412 results match your criteria Biochimica et biophysica acta. Gene regulatory mechanisms[Journal]


The SAGA continues: The rise of cis- and trans-histone crosstalk pathways.

Biochim Biophys Acta Gene Regul Mech 2020 Jul 6:194600. Epub 2020 Jul 6.

Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, Hansen Life Science Research Building, 201S, University Street, West Lafayette, IN 47907; USA. Electronic address:

Fueled by key technological innovations during the last several decades, chromatin-based research has greatly advanced our mechanistic understanding of how genes are regulated by epigenetic factors and their associated histone-modifying activities. Most notably, the landmark finding that linked histone acetylation by Gcn5 of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex to gene activation ushered in a new area of chromatin research and a realization that histone-modifying activities have integral genome functions. This review will discuss past and recent studies that have shaped our understanding of how the histone-modifying activities of SAGA are regulated by, and modulate the outcomes of, other histone modifications during gene transcription. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194600DOI Listing

Altered expressions and splicing profiles of Acin1 transcripts differentially modulate brown adipogenesis through an alternative splicing mechanism.

Biochim Biophys Acta Gene Regul Mech 2020 Jul 3:194601. Epub 2020 Jul 3.

School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan. Electronic address:

Apoptotic chromatin condensation inducer in the nucleus (also referred as Acin1) was first characterized as an RNA-binding protein involved in apoptosis. In later reports, Acin1 was identified as an auxiliary component of the exon junction complex (EJC) which is assembled throughout pre-messenger RNA splicing. In this study, results of whole-transcriptome analyses revealed reduced expressions and reprogrammed splicing profiles of Acin1 transcripts throughout development of brown adipose tissues (BATs) that execute non-shivering thermogenesis in small rodents and infants by consuming lipids. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194601DOI Listing

RNA and gene control in bacteria.

Biochim Biophys Acta Gene Regul Mech 2020 Jul 1:194602. Epub 2020 Jul 1.

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http://dx.doi.org/10.1016/j.bbagrm.2020.194602DOI Listing

Sp4 controls constitutive expression of neuronal serine racemase and NF-E2-related factor-2 mediates its induction by valproic acid.

Biochim Biophys Acta Gene Regul Mech 2020 Jun 27;1863(9):194597. Epub 2020 Jun 27.

School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, China; State Key Laboratory of Optometry, Ophthalmology, and Visual Science, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China. Electronic address:

Serine racemase (SR) synthesizes l-type serine to its enantimor, d-serine which participates in physiological processes and in pathological conditions. In the central nervous system, SR is highly expressed in neurons and astrocytes but expressed at relatively lower amount in microglia. However, the mechanism by which SR is highly expessed in neurons is hitherto unknown. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194597DOI Listing

Chromatin remodeling and transcription of the TPK1 subunit of PKA during stress in Saccharomyces cerevisiae.

Biochim Biophys Acta Gene Regul Mech 2020 Jun 26;1863(9):194599. Epub 2020 Jun 26.

Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica, Buenos Aires, Argentina; CONICET- Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina. Electronic address:

In response to environmental changes cells rapidly rearrange their gene expression pattern in order to adapt to the new conditions. Chromatin remodeling is critical for this process playing a major role in the induction of genes involved in stress responses. We demonstrated previously that TPK1, encoding one of the catalytic subunits of PKA from Saccharomyces cerevisiae, is upregulated under heat shock. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194599DOI Listing

The emerging roles of GCN5L1 in mitochondrial and vacuolar organelle biology.

Biochim Biophys Acta Gene Regul Mech 2020 Jun 26:194598. Epub 2020 Jun 26.

Cardiovascular Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, 20892, USA. Electronic address:

General control of amino acid synthesis 5 like 1 (GCN5L1) was named due to its loose sequence alignment to GCN5, a catalytic subunit of numerous histone N-acetyltransferase complexes. Further studies show that GCN5L1 has mitochondrial and cytosolic isoforms, although functional-domain sequence alignment and experimental studies show that GCN5L1 itself does not possess intrinsic acetyltransferase activity. Nevertheless, GCN5L1 does support protein acetylation in the mitochondria and cytosol and functions as a subunit of numerous intracellular multiprotein complexes that control intracellular vacuolar organelle positioning and function. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194598DOI Listing

RNA-binding activity and regulatory functions of the emerging sRNA-binding protein ProQ.

