scholarly journals Dissecting super-enhancer hierarchy based on chromatin interactions

2017 ◽  
Author(s):  
Jialiang Huang ◽  
Kailong Li ◽  
Wenqing Cai ◽  
Xin Liu ◽  
Yuannyu Zhang ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Binding Sites ◽  
Structural Organization ◽  
Gene Activation ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Intrinsic Properties ◽  
Genetic Ablation ◽  
Chromatin Interactions ◽  
Super Enhancer

AbstractRecent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization.

scholarly journals Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hong Wang ◽  
Aiping Duan ◽  
Jing Zhang ◽  
Qi Wang ◽  
Yuexian Xing ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Glucocorticoid Receptor ◽  
Protective Effect ◽  
Histone Modification ◽  
Regulatory Networks ◽  
Target Gene ◽  
Regulatory Elements ◽  
Chromatin Interactions ◽  
Super Enhancer

AbstractElucidating transcription mediated by the glucocorticoid receptor (GR) is crucial for understanding the role of glucocorticoids (GCs) in the treatment of diseases. Podocyte is a useful model for studying GR regulation because GCs are the primary medication for podocytopathy. In this study, we integrated data from transcriptome, transcription factor binding, histone modification, and genome topology. Our data reveals that the GR binds and activates selective regulatory elements in podocyte. The 3D interactome captured by HiChIP facilitates the identification of remote targets of GR. We found that GR in podocyte is enriched at transcriptional interaction hubs and super-enhancers. We further demonstrate that the target gene of the top GR-associated super-enhancer is indispensable to the effective functioning of GC in podocyte. Our findings provided insights into the mechanisms underlying the protective effect of GCs on podocyte, and demonstrate the importance of considering transcriptional interactions in order to fine-map regulatory networks of GR.

scholarly journals CREAM: Clustering of genomic REgions Analysis Method

2017 ◽  
Author(s):  
Seyed Ali Madani Tonekaboni ◽  
Parisa Mazrooei ◽  
Victor Kofia ◽  
Benjamin Haibe-Kains ◽  
Mathieu Lupien
Keyword(s):  
Expression Profiles ◽  
Gene Expression Profiles ◽  
R Package ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Analysis Method ◽  
Chromatin Interactions ◽  
Super Enhancer ◽  
Highly Expressed Genes ◽  
Genomic Regions

ABSTRACTCellular identity relies on cell type-specific gene expression profiles controlled by cis-regulatory elements (CREs), such as promoters, enhancers and anchors of chromatin interactions. CREs are unevenly distributed across the genome, giving rise to distinct subsets such as individual CREs and Clusters Of cis-Regulatory Elements (COREs), also known as super-enhancers. Identifying COREs is a challenge due to technical and biological features that entail variability in the distribution of distances between CREs within a given dataset. To address this issue, we developed a new unsupervised machine learning approach termed Clustering of genomic REgions Analysis Method (CREAM) that outperforms the Ranking Of Super Enhancer (ROSE) approach. Specifically CREAM identified COREs are enriched in CREs strongly bound by master transcription factors according to ChIP-seq signal intensity, are proximal to highly expressed genes, are preferentially found near genes essential for cell growth and are more predictive of cell identity. Moreover, we show that CREAM enables subtyping primary prostate tumor samples according to their CORE distribution across the genome. We further show that COREs are enriched compared to individual CREs at TAD boundaries and these are preferentially bound by CTCF and factors of the cohesin complex (e.g.: RAD21 and SMC3). Finally, using CREAM against transcription factor ChIP-seq reveals CTCF and cohesin-specific COREs preferentially at TAD boundaries compared to intra-TADs. CREAM is available as an open source R package (https://CRAN.R-project.org/package=CREAM) to identify COREs from cis-regulatory annotation datasets from any biological samples.

scholarly journals RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

2021 ◽  
Vol 119 (1) ◽  
pp. e2116222119
Author(s):  
Alexey A. Gavrilov ◽  
Rinat I. Sultanov ◽  
Mikhail D. Magnitov ◽  
Aleksandra A. Galitsyna ◽  
Erdem B. Dashinimaev ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Wide Spectrum ◽  
Noncoding Rnas ◽  
Ctcf Binding ◽  
Polycomb Repressive Complex 2 ◽  
Proximity Ligation ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Architectural Protein

Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However, neither of these techniques examines proteins involved in RNA–chromatin interactions. Here, we introduce RedChIP, a technique combining RNA–DNA proximity ligation and chromatin immunoprecipitation for identifying RNA–chromatin interactions mediated by a particular protein. Using antibodies against architectural protein CTCF and the EZH2 subunit of the Polycomb repressive complex 2, we identify a spectrum of cis- and trans-acting ncRNAs enriched at Polycomb- and CTCF-binding sites in human cells, which may be involved in Polycomb-mediated gene repression and CTCF-dependent chromatin looping. By providing a protein-centric view of RNA–DNA interactions, RedChIP represents an important tool for studies of nuclear ncRNAs.

scholarly journals The transcription factor STAT5 binds to distinct super-enhancer sites and controls Lrrc32 expression in a prominent autoimmune and allergic disease risk locus

2020 ◽  
Author(s):  
Lothar Hennighausen ◽  
Hye Kyung Lee
Keyword(s):  
Transcription Factor ◽  
Genetic Variants ◽  
Binding Sites ◽  
Disease Risk ◽  
Mammary Epithelium ◽  
Cell Type ◽  
Super Enhancer ◽  
Functional Understanding ◽  
Risk Locus ◽  
Definition Of

SummaryGenetic variants associated with diseases are enriched in genomic sequences linked to regulatory regions, such as enhancers, super-enhancers and possibly repressors, that control nearby and distant genes. A known allergic and autoimmune risk locus at chromosome 11q13.51,2 is associated with the LRRC32 gene, which encodes GARP, a protein critical for TGF-β delivery3. This region coincides with a candidate enhancer that was predicted by the presence of activating chromatin marks and contains a polymorphism significantly associated with GARP expression on CD4+CD127-CD25+ Treg cells4. In the mouse, binding of the cytokine-induced transcription factor STAT5 was detected at two sites within the expansive candidate enhancer region and a 2.3 kb deletion resulted in reduced Lrrc32 expression4. However, a clear definition of the enhancer units controlled by STAT5 and a functional understanding of STAT5 in the regulation of Lrrc32 are needed. Here we use high-resolution ChIP-seq and identify three STAT5 binding sites within the Lrrc32 super-enhancer, one shared between Treg cells and mammary epithelium and one specific to each respective cell type. Using mice that express only 10% of normal STAT5 levels we demonstrate the defining contribution of STAT5 in the activation of the Lrrc32 super-enhancer.

scholarly journals Gene activation and repression by the glucocorticoid receptor are mediated by sequestering Ep300 and two modes of chromatin binding

2019 ◽  
Author(s):  
Avital Sarusi Portuguez ◽  
Ivana Grbesa ◽  
Moran Tal ◽  
Rachel Deitch ◽  
Dana Raz ◽  
...  
Keyword(s):  
Glucocorticoid Receptor ◽  
Binding Sites ◽  
Gene Activation ◽  
Spatial Separation ◽  
Regulatory Elements ◽  
Chromatin Interaction ◽  
Chromatin Binding ◽  
Physiological Processes ◽  
Regulatory Loci ◽  
Open Question

ABSTRACTThe transcription factor glucocorticoid receptor (GR) is a key mediator of stress response and a broad range of physiological processes. How can GR rapidly activate the expression of some genes while repress others, remains an open question due to the challenge to associate GR binding sites (GBSs) to their distant gene targets. Mapping the full 3D scope of GR-responsive promoters using high-resolution 4C-seq unravelled spatial separation between chromatin interaction networks of GR-activated and repressed genes. Analysing GR binding sites and other regulatory loci in their functional 3D context revealed that GR sequesters the co-activator Ep300 from active non-GBS enhancers in both activated and repressed gene compartments. While this is sufficient for rapid gene repression, gene activation is countered by productive recruitment of Ep300 to GBS. Importantly, in GR-activated compartments Klf4 binding at non-GBS regulatory elements cluster in 3D with GBS and antagonizes GR activation. In addition, we revealed ROR and Rev-erb transcription factors as novel co-regulators for GR-mediated gene expression.

scholarly journals Controlling gene activation by enhancers through a drug-inducible topological insulator

2019 ◽  
Author(s):  
Taro Tsujimura ◽  
Osamu Takase ◽  
Masahiro Yoshikawa ◽  
Etsuko Sano ◽  
Matsuhiko Hayashi ◽  
...  
Keyword(s):  
Pluripotent Stem Cells ◽  
Binding Sites ◽  
Time Course ◽  
Gene Activation ◽  
Ctcf Binding ◽  
Control Gene ◽  
Expression Change ◽  
Krab Domain ◽  
Gene Enhancer ◽  
Drug Induction

