Regulation of Histone Deacetylase 4 Expression by the SP Family of Transcription Factors

Histone deacetylases mediate critical cellular functions but relatively little is known about mechanisms controlling their expression, including expression of HDAC4, a class II HDAC implicated in the modulation of cellular differentiation and viability. Endogenous HDAC4 mRNA, protein levels and promoter activity were all readily repressed by mithramycin, suggesting regulation by GC-rich DNA sequences. We validated consensus binding sites for Sp1/Sp3 transcription factors in the HDAC4 promoter through truncation studies and targeted mutagenesis. Specific and functional binding by Sp1/Sp3 at these sites was confirmed with chromatin immunoprecipitation (ChIP) and electromobility shift assays (EMSA). Cotransfection of either Sp1 or Sp3 with a reporter driven by the HDAC4 promoter led to high activities in SL2 insect cells (which lack endogenous Sp1/Sp3). In human cells, restored expression of Sp1 and Sp3 up-regulated HDAC4 protein levels, whereas levels were decreased by RNA-interference-mediated knockdown of either protein. Finally, variable levels of Sp1 were in concordance with that of HDAC4 in a number of human tissues and cancer cell lines. These studies together characterize for the first time the activity of the HDAC4 promoter, through which Sp1 and Sp3 modulates expression of HDAC4 and which may contribute to tissue or cell-line-specific expression of HDAC4.

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Association with Class IIa Histone Deacetylases Upregulates the Sumoylation of MEF2 Transcription Factors

Molecular and Cellular Biology ◽

10.1128/mcb.25.6.2273-2287.2005 ◽

2005 ◽

Vol 25 (6) ◽

pp. 2273-2287 ◽

Cited By ~ 145

Author(s):

Serge Grégoire ◽

Xiang-Jiao Yang

Keyword(s):

Transcription Factors ◽

Transcriptional Activation ◽

Histone Deacetylases ◽

Myocyte Enhancer Factor 2 ◽

Transcriptional Activation Domain ◽

Sumo Protease ◽

T Cell Apoptosis ◽

Extracellular Signal ◽

Histone Deacetylase 4

ABSTRACT The myocyte enhancer factor-2 (MEF2) family of transcription factors plays an important role in regulating cellular programs like muscle differentiation, neuronal survival, and T-cell apoptosis. Multisite phosphorylation is known to control the transcriptional activity of MEF2 proteins, but it is unclear whether other modifications are involved. Here, we report that human MEF2D, as well as MEF2C, is modified by SUMO2 and SUMO3 at a motif highly conserved among MEF2 proteins from diverse organisms. This motif is located within the C-terminal transcriptional activation domain, and its sumoylation inhibits transcription. As a transcriptional corepressor of MEF2, histone deacetylase 4 (HDAC4) potentiates sumoylation. This potentiation is dependent on the N-terminal region but not the C-terminal deacetylase domain of HDAC4 and is inhibited by the sumoylation of HDAC4 itself. Moreover, HDAC5, HDAC7, and an HDAC9 isoform also stimulate sumoylation of MEF2. Opposing the action of class IIa deacetylases, the SUMO protease SENP3 reverses the sumoylation to augment the transcriptional and myogenic activities of MEF2. Similarly, the calcium M kinase and extracellular signal-regulated kinase 5 signaling pathways negatively regulate the sumoylation. These results thus identify sumoylation as a novel regulatory mechanism for MEF2 and suggest that this modification interplays with phosphorylation to promote intramolecular signaling for coordinated regulation in vivo.

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hTFtarget: a comprehensive database for regulations of human transcription factors and their targets

10.1101/843656 ◽

2019 ◽

Cited By ~ 1

Author(s):

