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.

scholarly journals In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

2021 ◽  
Author(s):  
Chiara Anania ◽  
Rafael D. Acemel ◽  
Johanna Jedamzick ◽  
Adriano Bolondi ◽  
Giulia Cova ◽  
...  
Keyword(s):  
Target Genes ◽  
Domain Boundary ◽  
Boundary Function ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Multiple Levels ◽  
Developmental Principles

Vertebrate genomes organize into topologically associating domains (TADs), delimited by boundaries that insulate regulatory elements from non-target genes. However, how boundary function is established is not well understood. Here, we combine genome-wide analyses and transgenic mouse assays to dissect the regulatory logic of clustered-CTCF boundaries in vivo, interrogating their function at multiple levels: chromatin interactions, transcription and phenotypes. Individual CTCF binding sites (CBS) deletions revealed that the characteristics of specific sites can outweigh other factors like CBS number and orientation. Combined deletions demonstrated that CBS cooperate redundantly and provide boundary robustness. We show that divergent CBS signatures are not strictly required for effective insulation and that chromatin loops formed by non-convergently oriented sites could be mediated by a loop interference mechanism. Further, we observe that insulation strength constitutes a quantitative modulator of gene expression and phenotypes. Our results highlight the modular nature of boundaries and their control over developmental processes.

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.

An emerging role of chromatin-interacting RNA-binding proteins in transcription regulation

2020 ◽  
Vol 64 (6) ◽  
pp. 907-918
Author(s):  
Xian Du ◽  
Rui Xiao
Keyword(s):  
Transcription Regulation ◽  
Transcriptional Control ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Key Factors ◽  
Transcription Control ◽  
Chromatin Interactions ◽  
Genome Wide

Abstract Transcription factors (TFs) are well-established key factors orchestrating gene transcription, and RNA-binding proteins (RBPs) are mainly thought to participate in post-transcriptional control of gene. In fact, these two steps are functionally coupled, offering a possibility for reciprocal communications between transcription and regulatory RNAs and RBPs. Recently, a series of exploratory studies, utilizing functional genomic strategies, have revealed that RBPs are prevalently involved in transcription control genome-wide through their interactions with chromatin. Here, we present a refined census of RBPs to grope for such an emerging role and discuss the global view of RBP–chromatin interactions and their functional diversities in transcription regulation.

scholarly journals Deciphering essential cistromes using genome-wide CRISPR screens

2019 ◽  
Vol 116 (50) ◽  
pp. 25186-25195 ◽  
Author(s):  
Teng Fei ◽  
Wei Li ◽  
Jingyu Peng ◽  
Tengfei Xiao ◽  
Chen-Hao Chen ◽  
...  
Keyword(s):  
Predictive Models ◽  
Binding Sites ◽  
Regulatory Elements ◽  
High Accuracy ◽  
Essential Genes ◽  
Ctcf Binding ◽  
Prostate Cancer Cells ◽  
Regression Methods ◽  
Genome Wide ◽  
Breast And Prostate Cancer

Although millions of transcription factor binding sites, or cistromes, have been identified across the human genome, defining which of these sites is functional in a given condition remains challenging. Using CRISPR/Cas9 knockout screens and gene essentiality or fitness as the readout, we systematically investigated the essentiality of over 10,000 FOXA1 and CTCF binding sites in breast and prostate cancer cells. We found that essential FOXA1 binding sites act as enhancers to orchestrate the expression of nearby essential genes through the binding of lineage-specific transcription factors. In contrast, CRISPR screens of the CTCF cistrome revealed 2 classes of essential binding sites. The first class of essential CTCF binding sites act like FOXA1 sites as enhancers to regulate the expression of nearby essential genes, while a second class of essential CTCF binding sites was identified at topologically associated domain (TAD) boundaries and display distinct characteristics. Using regression methods trained on our screening data and public epigenetic profiles, we developed a model to predict essential cis-elements with high accuracy. The model for FOXA1 essentiality correctly predicts noncoding variants associated with cancer risk and progression. Taken together, CRISPR screens of cis-regulatory elements can define the essential cistrome of a given factor and can inform the development of predictive models of cistrome function.

scholarly journals CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

2019 ◽  
Author(s):  
Christopher T. Clarkson ◽  
Emma A. Deeks ◽  
Ralph Samarista ◽  
Hulkar Mamayusupova ◽  
Victor B. Zhurkin ◽  
...  
Keyword(s):  
Neural Progenitor Cells ◽  
Embryonic Stem ◽  
Cell Types ◽  
Ctcf Binding ◽  
Embryonic Fibroblasts ◽  
Genome Wide ◽  
Binding Factor ◽  
Chromatin Boundary ◽  
Nucleosome Array ◽  
The Relationship

AbstractThe CCCTC-binding factor (CTCF) organises the genome in 3D through DNA loops and in 1D by setting boundaries isolating different chromatin states, but these processes are not well understood. Here we focus on the relationship between CTCF binding and the decrease of the Nucleosome Repeat Length (NRL) for ∼20 adjacent nucleosomes, affecting up to 10% of the mouse genome. We found that the chromatin boundary near CTCF is created by the nucleosome-depleted region (NDR) asymmetrically located >40 nucleotides 5’-upstream from the centre of CTCF motif. The strength of CTCF binding to DNA is correlated with the decrease of NRL near CTCF and anti-correlated with the level of asymmetry of the nucleosome array. Individual chromatin remodellers have different contributions, with Snf2h having the strongest effect on the NRL decrease near CTCF and Chd4 playing a major role in the symmetry breaking. Upon differentiation of embryonic stem cells to neural progenitor cells and embryonic fibroblasts, a subset of common CTCF sites preserved in all three cell types maintains a relatively small local NRL despite genome-wide NRL increase. The sites which lost CTCF upon differentiation are characterised by nucleosome rearrangement 3’-downstream, but the boundary defined by the NDR 5’-upstream of CTCF motif remains.