AbstractWhile regulation of gene-enhancer interaction is better understood, its application remains limited. Here, we reconstituted arrays of CTCF binding sites and devised a synthetic topological insulator with tetO for chromatin-engineering (STITCH). By coupling STITCH with tetR linked to the KRAB domain to induce heterochromatin and disable the insulation, we developed a drug-inducible system to control gene activation by enhancers. We applied this to dissect MYC regulation in human pluripotent stem cells. Insertion of STITCH between MYC and the enhancer down-regulated MYC and affected its target transcriptome. Progressive mutagenesis of STITCH led to preferential escalation of the gene-enhancer interaction, corroborating the strong insulation ability of STITCH. The STITCH insertion altered epigenetic states around MYC. Time-course analysis by drug induction uncovered deposition and removal of H3K27me3 repressive marks follows and reflects, but does not precede and determine, the expression change. Thus the tool provided important insights in gene regulation, demonstrating its potency.

scholarly journals A super enhancer controls expression and chromatin architecture within the MHC class II locus

2019 ◽  
Vol 217 (2) ◽  
Author(s):  
Parimal Majumder ◽  
Joshua T. Lee ◽  
Andrew R. Rahmberg ◽  
Gaurav Kumar ◽  
Tian Mi ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
Three Dimensional ◽  
Class Ii ◽  
Ctcf Binding ◽  
Specific Gene ◽  
Mhc Ii ◽  
Chromatin Interactions ◽  
Super Enhancer ◽  
Cell Type Specific ◽  
Hla Dqa1

Super enhancers (SEs) play critical roles in cell type–specific gene regulation. The mechanisms by which such elements work are largely unknown. Two SEs termed DR/DQ-SE and XL9-SE are situated within the human MHC class II locus between the HLA-DRB1 and HLA-DQA1 genes and are highly enriched for disease-causing SNPs. To test the function of these elements, we used CRISPR/Cas9 to generate a series of mutants that deleted the SE. Deletion of DR/DQ-SE resulted in reduced expression of HLA-DRB1 and HLA-DQA1 genes. The SEs were found to interact with each other and the promoters of HLA-DRB1 and HLA-DQA1. DR/DQ-SE also interacted with neighboring CTCF binding sites. Importantly, deletion of DR/DQ-SE reduced the local chromatin interactions, implying that it functions as the organizer for the local three-dimensional architecture. These data provide direct mechanisms by which an MHC-II SE contributes to expression of the locus and suggest how variation in these SEs may contribute to human disease and altered immunity.

scholarly journals Genome-wide binding and mechanistic analyses of Smchd1-mediated epigenetic regulation

2015 ◽  
Vol 112 (27) ◽  
pp. E3535-E3544 ◽  
Author(s):  
Kelan Chen ◽  
Jiang Hu ◽  
Darcy L. Moore ◽  
Ruijie Liu ◽  
Sarah A. Kessans ◽  
...  
Keyword(s):  
Epigenetic Regulation ◽  
Transcriptional Control ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Dna And Rna ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Binding Factor ◽  
Structural Maintenance Of Chromosomes ◽  
Hinge Domain

Structural maintenance of chromosomes flexible hinge domain containing 1 (Smchd1) is an epigenetic repressor with described roles in X inactivation and genomic imprinting, but Smchd1 is also critically involved in the pathogenesis of facioscapulohumeral dystrophy. The underlying molecular mechanism by which Smchd1 functions in these instances remains unknown. Our genome-wide transcriptional and epigenetic analyses show that Smchd1 binds cis-regulatory elements, many of which coincide with CCCTC-binding factor (Ctcf) binding sites, for example, the clustered protocadherin (Pcdh) genes, where we show Smchd1 and Ctcf act in opposing ways. We provide biochemical and biophysical evidence that Smchd1–chromatin interactions are established through the homodimeric hinge domain of Smchd1 and, intriguingly, that the hinge domain also has the capacity to bind DNA and RNA. Our results suggest Smchd1 imparts epigenetic regulation via physical association with chromatin, which may antagonize Ctcf-facilitated chromatin interactions, resulting in coordinated transcriptional control.

Human IL-12(p35) gene activation involves selective remodeling of a single nucleosome within a region of the promoter containing critical Sp1-binding sites

Blood ◽  
2003 ◽  
Vol 101 (12) ◽  
pp. 4894-4902 ◽  
Author(s):  
Stanislas Goriely ◽  
Dominique Demonté ◽  
Séverine Nizet ◽  
Dominique De Wit ◽  
Fabienne Willems ◽  
...  
Keyword(s):  
Cell Line ◽  
Chromatin Remodeling ◽  
Binding Sites ◽  
Gene Activation ◽  
Regulatory Elements ◽  
Micrococcal Nuclease ◽  
Interleukin 12 ◽  
P35 Gene ◽  
Free Region ◽  
Ifn Γ