Biochim Biophys Acta Gene Regul Mech 2020 Jun 19;1863(9):194596. Epub 2020 Jun 19.

Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, Husargatan 3, S-75124 Uppsala, Sweden.

Regulatory small RNAs (sRNAs) ubiquitously impact bacterial physiology through antisense-mediated control of mRNA translation and stability. In Gram negative bacteria, sRNAs often associate with RNA-binding proteins (RBPs), both to gain cellular stability and to enable regulatory efficiency. The Hfq and CsrA proteins were for long the only known global RBPs implicated in sRNA biology. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194596DOI Listing

Sequential recruitment of the mRNA decay machinery to the iron-regulated protein Cth2 in Saccharomyces cerevisiae.

Biochim Biophys Acta Gene Regul Mech 2020 Jun 19;1863(9):194595. Epub 2020 Jun 19.

Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna (Valencia), Spain. Electronic address:

Post-transcriptional factors importantly contribute to the rapid and coordinated expression of the multiple genes required for the adaptation of living organisms to environmental stresses. In the model eukaryote Saccharomyces cerevisiae, a conserved mRNA-binding protein, known as Cth2, modulates the metabolic response to iron deficiency. Cth2 is a tandem zinc-finger (TZF)-containing protein that co-transcriptionally binds to adenine/uracil-rich elements (ARE) present in the 3'-untranslated region of iron-related mRNAs to promote their turnover. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194595DOI Listing

Novel therapeutic strategies for MLL-rearranged leukemias.

Biochim Biophys Acta Gene Regul Mech 2020 Jun 10;1863(9):194584. Epub 2020 Jun 10.

Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK. Electronic address:

MLL rearrangement is one of the key drivers and generally regarded as an independent poor prognostic marker in acute leukemias. The standard of care for MLL-rearranged (MLL-r) leukemias has remained largely unchanged for the past 50 years despite unsatisfying clinical outcomes, so there is an urgent need for novel therapeutic strategies. An increasing body of evidence demonstrates that a vast number of epigenetic regulators are directly or indirectly involved in MLL-r leukemia, and they are responsible for supporting the aberrant gene expression program mediated by MLL-fusions. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194584DOI Listing
June 2020
6.332 Impact Factor

The Sponge RNAs of bacteria - How to find them and their role in regulating the post-transcriptional network.

Authors:
Emma L Denham

Biochim Biophys Acta Gene Regul Mech 2020 Aug 28;1863(8):194565. Epub 2020 May 28.

University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom. Electronic address:

In bacteria small regulatory RNAs (sRNAs) interact with their mRNA targets through non-consecutive base-pairing. The loose base-pairing specificity allows sRNAs to regulate large numbers of genes, either affecting the stability and/or the translation of mRNAs. Mechanisms enabling post-transcriptional regulation of the sRNAs themselves have also been described involving so-called sponge RNAs. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194565DOI Listing

Cap-independent translation initiation of the unspliced RNA of retroviruses.

Biochim Biophys Acta Gene Regul Mech 2020 May 23;1863(9):194583. Epub 2020 May 23.

Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile. Electronic address:

Retroviruses are a unique family of RNA viruses that utilize a virally encoded reverse transcriptase (RT) to replicate their genomic RNA (gRNA) through a proviral DNA intermediate. The provirus is permanently integrated into the host cell chromosome and is expressed by the host cell transcription, RNA processing, and translation machinery. Retroviral messenger RNAs (mRNAs) entirely resemble a cellular mRNA as they have a 5'cap structure, 5'untranslated region (UTR), an open reading frame (ORF), 3'UTR, and a 3'poly(A) tail. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194583DOI Listing

ABI3 mediated repression of RAV1 gene expression promotes efficient dehydration stress response in Arabidopsis thaliana.

Biochim Biophys Acta Gene Regul Mech 2020 May 19;1863(9):194582. Epub 2020 May 19.

Department of Biotechnology, St. Xavier's College, 30, Mother Teresa Sarani, Kolkata 700016. India. Electronic address:

Dehydration stress response is a complex mechanism in plants involving several factors and hormone signalling pathways. RAV1 is a member of the AP2/ERF family of transcription factors that works in various developmental pathways. Here we show that downregulation of RAV1 gene expression is important for efficient dehydration stress response. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194582DOI Listing

LDB1 and the SWI/SNF complex participate in both transcriptional activation and repression by Caenorhabditis elegans BLIMP1/PRDM1.