Qiong Zhang

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Dna Sequences ◽

Chromatin Immunoprecipitation ◽

Target Genes ◽

Gene Expression Regulation ◽

Epigenetic Modification ◽

Wide Range ◽

Chromatin Immunoprecipitation Sequencing ◽

User Friendly

Transcription factors (TFs) as key regulators play crucial roles in biological processes. The identification of TF-target regulatory relationships is a key step for revealing functions of TFs and their regulations on gene expression. The accumulated data of Chromatin immunoprecipitation sequencing (ChIP-Seq) provides great opportunities to discover the TF-target regulations across different conditions. In this study, we constructed a database named hTFtarget, which integrated huge human TF target resources (7,190 ChIP-Seq samples of 659 TFs and high confident TF binding sites of 699 TFs) and epigenetic modification information to predict accurate TF-target regulations. hTFtarget offers the following functions for users to explore TF-target regulations: 1) Browse or search general targets of a query TF across datasets; 2) Browse TF-target regulations for a query TF in a specific dataset or tissue; 3) Search potential TFs for a given target gene or ncRNA; 4) Investigate co-association between TFs in cell lines; 5) Explore potential co-regulations for given target genes or TFs; 6) Predict candidate TFBSs on given DNA sequences; 7) View ChIP-Seq peaks for different TFs and conditions in genome browser. hTFtarget provides a comprehensive, reliable and user-friendly resource for exploring human TF-target regulations, which will be very useful for a wide range of users in the TF and gene expression regulation community. hTFtarget is available at http://bioinfo.life.hust.edu.cn/hTFtarget.

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Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes

10.1101/265538 ◽

2018 ◽

Author(s):

Langyu Gu ◽

Canwei Xia

Keyword(s):

Transcription Factors ◽

Cluster Expansion ◽

Expression Patterns ◽

3D Structure ◽

Teleost Fishes ◽

Duplicated Genes ◽

Specific Expression ◽

Forkhead Transcription Factors ◽

Apolipoprotein D ◽

First Time

AbstractBackgroundGene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attentions considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the ligand (e.g., pheromone and hormone)-transporter genes, apolipoprotein D (ApoD) genes in a cluster, specific to teleost fishes.ResultsThe single ApoD gene in the ancestor expands in two clusters with a dynamic evolutionary pattern in teleost fishes. Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, evolutionary rate detection and breakpoint detection, orthologous genes show conserved expression patterns. Lineage-specific duplicated genes that are under positive selection evolved specific and even new expression profiles. Different duplicates show high tissue-specific expression patterns (e.g., skin, eye, anal fin pigmentation patterns, gonads, gills, spleen and lower pharyngeal jaw). Cluster analyses based on protein 3D structure comparisons, especially the four loops at the opening side, show segregation patterns with different duplicates. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes, and they are located next to the breakpoints of genome rearrangements.ConclusionsHere, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both protein and expression levels after duplication. Evidence from different aspects, i.e. abnormal expression induced disease in human, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, highly specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes that are under positive selection, and their locations next to breakpoints of genome rearrangement, suggests the potential advantageous roles of ApoD genes in teleost fishes. Cluster expansion of ApoD genes specific to teleost fishes thus provides an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.

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Mechanism of thiamine uptake by human colonocytes: studies with cultured colonic epithelial cell line NCM460

AJP Gastrointestinal and Liver Physiology ◽

10.1152/ajpgi.2001.281.1.g144 ◽

2001 ◽

Vol 281 (1) ◽

pp. G144-G150 ◽

Cited By ~ 48

Author(s):

Hamid M. Said ◽

Alvaro Ortiz ◽

Veedamali S. Subramanian ◽

Ellis J. Neufeld ◽

Mary Pat Moyer ◽

...

Keyword(s):

Large Intestine ◽

Epithelial Cell Line ◽

Cellular Functions ◽

Protein Levels ◽

Normal Microflora ◽

Colonic Epithelial Cell Line ◽

Intracellular Ca ◽

Energy Dependent ◽

First Time ◽

Slc19a2 Gene

Thiamine (vitamin B1) is essential for normal cellular functions and growth. Mammals cannot synthesize thiamine and thus must obtain the vitamin via intestinal absorption. The intestine is exposed to a dietary thiamine source and a bacterial source in which the vitamin is synthesized by the normal microflora of the large intestine. Very little is known about thiamine uptake in the large intestine. The aim of this study was, therefore, to address this issue. Our results with human-derived colonic epithelial NCM460 cells as a model system showed thiamine uptake to be 1) temperature- and energy dependent, 2) Na+ independent, 3) increased with increasing buffer pH from 5 to 8 and after cell acidification but inhibited by amiloride, 4) saturable as a function of concentration, 5) inhibited by thiamine structural analogs but not by unrelated organic cations, and 6) inhibited by modulators of a Ca2+/calmodulin-mediated pathway. NCM460 cells and native human colonic mucosa expressed the recently cloned human thiamine transporter THTR-1 (product of the SLC19A2 gene) at both mRNA and protein levels. These results demonstrate for the first time that human NCM460 colonocytes possess a specific carrier-mediated system for thiamine uptake that appears to be under the regulation of an intracellular Ca2+/calmodulin-mediated pathway. It is suggested that bacterially synthesized thiamine in the large intestine may contribute to thiamine nutrition of the host, especially toward cellular nutrition of the local colonocytes.