AbstractTo get insight into the regulation of human interleukin-12 (IL-12) synthesis, we determined the chromatin organization of the IL-12(p35) promoter region. First, we determined positioning of nucleosomes within the IL-12(p35) promoter using the indirect end-labeling technique in the THP-1 monocytic cell line. On stimulation with bacterial lipopolysaccharide (LPS) and interferon-γ (IFN-γ), hypersensitivity to digestion with DNase I, micrococcal nuclease, and specific restriction enzymes was detected in the region encompassing nucleotide (nt) –310 to –160, indicating selective inducible chromatin remodeling involving disruption of a single nucleosome (named nuc-2). Using p35 promoter deletion mutants and reporter gene assays, we demonstrated that the –396/–241 region contained critical cis-acting elements. Within this latter region, we characterized physically and functionally 2 Sp1-binding sites, which were acting as key regulatory elements for both basal and LPS/IFN-γ–inducible p35 gene expression: Sp1#1 lies within the remodeled nuc-2 region and Sp1#2 is located in the nucleosome-free region immediately upstream of nuc-2. Finally, we extended the chromatin structure analysis to dendritic cells (DCs) derived from human monocytes and observed the same nucleosomal organization and remodeling as in the THP-1 cell line. Moreover, we found that in DCs, LPS and IFN-γ synergized in the induction of nucleosomal remodeling and that chromatin remodeling at the p35 locus immediately preceded IL-12(p35) mRNA synthesis. Taken together, our results demonstrate that IL-12(p35) gene activation in the course of DC maturation involves selective and rapid remodeling of a single positioned nucleosome within a region of the promoter containing critical Sp1-binding sites.

CTCF function is modulated by neighboring DNA binding factors

2011 ◽  
Vol 89 (5) ◽  
pp. 459-468 ◽  
Author(s):  
Oliver Weth ◽  
Rainer Renkawitz
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Zinc Finger ◽  
Binding Sites ◽  
Zinc Finger Protein ◽  
Gene Activation ◽  
Ctcf Binding ◽  
Paternal Allele ◽  
Ctcf Binding Site ◽  
Enhancer Blocking

The zinc-finger protein CTCF was originally identified in the context of gene silencing and gene repression (Baniahmad et al. 1990; Lobanenkov et al. 1990). CTCF was later shown to be involved in several transcriptional mechanisms such as gene activation (Vostrov et al. 2002) and enhancer blocking (Filippova et al. 2001; Hark et al. 2000; Kanduri et al. 2000; Lutz et al. 2003; Szabó et al. 2000; Tanimoto et al. 2003; Phillips and Corces 2009; Bell et al. 1999; Zlatanova and Caiafa 2009a, 2009b). Insulators block the action of enhancers when positioned between enhancer and promoter. CTCF was found to be required in almost all cases of enhancer blocking tested in vertebrates. This CTCF-mediated enhancer blocking is in many instances conferred by constitutive CTCF action. For some examples however, a modulation of the enhancer blocking activity was documented (Lutz et al. 2003; Weth et al. 2010). One mechanism is achieved by regulation of binding to DNA. It was shown that CTCF is not able to bind to those binding-sites containing methylated CpG sequences. At the imprinting control region (ICR) of the Igf2/H19 locus the binding-site for CTCF on the paternal allele is methylated. This prevents DNA-binding of CTCF, resulting in the loss of enhancer blocking (Bell and Felsenfeld 2000; Chao et al. 2002; Filippova et al. 2001; Hark et al. 2000; Kanduri et al. 2000, 2002; Szabó et al. 2000; Takai et al. 2001). Not only can DNA methylation interfere with CTCF binding to DNA, it was also shown in one report that RNA transcription through the CTCF binding site results in CTCF eviction (Lefevre et al. 2008). In contrast to these cases most of the DNA sites are not differentially bound by CTCF. Even CTCF interaction with its cofactor cohesin does not seem to differ in different cell types (Schmidt et al. 2010). These results indicate that regulation of CTCF activity might be achieved by neighboring factors bound to DNA. In fact, whole genome analyses of CTCF binding sites identified several classes of neighboring sequences (Dickson et al. 2010; Boyle et al. 2010; Essien et al. 2009). Therefore, in this review we will summarize those results for which a combined action of CTCF with factors bound adjacently was found. These neighboring factors include the RNA polymerases I, II and III, another zinc finger factor VEZF1 and the factors YY1, SMAD, TR and Oct4. Each of these seems to influence, modulate or determine the function of CTCF. Thereby, at least some of the pleiotropic effects of CTCF can be explained.

Sign in / Sign up

Export Citation Format

Share Document