Biochim Biophys Acta Gene Regul Mech 2020 May 14;1863(9):194577. Epub 2020 May 14.

Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore. Electronic address:

Transcription factors of the BLIMP1/PRDM1 family are important regulators of development. BLIMP1/PRDM1 can both activate and repress gene expression, however, the mechanism of activation is not well understood. Therefore, we looked for factors involved in gene activation by C. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194577DOI Listing

CREB-binding protein regulates metamorphosis and compound eye development in the yellow fever mosquito, Aedes aegypti.

Biochim Biophys Acta Gene Regul Mech 2020 Aug 7;1863(8):194576. Epub 2020 May 7.

Department of Entomology, University of Kentucky, Lexington, KY 40546, USA. Electronic address:

Juvenile hormones (JH) and ecdysone coordinately regulate metamorphosis in Aedes aegypti. We studied the function of an epigenetic regulator and multifunctional transactivator, CREB binding protein (CBP) in A. aegypti. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7339023PMC

The MLL/SET family and haematopoiesis.

Biochim Biophys Acta Gene Regul Mech 2020 Aug 7;1863(8):194579. Epub 2020 May 7.

MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, Scotland, UK. Electronic address:

As demonstrated through early work in Drosophila, members of the MLL/SET family play essential roles during embryonic development through their participation in large protein complexes that are central to epigenetic regulation of gene expression. One of its members, MLL1, has additionally received a lot of attention as it is a potent oncogenic driver in different types of leukaemia when aberrantly fused to a large variety of partners as a result of chromosomal translocations. Its exclusive association with cancers of the haematopoietic system has prompted a large number of investigations into the role of MLL/SET proteins in haematopoiesis, a summary of which was attempted in this review. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7294230PMC

The role of SETD1A and SETD1B in development and disease.

Biochim Biophys Acta Gene Regul Mech 2020 Aug 8;1863(8):194578. Epub 2020 May 8.

Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany. Electronic address:

The Trithorax-related Set1 H3K4 methyltransferases are conserved from yeast to human. In yeast loss of Set1 causes pleiotropic effects but is compatible with life. In contrast, both mammalian Set1 orthologs: SETD1A and SETD1B are essential for embryonic development, however they have distinct functions. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194578DOI Listing

A survey of transcripts generated by spinal muscular atrophy genes.

Biochim Biophys Acta Gene Regul Mech 2020 Aug 6;1863(8):194562. Epub 2020 May 6.

Department of Biomedical Science, Iowa State University, Ames, IA, 50011, United States of America. Electronic address:

Human Survival Motor Neuron (SMN) genes code for SMN, an essential multifunctional protein. Complete loss of SMN is embryonic lethal, while low levels of SMN lead to spinal muscular atrophy (SMA), a major genetic disease of children and infants. Reduced levels of SMN are associated with the abnormal development of heart, lung, muscle, gastro-intestinal system and testis. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7302838PMC
August 2020
6.332 Impact Factor

The molecular basis of selective DNA binding by the BRG1 AT-hook and bromodomain.

Biochim Biophys Acta Gene Regul Mech 2020 Aug 3;1863(8):194566. Epub 2020 May 3.

Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States. Electronic address:

The ATP-dependent BAF chromatin remodeling complex plays a critical role in gene regulation by modulating chromatin architecture, and is frequently mutated in cancer. Indeed, subunits of the BAF complex are found to be mutated in >20% of human tumors. The mechanism by which BAF properly navigates chromatin is not fully understood, but is thought to involve a multivalent network of histone and DNA contacts. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194566DOI Listing

MLL-rearranged infant leukaemia: A 'thorn in the side' of a remarkable success story.

Biochim Biophys Acta Gene Regul Mech 2020 Aug 3;1863(8):194564. Epub 2020 May 3.

Department of Paediatrics, University of Oxford, Oxford, UK. Electronic address:

Advances in treatment of childhood leukaemia has led to vastly improved survival rates, however some subtypes such as those characterised by MLL gene rearrangement (MLL-r), especially in infants, continue to have high relapse rates and poor survival. Natural history and molecular studies indicate that infant acute lymphoblastic leukaemia (ALL) originates in utero, is distinct from childhood ALL, and most cases are caused by MLL-r resulting in an oncogenic MLL fusion protein. Unlike childhood ALL, only a very small number of additional mutations are present in infant ALL, indicating that MLL-r alone may be sufficient to give rise to this rapid onset, aggressive leukaemia in an appropriate fetal cell context. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194564DOI Listing

Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation.