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Disruption of cardiac Med1 inhibits RNA polymerase II promoter occupancy and promotes chromatin remodeling

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.00580.2018 ◽

2019 ◽

Vol 316 (2) ◽

pp. H314-H325 ◽

Cited By ~ 3

Author(s):

Duane D. Hall ◽

Kathryn M. Spitler ◽

Chad E. Grueter

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Chromatin Immunoprecipitation ◽

Chromatin Accessibility ◽

Gene Promoters ◽

Specific Expression ◽

Pol Ii ◽

Transcriptional Start Sites

The Mediator coactivator complex directs gene-specific expression by binding distal enhancer-bound transcription factors through its Med1 subunit while bridging to RNA polymerase II (Pol II) at gene promoters. In addition, Mediator scaffolds epigenetic modifying enzymes that determine local DNA accessibility. Previously, we found that deletion of Med1 in cardiomyocytes deregulates more than 5,000 genes and promotes acute heart failure. Therefore, we hypothesized that Med1 deficiency disrupts enhancer-promoter coupling. Using chromatin immunoprecipitation-coupled deep sequencing (ChIP-seq; n = 3/ChIP assay), we found that the Pol II pausing index is increased in Med1 knockout versus floxed control mouse hearts primarily due to a decrease in Pol II occupancy at the majority of transcriptional start sites without a corresponding increase in elongating species. Parallel ChIP-seq assays reveal that Med1-dependent gene expression correlates strongly with histone H3 K27 acetylation, which is indicative of open and active chromatin at transcriptional start sites, whereas H3 K27 trimethylated levels, representing condensed and repressed DNA, are broadly increased and inversely correlate with absolute expression levels. Furthermore, Med1 deletion leads to dynamic changes in acetyl-K27 associated superenhancer regions and their enriched transcription factor-binding motifs that are consistent with altered gene expression. Our findings suggest that Med1 is important in establishing enhancer-promoter coupling in the heart and supports the proposed role of Mediator in establishing preinitiation complex formation. We also found that Med1 determines chromatin accessibility within genes and enhancer regions and propose that the composition of transcription factors associated with superenhancer changes to direct gene-specific expression. NEW & NOTEWORTHY Based on our previous findings that transcriptional homeostasis and cardiac function are disturbed by cardiomyocyte deletion of the Mediator coactivator Med1 subunit, we investigated potential underlying changes in RNA polymerase II localization and global chromatin accessibility. Using chromatin immunoprecipitation sequencing, we found that disrupted transcription arises from a deficit in RNA polymerase II recruitment to gene promoters. Furthermore, active versus repressive chromatin marks are redistributed within gene loci and at enhancer regions correlated with gene expression changes.

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Ubiquitin-dependent degradation of HDAC4, a new regulator of random cell motility

Molecular Biology of the Cell ◽

10.1091/mbc.e10-07-0616 ◽

2011 ◽

Vol 22 (2) ◽

pp. 278-289 ◽

Cited By ~ 44

Author(s):

Nadia Cernotta ◽

Andrea Clocchiatti ◽

Cristina Florean ◽

Claudio Brancolini

Keyword(s):

