components were then manipulated to delineate their relative impacts on root growth. The new transcription factor mutant myc2-322B was isolated. In vitro transcription assays and whole-plant approaches revealed that myc2-322B is a dosage-dependent gain-of-function mutant that can amplify JA growth responses. Moreover, myc2-322B displayed extreme hypersensitivity to JA that totally suppressed root elongation. The mutation weakly reduced root growth in undamaged plants but, when the upstream negative regulator NINJA was genetically removed, myc2-322B powerfully repressed root growth through its effects on cell division and cell elongation. Furthermore, in a JA-deficient mutant background, ninja1 myc2-322B still repressed root elongation, indicating that it is possible to generate JA-responses in the absence of JA. We show that NINJA forms a broadly expressed regulatory layer that is required to inhibit JA signalling in the apex of roots grown under basal conditions. By contrast, MYC2, MYC3 and MYC4 displayed cell layer-specific localisations and MYC3 and MYC4 were expressed in mutually exclusive regions. In nature, growing roots are likely subjected to constant mechanical stress during soil penetration that could lead to JA production and subsequent detrimental effects on growth. Our data reveal how distinct negative regulatory layers, including both NINJA-dependent and -independent mechanisms, restrain JA responses to allow normal root growth. Mechanistic insights from this work underline the importance of mapping JA signalling components to specific cell types in order to understand and potentially engineer the growth reduction that follows physical damage.
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http://dx.doi.org/10.1371/journal.pgen.1005300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466561PMC
June 2015

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools.

Nucleic Acids Res 2015 Jan 6;43(Database issue):D92-6. Epub 2014 Nov 6.

Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland

We present an update of EPDNew (http://epd.vital-it.ch), a recently introduced new part of the Eukaryotic Promoter Database (EPD) which has been described in more detail in a previous NAR Database Issue. EPD is an old database of experimentally characterized eukaryotic POL II promoters, which are conceptually defined as transcription initiation sites or regions. EPDnew is a collection of automatically compiled, organism-specific promoter lists complementing the old corpus of manually compiled promoter entries of EPD. This new part is exclusively derived from next generation sequencing data from high-throughput promoter mapping experiments. We report on the recent growth of EPDnew, its extension to additional model organisms and its improved integration with other bioinformatics resources developed by our group, in particular the Signal Search Analysis and ChIP-Seq web servers.
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http://dx.doi.org/10.1093/nar/gku1111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383928PMC
January 2015

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era.

Nucleic Acids Res 2013 Jan 27;41(Database issue):D157-64. Epub 2012 Nov 27.

Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.

The Eukaryotic Promoter Database (EPD), available online at http://epd.vital-it.ch, is a collection of experimentally defined eukaryotic POL II promoters which has been maintained for more than 25 years. A promoter is represented by a single position in the genome, typically the major transcription start site (TSS). EPD primarily serves biologists interested in analysing the motif content, chromatin structure or DNA methylation status of co-regulated promoter subsets. Initially, promoter evidence came from TSS mapping experiments targeted at single genes and published in journal articles. Today, the TSS positions provided by EPD are inferred from next-generation sequencing data distributed in electronic form. Traditionally, EPD has been a high-quality database with low coverage. The focus of recent efforts has been to reach complete gene coverage for important model organisms. To this end, we introduced a new section called EPDnew, which is automatically assembled from multiple, carefully selected input datasets. As another novelty, we started to use chromatin signatures in addition to mRNA 5'tags to locate promoters of weekly expressed genes. Regarding user interfaces, we introduced a new promoter viewer which enables users to explore promoter-defining experimental evidence in a UCSC genome browser window.
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http://dx.doi.org/10.1093/nar/gks1233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531148PMC
January 2013

Genetic and physiological analysis of Rht8 in bread wheat: an alternative source of semi-dwarfism with a reduced sensitivity to brassinosteroids.

J Exp Bot 2012 Jul 12;63(12):4419-36. Epub 2012 Jul 12.

Crop Genetics Department, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH UK.