Biochim Biophys Acta Gene Regul Mech 2020 Aug 29;1863(8):194567. Epub 2020 Apr 29.

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom. Electronic address:

The precise regulation of gene transcription is required to establish and maintain cell type-specific gene expression programs during multicellular development. In addition to transcription factors, chromatin, and its chemical modification, play a central role in regulating gene expression. In vertebrates, DNA is pervasively methylated at CG dinucleotides, a modification that is repressive to transcription. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7294231PMC

Keeping RNA polymerase II on the run: Functions of MLL fusion partners in transcriptional regulation.

Biochim Biophys Acta Gene Regul Mech 2020 Aug 27;1863(8):194563. Epub 2020 Apr 27.

Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India. Electronic address:

Since the identification of key MLL fusion partners as transcription elongation factors regulating expression of HOX cluster genes during hematopoiesis, extensive work from the last decade has resulted in significant progress in our overall mechanistic understanding of role of MLL fusion partner proteins in transcriptional regulation of diverse set of genes beyond just the HOX cluster. In this review, we are going to detail overall understanding of role of MLL fusion partner proteins in transcriptional regulation and thus provide mechanistic insights into possible MLL fusion protein-mediated transcriptional misregulation leading to aberrant hematopoiesis and leukemogenesis. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194563DOI Listing

Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription.

Biochim Biophys Acta Gene Regul Mech 2020 Aug 25;1863(8):194568. Epub 2020 Apr 25.

Institute of Physiology, University of Zürich, CH-8057 Zürich, Switzerland; National Centre of Competence in Research "Kidney.CH", Switzerland. Electronic address:

One of the widely used applications of the popular Cre-loxP method for targeted recombination is the permanent activation of marker genes, such as reporter genes or antibiotic resistance genes, by excision of a preceding transcriptional stop signal. The STOP cassette consists of three identical SV40-derived poly(A) signal repeats and is flanked by two loxP sites. We found that in addition to complete loxP-mediated recombination, limiting levels of the Cre recombinase also cause incomplete recombination of the STOP cassette. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194568DOI Listing

The molecular functions of common and atypical MLL fusion protein complexes.

Biochim Biophys Acta Gene Regul Mech 2020 Jul 19;1863(7):194548. Epub 2020 Apr 19.

Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan; National Cancer Center Research Institute, Tokyo, Japan. Electronic address:

Mixed-lineage leukemia (MLL) fuses with a variety of partners to produce a functionally altered MLL complex that is not expressed in normal cells, which transforms normal hematopoietic progenitors into leukemia cells. Because more than 80 fusion partners have been identified to date, the molecular functions of MLL fusion protein complexes appear diverse. However, over the past decade, the common functions utilized for leukemic transformation have begun to be elucidated. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194548DOI Listing

Learning from mouse models of MLL fusion gene-driven acute leukemia.

Authors:
Juerg Schwaller

Biochim Biophys Acta Gene Regul Mech 2020 Aug 19;1863(8):194550. Epub 2020 Apr 19.

University Children's Hospital Beider Basel (UKBB), Basel, Switzerland; Department of Biomedicine, University of Basel, Switzerland. Electronic address:

5-10% of human acute leukemias carry chromosomal translocations involving the mixed lineage leukemia (MLL) gene that result in the expression of chimeric protein fusing MLL to >80 different partners of which AF4, ENL and AF9 are the most prevalent. In contrast to many other leukemia-associated mutations, several MLL-fusions are powerful oncogenes that transform hematopoietic stem cells but also more committed progenitor cells. Here, I review different approaches that were used to express MLL fusions in the murine hematopoietic system which often, but not always, resulted in highly penetrant and transplantable leukemias that closely phenocopied the human disease. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194550DOI Listing

Insights on the regulation of the MLL/SET1 family histone methyltransferases.

Biochim Biophys Acta Gene Regul Mech 2020 Jul 15;1863(7):194561. Epub 2020 Apr 15.