Growth Factors ◽

Cell Motility ◽

Histone Deacetylases ◽

Glycogen Synthase ◽

Consensus Sequence ◽

Ubiquitin Proteasome System ◽

Serum Starvation ◽

Cellular Functions ◽

Histone Deacetylase 4

HDAC4 (histone deacetylase 4) belongs to class IIa of histone deacetylases, which groups important regulators of gene expression, controlling pleiotropic cellular functions. Here we show that, in addition to the well-defined nuclear/cytoplasmic shuttling, HDAC4 activity is modulated by the ubiquitin–proteasome system. Serum starvation elicits the poly-ubiquitination and degradation of HDAC4 in nontransformed cells. Phosphorylation of serine 298 within the PEST1 sequence plays an important role in the control of HDAC4 stability. Serine 298 lies within a glycogen synthase kinase 3β consensus sequence, and removal of growth factors fails to trigger HDAC4 degradation in cells deficient in this kinase. GSK3β can phosphorylate HDAC4 in vitro, and phosphorylation of serine 302 seems to play the role of priming phosphate. We have also found that HDAC4 modulates random cell motility possibly through the regulation of KLF2 transcription. Apoptosis, autophagy, cell proliferation, and growth arrest were unaffected by HDAC4. Our data suggest a link between regulation of HDAC4 degradation and the control of cell motility as operated by growth factors.

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BRD2 regulation of sigma-2 receptor expression upon cytosolic cholesterol deprivation

10.1101/748236 ◽

2019 ◽

Cited By ~ 1

Author(s):

Hongtao Shen ◽

Jing Li ◽

Xiujie Xie ◽

Huan Yang ◽

Mengxue Zhang ◽

...

Keyword(s):

Transcriptional Regulation ◽

Transcription Factors ◽

Fatty Acid ◽

Chromatin Immunoprecipitation ◽

Acid Metabolism ◽

Gene Promoter ◽

Cholesterol Homeostasis ◽

Receptor Expression ◽

Antipsychotic Treatment ◽

Protein Levels

AbstractTraditionally a pharmacologic target for antipsychotic treatment, the sigma-2 receptor (S2R) was recently implicated in cholesterol homeostasis. Here we investigated the transcriptional regulation of S2R by the Bromo/ExtraTerminal epigenetic reader family (BETs, including BRD2, 3, 4) upon cholesterol perturbation.Cytosolic cholesterol deprivation was induced using an export blocker of lysosomal cholesterol in ARPE19 cells. This condition upregulated mRNA and protein levels of S2R, and of SREBP2 but not SREBP1, transcription factors key to cholesterol/fatty acid metabolism. Silencing BRD2 but not BRD4 (though widely deemed as a master regulator) or BRD3 prevented S2R upregulation induced by cholesterol deprivation. Silencing SREBP2 but not SREBP1 diminished S2R expression. Furthermore, BRD2 co-immunoprecipitated with the SREBP2 transcription-active N-terminal domain, and chromatin immunoprecipitation-qPCR showed a BRD2 occupancy at the S2R gene promoter.In summary, this study reveals a novel BRD2/SREBP2 cooperative regulation of S2R transcription in response to cytosolic cholesterol deprivation, thus shedding new light on epigenetic control of cholesterol biology.

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ChromWave: Deciphering the DNA-encoded competition between transcription factors and nucleosomes with deep neural networks

10.1101/2021.03.19.436198 ◽

2021 ◽

Author(s):

Sera Aylin Cakiroglu ◽

Sebastian Steinhauser ◽

Jon Smith ◽

Wei Xing ◽

Nicholas M. Luscombe

Keyword(s):

Transcription Factors ◽

Dna Sequences ◽

Genomic Sequence ◽

Local Level ◽

Regulatory Elements ◽

Training Data ◽

Yeast Genome ◽

Knock Out ◽

Causal Variants ◽

First Time

SummaryTranscription factors (TFs) regulate gene expression by recognising and binding specific DNA sequences. At times, these regulatory elements may be occluded by nucleosomes, making them inaccessible for TF-binding. The competition for DNA occupancy between TFs and nucleosomes, and associated gene regulatory outputs, are important consequences of the cis-regulatory information encoded in the genome. However, these sequence patterns are subtle and remain difficult to interpret. Here, we introduce ChromWave, a deep-learning model that, for the first time, predicts the competing profiles for TF and nucleosomes occupancies with remarkable accuracy. Models trained using short- and long-fragment MNase-Seq data successfully learn the sequence preferences underlying TF and nucleosome occupancies across the entire yeast genome. They recapitulate nucleosome evictions from regions containing “strong” TF binding sites and knock-out simulations show nucleosomes gaining occupancy in the absence of these TFs, accompanied by lateral rearrangement of adjacent nucleosomes. At a local level, models anticipate with high accuracy the outcomes of detailed experimental analysis of partially unwrapped nucleosomes at the GAL4 UAS locus. Finally, we trained a ChromWave model that successfully predicts nucleosome positions at promoters in the human genome. We find that human promoters generally contain few sites at which simple sequence changes can alter nucleosome occupancies and that these positions align well with causal variants linked to DNase hypersensitivity. ChromWave is readily combined with diverse genomic datasets and can be trained to predict any output that is linked to the underlying genomic sequence. ChromWave’s application is limited only by the user’s imagination and availability of training data.