Over the next decade, wheat grain production must increase to meet the demand of a fast growing human population. One strategy to meet this challenge is to raise wheat productivity by optimizing plant stature. The Reduced height 8 (Rht8) semi-dwarfing gene is one of the few, together with the Green Revolution genes, to reduce stature of wheat (Triticum aestivum L.), and improve lodging resistance, without compromising grain yield. Rht8 is widely used in dry environments such as Mediterranean countries where it increases plant adaptability. With recent climate change, its use could become increasingly important even in more northern latitudes. In the present study, the characterization of Rht8 was furthered. Morphological analyses show that the semi-dwarf phenotype of Rht8 lines is due to shorter internodal segments along the wheat culm, achieved through reduced cell elongation. Physiological experiments show that the reduced cell elongation is not due to defective gibberellin biosynthesis or signalling, but possibly to a reduced sensitivity to brassinosteroids. Using a fine-resolution mapping approach and screening 3104 F(2) individuals of a newly developed mapping population, the Rht8 genetic interval was reduced from 20.5 cM to 1.29 cM. Comparative genomics with model genomes confined the Rht8 syntenic intervals to 3.3 Mb of the short arm of rice chromosome 4, and to 2 Mb of Brachypodium distachyon chromosome 5. The very high resolution potential of the plant material generated is crucial for the eventual cloning of Rht8.
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http://dx.doi.org/10.1093/jxb/ers138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3421992PMC
July 2012

RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription.

Proc Natl Acad Sci U S A 2011 May 2;108(20):8508-13. Epub 2011 May 2.

Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom.

The RNA-binding proteins FCA and FPA were identified based on their repression of the flowering time regulator FLC but have since been shown to have widespread roles in the Arabidopsis thaliana genome. Here, we use whole-genome tiling arrays to show that a wide spectrum of genes and transposable elements are misexpressed in the fca-9 fpa-7 (fcafpa) double mutant at two stages of seedling development. There was a significant bias for misregulated genomic segments mapping to the 3' region of genes. In addition, the double mutant misexpressed a large number of previously unannotated genomic segments corresponding to intergenic regions. We characterized a subset of these misexpressed unannotated segments and established that they resulted from extensive transcriptional read-through, use of downstream polyadenylation sites, and alternative splicing. In some cases, the transcriptional read-through significantly reduced expression of the associated genes. FCA/FPA-dependent changes in DNA methylation were found at several loci, supporting previous associations of FCA/FPA function with chromatin modifications. Our data suggest that FCA and FPA play important roles in the A. thaliana genome in RNA 3' processing and transcription termination, thus limiting intergenic transcription.
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http://dx.doi.org/10.1073/pnas.1105334108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3100917PMC
May 2011

Arabidopsis plant homeodomain finger proteins operate downstream of auxin accumulation in specifying the vasculature and primary root meristem.

Plant J 2009 Aug 24;59(3):426-36. Epub 2009 Mar 24.

John Innes Centre, Norwich Research Park, Norwich, UK.

In Arabidopsis thaliana, auxin is a key regulator of tissue patterning in the developing embryo. We have identified a group of proteins that act downstream of auxin accumulation in auxin-mediated root and vascular development in the embryo. Combined mutations in OBERON1 (OBE1) and OBERON2 (OBE2) give rise to obe1 obe2 double mutant seedlings that closely phenocopy the monopteros (mp) mutant phenotype, with an absence of roots and defective development of the vasculature. We show that, in contrast to the situation in mp mutants, obe1 obe2 double mutant embryos show auxin maxima at the root pole and in the provascular region, and that the SCF(TIR1) pathway, which translates auxin accumulation into transcriptional activation of auxin-responsive genes, remains intact. Although we focus on the impact of obe mutations on aspects of embryo development, the effect of such mutations on a broad range of auxin-related gene expression and the tissue expression patterns of OBE genes in seedlings suggest that OBE proteins have a wider role to play in growth and development. We suggest that OBE1 and OBE2 most likely control the transcription of genes required for auxin responses through the action of their PHD finger domains.
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http://dx.doi.org/10.1111/j.1365-313X.2009.03874.xDOI Listing
August 2009

The cytosolic protein response as a subcomponent of the wider heat shock response in Arabidopsis.

Plant Cell 2009 Feb 24;21(2):642-54. Epub 2009 Feb 24.

John Ines Centre, Colney, Norwich NR4 7UH, United Kingdom.