Department of Pathology, University of Michigan, Ann Arbor, United States of America; Department of Biological Chemistry, University of Michigan, Ann Arbor, United States of America. Electronic address:

In eukaryotes, histone H3K4 methylation by the MLL/SET1 family histone methyltransferases is enriched at transcription regulatory elements including gene promoters and enhancers. The level of H3K4 methylation is highly correlated with transcription activation and is one of the most frequently used histone post-translational modifications to predict transcriptional outcome. Recently, it has been shown that rearrangement of the cellular landscape of H3K4 mono-methylation at distal enhancers precedes cell fate transition and is used for identification of novel regulatory elements for development and disease progression. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236755PMC

The complex activities of the SET1/MLL complex core subunits in development and disease.

Authors:
Hao Jiang

Biochim Biophys Acta Gene Regul Mech 2020 Jul 15;1863(7):194560. Epub 2020 Apr 15.

Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA. Electronic address:

In mammalian cells, the SET1/MLL complexes are the main writers of the H3K4 methyl mark that is associated with active gene expression. The activities of these complexes are critically dependent on the association of the catalytic subunit with their shared core subunits, WDR5, RBBP5, ASH2L, and DPY30, collectively referred as WRAD. In addition, some of these core subunits can bind to proteins other than the SET1/MLL complex components. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236065PMC
July 2020
6.332 Impact Factor

The reciprocal world of MLL fusions: A personal view.

Authors:
Rolf Marschalek

Biochim Biophys Acta Gene Regul Mech 2020 Jul 12;1863(7):194547. Epub 2020 Apr 12.

Institute Pharm Biology/DCAL, Goethe-University, Max-von-Laue-Str.9, 60438 Frankfurt/Main, Germany. Electronic address:

Over the last 15 years the Diagnostic Center of Acute Leukemia (DCAL) at the Frankfurt University has diagnosed and elucidated the Mixed Lineage Leukemia (MLL) recombinome with >100 MLL fusion partners. When analyzing all these different events, balanced chromosomal translocations were found to comprise the majority of these cases (~70%), while other types of genetic rearrangements (3-way-translocations, spliced fusions, 11q inversions, interstitial deletions or insertion of chromosomal fragments into other chromosomes) account for about 30%. In nearly all those complex cases, functional fusion proteins can be produced by transcription, splicing and translation. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194547DOI Listing

Selective repression of the Drosophila cyclin B promoter by retinoblastoma and E2F proteins.

Biochim Biophys Acta Gene Regul Mech 2020 Jul 8;1863(7):194549. Epub 2020 Apr 8.

Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States of America; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States of America. Electronic address:

The Cyclin B1 gene encodes a G2/M cyclin that is deregulated in various human cancers, however, the transcriptional regulation of this gene is incompletely understood. The E2F and retinoblastoma family of proteins are involved in this gene's regulation, but there is disagreement on which of the E2F and retinoblastoma proteins interact with the promoter to regulate this gene. Here, we dissect the promoter region of the Drosophila CycB gene, and study the role of Rbf and E2F factors in its regulation. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7330510PMC

Regulatory interplay between small RNAs and transcription termination factor Rho.

Biochim Biophys Acta Gene Regul Mech 2020 Jul 23;1863(7):194546. Epub 2020 Mar 23.

Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, 45071 Orléans cedex 2, France.

The largest and best studied group of regulatory small RNAs (sRNAs) in bacteria act by modulating translation or turnover of messenger RNAs (mRNAs) through base-pairing interactions that typically take place near the 5' end of the mRNA. This allows the sRNA to bind the complementary target sequence while the remainder of the mRNA is still being made, creating conditions whereby the action of the sRNA can extend to transcriptional steps, most notably transcription termination. Increasing evidence corroborates the existence of a functional interplay between sRNAs and termination factor Rho. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194546DOI Listing

Transcriptional regulation by the KMT2 histone H3K4 methyltransferases.

Biochim Biophys Acta Gene Regul Mech 2020 Jul 16;1863(7):194545. Epub 2020 Mar 16.

Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea. Electronic address:

Histone lysine methyltransferase 2 (KMT2) proteins form multimeric enzymatic complexes that methylate lysine 4 on histone H3 (H3K4) at transcription regulatory elements in the genome. A strong association of H3K4 methylation with active transcription has led to intense efforts to reveal the functional involvement of KMT2 complexes in transcriptional regulation. A number of biochemical and cellular studies have shown that KMT2 complexes regulate transcription of target genes via H3K4 methylation. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194545DOI Listing

Interoperable RNA-Seq analysis in the cloud.

