The ubiquitous transcription factor CTCF promotes lineage-specific epigenomic remodeling and establishment of transcriptional networks driving cell differentiation

Dubois-Chevalier, Julie; Staels, Bart; Lefèbvre, Philippe; Eeckhoute, Jérôme

doi:10.1080/19491034.2015.1004258

Cited by 9 publications

(8 citation statements)

References 48 publications

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“…The factor peroxisome proliferator-activated receptor gamma ( PPARG ) is reported to be an important regulator in adipogenesis. The cooperation of CTCF with PPARG and its effects on the transcriptional activity of PPARG are well documented in [62, 63]. SMAD factors are known to form complexes with KLF 4 and to mediate its phosphorylation, which is necessary for the recruitment of other factors such as PPARG [64, 65].…”

Section: Resultsmentioning

confidence: 99%

Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues

et al. 2019

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Transcription factors (TFs) are a special class of DNA-binding proteins that orchestrate gene transcription by recruiting other TFs, co-activators or co-repressors. Their combinatorial interplay in higher organisms maintains homeostasis and governs cell identity by finely controlling and regulating tissue-specific gene expression. Despite the rich literature on the importance of cooperative TFs for deciphering the mechanisms of individual regulatory programs that control tissue specificity in several organisms such as human, mouse, or Drosophila melanogaster , to date, there is still need for a comprehensive study to detect specific TF cooperations in regulatory processes of cattle tissues. To address the needs of knowledge about specific combinatorial gene regulation in cattle tissues, we made use of three publicly available RNA-seq datasets and obtained tissue-specific gene (TSG) sets for ten tissues (heart, lung, liver, kidney, duodenum, muscle tissue, adipose tissue, colon, spleen and testis). By analyzing these TSG-sets, tissue-specific TF cooperations of each tissue have been identified. The results reveal that similar to the combinatorial regulatory events of model organisms, TFs change their partners depending on their biological functions in different tissues. Particularly with regard to preferential partner choice of the transcription factors STAT 3 and NR 2 C 2, this phenomenon has been highlighted with their five different specific cooperation partners in multiple tissues. The information about cooperative TFs could be promising: i) to understand the molecular mechanisms of regulating processes; and ii) to extend the existing knowledge on the importance of single TFs in cattle tissues.

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Section: Resultsmentioning

confidence: 99%

Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues

et al. 2019

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“…TET2 protein does interact with both transcription factors, PPARg and CTCF, to promote DNA hydroxymethylation of 5mCGs at their associated enhancers, CCCTC-related sequences and PPAREs, respectively. Hence, TET activity appears to drive increases in constitutive and adipogenic gene expression during the development of 3T3-L1 preadipocytes into mature, lipid-rich adipocytes [ 40 , 41 ]. The likelihood of a specific relationship between PPARg and CTCF is further evidenced by that fact that during adipogenesis, CTCF binds disproportionately to enhancer sites that are near PPAREs and at most genes induced by PPARg [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

“…The likelihood of a specific relationship between PPARg and CTCF is further evidenced by that fact that during adipogenesis, CTCF binds disproportionately to enhancer sites that are near PPAREs and at most genes induced by PPARg [ 40 ]. It has been suggested that 3-dimensional chromatin loops bring these two enhancers into proximity to promote coordinated activity [ 41 ]. The resulting specific relationship of PPARg, TET activity, and 5hmC levels in adipocytes may also help explain the lower than average levels of 5hmC we observed in the gene bodies of the lowest quintile of expressed genes.…”

Section: Discussionmentioning

confidence: 99%

“…In general, 5hmCG dinucleotides mark a small subset of antiparallel CGs, which may or may not also be 5mC modified (5mCGs) in the antiparallel strand, such that increases in one of these two modifications at a site is not always correlated with the loss of the other. TET dioxygenase-catalyzed oxidation of 5mC to 5hmC at constitutive CTS (CTCF binding sites) and PPARg enhancers (PPAREs) appears to be part of and perhaps may be essential to adipogenesis [ 40 , 41 ]. The ADP-ribose polymer attached to parylated-PPARg binds TET enzymes to catalyze the localized conversion of 5mC to 5hmC [ 42 ], which begins to outline a mechanism connecting 5hmC modification and adipogenesis.…”

Section: Introductionmentioning

confidence: 99%

“…The gene-region-specific balance of these activities determines the levels of C, 5mC, and 5hmC. The diagram was modified from those in previous publications [ 41 , 115 ].…”

Section: Introductionmentioning

confidence: 99%

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Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine

Lee

et al. 2016

PLoS ONE

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The reprogramming of cellular memory in specific cell types, and in visceral adipocytes in particular, appears to be a fundamental aspect of obesity and its related negative health outcomes. We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We developed fluorescence nuclear cytometry (FNC) and fluorescence activated nuclear sorting (FANS) of cellular nuclei from visceral adipose tissue (VAT) using the levels of the pan-adipocyte protein, peroxisome proliferator-activated receptor gamma-2 (PPARg2), to distinguish classes of PPARg2-Positive (PPARg2-Pos) adipocyte nuclei from PPARg2-Negative (PPARg2-Neg) leukocyte and endothelial cell nuclei. PPARg2-Pos nuclei were 10-fold enriched for most adipocyte marker transcripts relative to PPARg2-Neg nuclei. PPARg2-Pos nuclei showed 2- to 50-fold higher levels of transcripts encoding most of the chromatin-remodeling factors assayed, which regulate the methylation of histones and DNA cytosine (e.g., DNMT1, TET1, TET2, KDM4A, KMT2C, SETDB1, PAXIP1, ARID1A, JMJD6, CARM1, and PRMT5). PPARg2-Pos nuclei were large with decondensed chromatin. TAB-seq demonstrated 5-hydroxymethylcytosine (5hmC) levels were remarkably dynamic in gene bodies of various classes of VAT nuclei, dropping 3.8-fold from the highest quintile of expressed genes to the lowest. In short, VAT-derived adipocytes appear to be more actively remodeling their chromatin than non-adipocytes.

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Atypical Modes of CTCF Binding Facilitate Tissue-Specific and Neuronal Activity-Dependent Gene Expression States

Crewe,

Segev,

Rueda

et al. 2023

Mol Neurobiol

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The ubiquitous transcription factor CTCF promotes lineage-specific epigenomic remodeling and establishment of transcriptional networks driving cell differentiation

Cited by 9 publications

References 48 publications

Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues

Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues

Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine

Atypical Modes of CTCF Binding Facilitate Tissue-Specific and Neuronal Activity-Dependent Gene Expression States

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