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Denaturing High Performance Liquid Chromatography and Bioinformatics - Two Modern Tools for Extracellular Superoxide Dismutase (SOD3) Gene Promoter Analysis

Revista de Chimie ◽

10.37358/rc.08.7.1893 ◽

2008 ◽

Vol 59 (7) ◽

Author(s):

Corina Samoila ◽

Alfa Xenia Lupea ◽

Andrei Anghel ◽

Marilena Motoc ◽

Gabriela Otiman ◽

...

Keyword(s):

High Performance Liquid Chromatography ◽

Transcription Factors ◽

Liquid Chromatography ◽

Dna Sequences ◽

High Performance ◽

Zinc Finger Protein ◽

High Capacity ◽

Gene Promoter ◽

Experimental Approaches ◽

Myeloid Zinc Finger

Denaturing High Performance Liquid Chromatography (DHPLC) is a relatively new method used for screening DNA sequences, characterized by high capacity to detect mutations/polymorphisms. This study is focused on the Transgenomic WAVETM DNA Fragment Analysis (based on DHPLC separation method) of a 485 bp fragment from human EC-SOD gene promoter in order to detect single nucleotide polymorphism (SNPs) associated with atherosclerosis and risk factors of cardiovascular disease. The fragment of interest was amplified by PCR reaction and analyzed by DHPLC in 100 healthy subjects and 70 patients characterized by atheroma. No different melting profiles were detected for the analyzed DNA samples. A combination of computational methods was used to predict putative transcription factors in the fragment of interest. Several putative transcription factors binding sites from the Ets-1 oncogene family: ETS member Elk-1, polyomavirus enhancer activator-3 (PEA3), protein C-Ets-1 (Ets-1), GABP: GA binding protein (GABP), Spi-1 and Spi-B/PU.1 related transcription factors, from the Krueppel-like family: Gut-enriched Krueppel-like factor (GKLF), Erythroid Krueppel-like factor (EKLF), Basic Krueppel-like factor (BKLF), GC box and myeloid zinc finger protein MZF-1 were identified in the evolutionary conserved regions. The bioinformatics results need to be investigated further in others studies by experimental approaches.

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MiRNA Expression in Neuroendocrine Neoplasms of Frequent Localizations

Non-Coding RNA ◽

10.3390/ncrna7030038 ◽

2021 ◽

Vol 7 (3) ◽

pp. 38

Author(s):

Alexandra Korotaeva ◽

Danzan Mansorunov ◽

Natalya Apanovich ◽

Anna Kuzevanova ◽

Alexander Karpukhin

Keyword(s):

Mirna Expression ◽

Malignant Tumors ◽

Neuroendocrine Neoplasms ◽

Specific Expression ◽

Clinical Biomarkers ◽

Different Types ◽

Functional Features ◽

First Time ◽

Potential Biomarkers

Neuroendocrine neoplasms (NEN) are infrequent malignant tumors of a neuroendocrine nature that arise in various organs. They occur most frequently in the lungs, intestines, stomach and pancreas. Molecular diagnostics and prognosis of NEN development are highly relevant. The role of clinical biomarkers can be played by microRNAs (miRNAs). This work is devoted to the analysis of data on miRNA expression in NENs. For the first time, a search for specificity or a community of their functional characteristics in different types of NEN was carried out. Their properties as biomarkers were also analyzed. To date, more than 100 miRNAs have been characterized as differentially expressed and significant for the development of NEN tumors. Only about 10% of the studied miRNAs are expressed in several types of NEN; differential expression of the remaining 90% was found only in tumors of specific localizations. A significant number of miRNAs have been identified as potential biomarkers. However, only a few miRNAs have values that characterized their quality as markers. The analysis demonstrates the predominant specific expression of miRNA in each studied type of NEN. This indicates that miRNA’s functional features are predominantly influenced by the tissue in which they are formed.

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