Biochim Biophys Acta Gene Regul Mech 2020 06 7;1863(6):194521. Epub 2020 Mar 7.

Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA; Library of Integrated Network-based Cellular Signatures, Data Coordination and Integration Center (BD2K-LINCS DCIC), USA; Knowledge Management Center for Illuminating the Druggable Genome (KMC-IDG), USA.

RNA-Sequencing (RNA-Seq) is currently the leading technology for genome-wide transcript quantification. Mapping the raw reads to transcript and gene level counts can be achieved by different aligners. Here we report an in-depth comparison of transcript quantification methods. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194521DOI Listing

The yeast Aft1 transcription factor activates ribonucleotide reductase catalytic subunit RNR1 in response to iron deficiency.

Biochim Biophys Acta Gene Regul Mech 2020 Jul 6;1863(7):194522. Epub 2020 Mar 6.

Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Agustín Escardino 7, Paterna 46980, Valencia, Spain. Electronic address:

Eukaryotic ribonucleotide reductases are iron-dependent enzymes that catalyze the rate-limiting step in the de novo synthesis of deoxyribonucleotides. Multiple mechanisms regulate the activity of ribonucleotide reductases in response to genotoxic stresses and iron deficiency. Upon iron starvation, the Saccharomyces cerevisiae Aft1 transcription factor specifically binds to iron-responsive cis elements within the promoter of a group of genes, known as the iron regulon, activating their transcription. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194522DOI Listing

Prevalence of small base-pairing RNAs derived from diverse genomic loci.

Biochim Biophys Acta Gene Regul Mech 2020 Jul 5;1863(7):194524. Epub 2020 Mar 5.

Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA.

Small RNAs (sRNAs) that act by base-pairing have been shown to play important roles in fine-tuning the levels and translation of their target transcripts across a variety of model and pathogenic organisms. Work from many different groups in a wide range of bacterial species has provided evidence for the importance and complexity of sRNA regulatory networks, which allow bacteria to quickly respond to changes in their environment. However, despite the expansive literature, much remains to be learned about all aspects of sRNA-mediated regulation, particularly in bacteria beyond the well-characterized Escherichia coli and Salmonella enterica species. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217754PMC

Gene network reverse engineering: The Next Generation.

Biochim Biophys Acta Gene Regul Mech 2020 06 5;1863(6):194523. Epub 2020 Mar 5.

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http://dx.doi.org/10.1016/j.bbagrm.2020.194523DOI Listing

Bacterial RNA in extracellular vesicles: A new regulator of host-pathogen interactions?

Biochim Biophys Acta Gene Regul Mech 2020 Jul 3;1863(7):194519. Epub 2020 Mar 3.

IRI Life Sciences, Humboldt University, 10115 Berlin, Germany. Electronic address:

Extracellular vesicles (EVs) are released by cells from all kingdoms and represent one form of cell-cell interaction. This universal system of communication blurs cells type boundaries, offering an new avenue for pathogens to infect their hosts. EVs carry with them an arsenal of virulence factors that have been the focus of numerous studies. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194519DOI Listing

TOPORS, a tumor suppressor protein, contributes to the maintenance of higher-order chromatin architecture.

Biochim Biophys Acta Gene Regul Mech 2020 05 27;1863(5):194518. Epub 2020 Feb 27.

The Fifth People's Hospital of Shanghai, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China. Electronic address:

In the nucleus, chromosomes are hierarchically folded into active (A) and inactive (B) compartments composed of topologically associating domains (TADs). Genomic regions interact with nuclear lamina, termed lamina-associated domains (LADs). However, the molecular mechanisms underlying these 3D chromatin architectures remain incompletely understood. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194518DOI Listing

Nuclear accumulation of MKL1 in luminal breast cancer cells impairs genomic activity of ERα and is associated with endocrine resistance.

Biochim Biophys Acta Gene Regul Mech 2020 05 27;1863(5):194507. Epub 2020 Feb 27.

Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000 Rennes, France. Electronic address:

Estrogen receptor (ERα) is central in driving the development of hormone-dependent breast cancers. A major challenge in treating these cancers is to understand and overcome endocrine resistance. The Megakaryoblastic Leukemia 1 (MKL1, MRTFA) protein is a master regulator of actin dynamic and cellular motile functions, whose nuclear translocation favors epithelial-mesenchymal transition. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194507DOI Listing

Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup.