In common with a range of environmental and biological stresses, heat shock results in the accumulation of misfolded proteins and a collection of downstream consequences for cellular homeostasis and growth. Within this complex array of responses, the sensing of and responses to misfolded proteins in specific subcellular compartments involves specific chaperones, transcriptional regulators, and expression profiles. Using biological (ectopic protein expression and virus infection) and chemical triggers for misfolded protein accumulation, we have profiled the transcriptional features of the response to misfolded protein accumulation in the cytosol (i.e., the cytoplasmic protein response [CPR]) and identified the effects as a subcomponent of the wider effects induced by heat shock. The CPR in Arabidopsis thaliana is associated with the heat shock promoter element and the involvement of specific heat shock factors (HSFs), notably HSFA2, which appears to be regulated by alternative splicing and non-sense-mediated decay. Characterization of Arabidopsis HSFA2 knockout and overexpression lines showed that HSFA2 is one of the regulatory components of the CPR.
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http://dx.doi.org/10.1105/tpc.108.062596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660624PMC
February 2009

High sequence variability of myticin transcripts in hemocytes of immune-stimulated mussels suggests ancient host-pathogen interactions.

Dev Comp Immunol 2008 26;32(3):213-26. Epub 2007 Jun 26.

Department of Biology, University of Trieste, Trieste, Italy.

Small cationic antimicrobial peptides (AMPs) are host defense molecules detected in virtually all groups of organisms. To investigate the immune response mechanisms of Mytilus galloprovincialis, primary and suppression subtractive hybridization libraries were prepared from hemolymph of mussels injected with heat-inactivated bacteria or poly I:C, the latter mimicking viral infection. After DNA sequencing, sequence processing and similarity searching, a remarkable abundance of AMP mRNAs were identified. In detail, 25.9% and 32.4% AMP sequences from mussels infected with bacteria and 43.4% and 40.6% from mussels stimulated with poly I:C were detected by selective amplification of 180 differentially expressed genes and random sequencing of 967 cDNA clones, respectively. The 232 ESTs matching with myticin A and B (Mytilus spp.) displayed considerable sequence variability and revealed a third cluster proposed here as myticin C. Phenetic analysis of the translated myticin ESTs yielded 74 and 25 variants of the precursor and active peptide, respectively, and confirmed the high polymorphism of the new form. Myticin C shows typical features of the CSalphabeta AMP family (eight-cysteine array and secretory signal peptide) as well as amino acid variation, mainly in the anionic C-terminal region. The sequencing of one intronic region from genomic DNA, allowed us to detect 13 variants in 9 individual mussels referring them to one gene only. In addition to hemolymph, myticin C transcripts were detected in various mussel tissues, oocytes and early larval stages. The striking sequence variability and expression levels of myticins in mussels confirm the fundamental role of these natural antibiotics in the ancient host-pathogen interplay of mutual inhibition, evasion and adaptation strategies.
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http://dx.doi.org/10.1016/j.dci.2007.05.008DOI Listing
April 2008

Differential responses of Coffea arabica L. leaves and roots to chemically induced systemic acquired resistance.

Genome 2006 Dec;49(12):1594-605

Department of Biology, University of Trieste, Trieste, Italy.

Coffea arabica is susceptible to several pests and diseases, some of which affect the leaves and roots. Systemic acquired resistance (SAR) is the main defence mechanism activated in plants in response to pathogen attack. Here, we report the effects of benzo(1,2,3)thiadiazole-7-carbothioic acid-S-methyl ester (BTH), a SAR chemical inducer, on the expression profile of C. arabica. Two cDNA libraries were constructed from the mRNA isolated from leaves and embryonic roots to create 1587 nonredundant expressed sequence tags (ESTs). We developed a cDNA microarray containing 1506 ESTs from the leaves and embryonic roots, and 48 NBS-LRR (nucleotide-binding site leucine-rich repeat) gene fragments derived from 2 specific genomic libraries. Competitive hybridization between untreated and BTH-treated leaves resulted in 55 genes that were significantly overexpressed and 16 genes that were significantly underexpressed. In the roots, 37 and 42 genes were over and underexpressed, respectively. A general shift in metabolism from housekeeping to defence occurred in the leaves and roots after BTH treatment. We observed a systemic increase in pathogenesis-related protein synthesis, in the oxidative burst, and in the cell wall strengthening processes. Moreover, responses in the roots and leaves varied significantly.
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http://dx.doi.org/10.1139/g06-125DOI Listing
December 2006