scholarly journals Intra- and inter-chromosomal chromatin interactions mediate genetic effects on regulatory networks

2017 ◽  
Author(s):  
O. Delaneau ◽  
M. Zazhytska ◽  
C. Borel ◽  
C. Howald ◽  
S. Kumar ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Cell Types ◽  
Regulatory Elements ◽  
Regulatory Domains ◽  
Regulatory Variants ◽  
Chromatin Interactions ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Cell Type Specific ◽  
Cis And Trans

SummaryGenome-wide studies on the genetic basis of gene expression and the structural properties of chromatin have considerably advanced our understanding of the function of the human genome. However, it remains unclear how structure relates to function and, in this work, we aim at bridging both by assembling a dataset that combines the activity of regulatory elements (e.g. enhancers and promoters), expression of genes and genetic variations of 317 individuals and across two cell types. We show that the regulatory activity is structured within 12,583 Cis Regulatory Domains (CRDs) that are cell type specific and highly reflective of the local (i.e. Topologically Associating Domains) and global (i.e. A/B nuclear compartments) nuclear organization of the chromatin. These CRDs essentially delimit the sets of active regulatory elements involved in the transcription of most genes, thereby capturing complex regulatory networks in which the effects of regulatory variants are propagated and combined to finally mediate expression Quantitative Trait Loci. Overall, our analysis reveals the complexity and specificity of cis and trans regulatory networks and their perturbation by genetic variation.

scholarly journals Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions

2020 ◽  
Vol 48 (17) ◽  
pp. 9606-9620
Author(s):  
Gongcheng Hu ◽  
Xiaotao Dong ◽  
Shixin Gong ◽  
Yawei Song ◽  
Andrew P Hutchins ◽  
...  
Keyword(s):  
Binding Sites ◽  
Wide Distribution ◽  
Ctcf Binding ◽  
Loop Formation ◽  
Systematic Screening ◽  
Chromatin Interactions ◽  
Binding Partners ◽  
Number Of Factors ◽  
Genome Wide ◽  
Localization Analysis

Abstract CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators by co-localization analysis with CTCF. We screened all factors that had ChIP-seq data in humans by co-localization analysis with human super conserved CTCF (hscCTCF) binding sites, and identified many new factors that overlapped with hscCTCF binding sites. Combined with CTCF loop information, we observed that clustered factors could promote CTCF loops. After in-depth mining of each factor, we found that many factors might have the potential to promote CTCF loops. Our data further demonstrated that BHLHE40 affected CTCF loops by regulating CTCF binding. Together, this study revealed that many factors have the potential to participate in or regulate CTCF loops, and discovered a new role for BHLHE40 in modulating CTCF loop formation.

scholarly journals A dementia-associated risk variant near TMEM106B alters chromatin architecture and gene expression

2017 ◽  
Author(s):  
Michael D. Gallagher ◽  
Marijan Posavi ◽  
Peng Huang ◽  
Travis L. Unger ◽  
Yosef Berlyand ◽  
...  
Keyword(s):  
Neurodegenerative Diseases ◽  
Genetic Variants ◽  
Frontotemporal Lobar Degeneration ◽  
Disease Risk ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Common Genetic Variants ◽  
Depth Analysis

ABSTRACTNeurodegenerative diseases pose an extraordinary threat to the world’s aging population, yet no disease-modifying therapies are available. While genome-wide association studies (GWAS) have identified hundreds of novel risk loci for neurodegeneration, the mechanisms by which these loci influence disease risk are largely unknown. Indeed, of the many thousands of SNP-trait associations identified by GWAS over the past ~10 years, very few are understood mechanistically. Here, we investigate the association of common genetic variants at the 7p21 locus with risk for the neurodegenerative disease frontotemporal lobar degeneration. We show that variants associated with disease risk correlate with increased brain expression of the 7p21 gene TMEM106B, and no other genes. Furthermore, incremental increases in TMEM106B levels result in incremental increases in lysosomal phenotypes and cell toxicity. We then combine fine-mapping, bioinformatics, and bench-based approaches to functionally characterize all candidate causal variants at this locus. This approach identified a noncoding variant, rs1990620, which differentially recruits CTCF, influencing CTCF-mediated long-range chromatin looping interactions between multiple cis-regulatory elements, including the TMEM106B promoter. Our findings thus provide an in-depth analysis of the 7p21 locus linked by GWAS to frontotemporal lobar degeneration, nominating a causal variant and a causal mechanism for allele-specific expression and disease association at this locus. Finally, we show that genetic variants associated with risk for neurodegenerative diseases beyond frontotemporal lobar degeneration are enriched in brain CTCF-binding sites genome-wide, implicating CTCF-mediated gene regulation in risk for neurodegeneration more generally.

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.

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