Biochim Biophys Acta Gene Regul Mech 2020 05 27;1863(5):194515. Epub 2020 Feb 27.

Laboratory of Biosystem Dynamics, BioMediTech, Faculty of Medicine and Health Technology, Tampere University, 33101 Tampere, Finland. Electronic address:

Positive supercoiling buildup (PSB) is a pervasive phenomenon in the transcriptional programs of Escherichia coli. After finding a range of Gyrase concentrations where the inverse of the transcription rate of a chromosome-integrated gene changes linearly with the inverse of Gyrase concentration, we apply a LineWeaver-Burk plot to dissect the expected in vivo transcription rate in absence of PSB. We validate the estimation by time-lapse microscopy of single-RNA production kinetics of the same gene when single-copy plasmid-borne, shown to be impervious to Gyrase inhibition. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194515DOI Listing

Noncoding RNAs in control of gene expression.

Authors:
Kotb Abdelmohsen

Biochim Biophys Acta Gene Regul Mech 2020 04 27;1863(4):194520. Epub 2020 Feb 27.

Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Blvd., Baltimore, MD 21224, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbagrm.2020.194520DOI Listing

ELL-associated factors EAF1/2 negatively regulate HIV-1 transcription through inhibition of Super Elongation Complex formation.

Biochim Biophys Acta Gene Regul Mech 2020 05 19;1863(5):194508. Epub 2020 Feb 19.

State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Fujian, China. Electronic address:

The ELL (ELL1 and ELL2)-containing Super Elongation Complex (SEC) is required for efficient HIV-1 transactivation by the viral-encoded Tat protein. EAF1 and EAF2 are ELL-associated factors and considered as positive regulators of ELL. However, their role in HIV-1 transcriptional control is unknown. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194508DOI Listing

Navigation through the twists and turns of RNA sequencing technologies: Application to bacterial regulatory RNAs.

Biochim Biophys Acta Gene Regul Mech 2020 03 14;1863(3):194506. Epub 2020 Feb 14.

Université de Strasbourg, CNRS, ARN UPR 9002, F-67000 Strasbourg, France. Electronic address:

Discovered in the 1980s, small regulatory RNAs (sRNAs) are now considered key actors in virtually all aspects of bacterial physiology and virulence. Together with transcriptional and translational regulatory proteins, they integrate and often are hubs of complex regulatory networks, responsible for bacterial response/adaptation to various perceived stimuli. The recent development of powerful RNA sequencing technologies has facilitated the identification and characterization of sRNAs (length, structure and expression conditions) and their RNA targets in several bacteria. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194506DOI Listing

sRNA-mediated control in bacteria: An increasing diversity of regulatory mechanisms.

Biochim Biophys Acta Gene Regul Mech 2020 05 9;1863(5):194504. Epub 2020 Mar 9.

Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark. Electronic address:

Small regulatory RNAs (sRNAs) act as post-transcriptional regulators controlling bacterial adaptation to environmental changes. Our current understanding of the mechanisms underlying sRNA-mediated control is mainly based on studies in Escherichia coli and Salmonella. Ever since the discovery of sRNAs decades ago, these Gram-negative species have served as excellent model organisms in the field of sRNA biology. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194504DOI Listing

MLL fusion proteins and transcriptional control.

Authors:
Robert K Slany

Biochim Biophys Acta Gene Regul Mech 2020 03 19;1863(3):194503. Epub 2020 Feb 19.

Department of Genetics, Friedrich-Alexander-University Erlangen-Nürnberg, Germany. Electronic address:

The highly leukemogenic MLL fusion proteins have a unique mechanism of action. This review summarizes the current knowledge of how MLL fusions interact with the transcriptional machinery and it proposes a hypothesis how these proteins modify transcriptional control to act as transcriptional amplifiers causing runaway production of certain RNAs that transform hematopoietic cells. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194503DOI Listing

Regulation of RNA processing and degradation in bacteria.

Biochim Biophys Acta Gene Regul Mech 2020 05 6;1863(5):194505. Epub 2020 Mar 6.

UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France. Electronic address:

Messenger RNA processing and decay is a key mechanism to control gene expression at the post-transcriptional level in response to ever-changing environmental conditions. In this review chapter, we discuss the main ribonucleases involved in these processes in bacteria, with a particular but non-exclusive emphasis on the two best-studied paradigms of Gram-negative and Gram-positive bacteria, E. coli and B. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194505DOI Listing

Bacterial growth physiology and RNA metabolism.

Biochim Biophys Acta Gene Regul Mech 2020 05 7;1863(5):194502. Epub 2020 Feb 7.

Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France. Electronic address:

Bacteria are sophisticated systems with high capacity and flexibility to adapt to various environmental conditions. Each prokaryote however possesses a defined metabolic network, which sets its overall metabolic capacity, and therefore the maximal growth rate that can be reached. To achieve optimal growth, bacteria adopt various molecular strategies to optimally adjust gene expression and optimize resource allocation according to the nutrient availability. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194502DOI Listing

Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins.

Biochim Biophys Acta Gene Regul Mech 2020 03 7;1863(3):194501. Epub 2020 Feb 7.

Department of biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada. Electronic address:

Riboswitches are RNA sensors that have been shown to modulate the expression of downstream genes by altering their structure upon metabolite binding. Riboswitches are unique among cellular regulators in that metabolite detection is strictly performed using RNA interactions with the sensed metabolite and in which no regulatory protein is needed to mediate the interaction. However, recent studies have shed light on riboswitch control mechanisms relying on protein regulators to harness metabolite binding for the mediation of gene expression, thereby increasing the range of cellular factors involved in riboswitch regulation. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194501DOI Listing

The interaction between the F55 virus-encoded transcription regulator and the RadA host recombinase reveals a common strategy in Archaea and Bacteria to sense the UV-induced damage to the host DNA.

Biochim Biophys Acta Gene Regul Mech 2020 05 31;1863(5):194493. Epub 2020 Jan 31.

Department of Biology, University of Naples Federico II, 80126 Naples, Italy. Electronic address:

Sulfolobus spindle-shaped virus 1 is the only UV-inducible member of the virus family Fuselloviridae. Originally isolated from Saccharolobus shibatae B12, it can also infect Saccharolobus solfataricus. Like the CI repressor of the bacteriophage λ, the SSV1-encoded F55 transcription repressor acts as a key regulator for the maintenance of the SSV1 carrier state. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194493DOI Listing

Transcriptomic landscape, gene signatures and regulatory profile of aging in the human brain.

Biochim Biophys Acta Gene Regul Mech 2020 06 8;1863(6):194491. Epub 2020 Feb 8.

Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IMBCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca (USAL), Campus Miguel de Unamuno s/n, 37007 Salamanca, Spain. Electronic address:

The molecular characteristics of aging that lead to increased disease susceptibility remain poorly understood. Here we present a transcriptomic profile of the human brain associated with age and aging, derived from a systematic integrative analysis of four independent cohorts of genome-wide expression data from 2202 brain samples (cortex, hippocampus and cerebellum) of individuals of different ages (from young infants, 5-10 years old, to elderly people, up to 100 years old) categorized in age stages by decades. The study provides a signature of 1148 genes detected in cortex, 874 genes in hippocampus and 657 genes in cerebellum, that present significant differential expression changes with age according to a robust gamma rank correlation profiling. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194491DOI Listing

The zinc-finger proteins WOC and ROW play distinct functions within the HP1c transcription complex.

Biochim Biophys Acta Gene Regul Mech 2020 03 30;1863(3):194492. Epub 2020 Jan 30.

Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain. Electronic address:

In Drosophila, the Heterochromatin Protein 1c (HP1c) forms a transcriptional complex with the zinc-finger proteins WOC and ROW, and the extraproteasomal ubiquitin receptor Dsk2. This complex localizes at promoters of active genes and it is required for transcription. The functions played by the different components of the HP1c complex are not fully understood. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194492DOI Listing

The functional role of the C-terminal tail of the human ribosomal protein uS19.

Biochim Biophys Acta Gene Regul Mech 2020 03 25;1863(3):194490. Epub 2020 Jan 25.

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia. Electronic address:

The eukaryotic ribosomal protein uS19 has a C-terminal tail that is absent in its bacterial homologue. This tail has been shown to be involved in the formation of the decoding site of human ribosomes. We studied here the previously unexplored functional significance of the 15 C-terminal amino acid residues of human uS19 for the assembly of ribosomes and translation using HEK293-based cell cultures capable of producing FLAG-labeled uS19 (uS19) or its mutant form deprived of the mentioned amino acid ones. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2020.194490DOI Listing