scholarly journals Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

2020 ◽  
Vol 6 (27) ◽  
pp. eaaz4012 ◽  
Author(s):  
Gustavo A. Ruiz Buendía ◽  
Marion Leleu ◽  
Flavia Marzetta ◽  
Ludovica Vanzan ◽  
Jennifer Y. Tan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Three Dimensional ◽  
Cag Repeat ◽  
Ctcf Binding ◽  
Chromatin Interaction ◽  
Chromatin Conformation ◽  
Repeat Instability ◽  
Ctg Repeats ◽  
Chromatin Interactions ◽  
Ctg Repeat

Expanded CAG/CTG repeats underlie 13 neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington’s disease (HD). Upon expansion, disease loci acquire heterochromatic characteristics, which may provoke changes to chromatin conformation and thereby affect both gene expression and repeat instability. Here, we tested this hypothesis by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD–derived cells. We find that allele sizes ranging from 15 to 1700 repeats displayed similar chromatin interaction profiles. This was true for both loci and for alleles with different DNA methylation levels and CTCF binding. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the conformation of the surrounding chromatin. We conclude that CAG/CTG repeat expansions are not enough to alter chromatin conformation in cis. Therefore, it is unlikely that changes in chromatin interactions drive repeat instability or changes in gene expression in these disorders.

scholarly journals Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

2019 ◽  
Author(s):  
Gustavo A. Ruiz Buendía ◽  
Marion Leleu ◽  
Flavia Marzetta ◽  
Ludovica Vanzan ◽  
Jennifer Y. Tan ◽  
...  
Keyword(s):  
Neurological Disorders ◽  
Three Dimensional ◽  
Repeat Expansion ◽  
Ctcf Binding ◽  
Chromatin Interaction ◽  
Ctg Repeats ◽  
Repeat Tract ◽  
Chromatin Interactions ◽  
Chromatin Folding ◽  
Ctg Repeat

AbstractExpanded CAG/CTG repeats underlie thirteen neurological disorders, including myotonic dystrophy (DM1) and Huntington’s disease (HD). Upon expansion, CAG/CTG repeat loci acquire heterochromatic characteristics. This observation raises the hypothesis that repeat expansion provokes changes to higher order chromatin folding and thereby affects both gene expression in cis and the genetic instability of the repeat tract. Here we tested this hypothesis directly by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD patient-derived cells. Surprisingly, chromatin contacts remain unchanged upon repeat expansion at both loci. This was true for loci with different DNA methylation levels and CTCF binding. Repeat sizes ranging from 15 to 1,700 displayed strikingly similar chromatin interaction profiles. Our findings argue that extensive changes in heterochromatic properties are not enough to alter chromatin folding at expanded CAG/CTG repeat loci. Moreover, the ectopic insertion of an expanded repeat tract did not change three-dimensional chromatin contacts. We conclude that expanded CAG/CTG repeats have little to no effect on chromatin conformation.

scholarly journals Transcriptionally Repressive Chromatin Remodelling and CpG Methylation in the Presence of Expanded CTG-Repeats at the DM1 Locus

2013 ◽  
Vol 2013 ◽  
pp. 1-16 ◽  
Author(s):  
Judith Rixt Brouwer ◽  
Aline Huguet ◽  
Annie Nicole ◽  
Arnold Munnich ◽  
Geneviève Gourdon
Keyword(s):  
Transgenic Mice ◽  
Trinucleotide Repeat ◽  
Cpg Methylation ◽  
Chromatin Remodelling ◽  
Ctcf Binding ◽  
Type I ◽  
Repeat Instability ◽  
Ctg Repeats ◽  
Repressive Chromatin ◽  
Ctg Repeat

An expanded CTG-repeat in the 3′ UTR of theDMPKgene is responsible for myotonic dystrophy type I (DM1). Somatic and intergenerational instability cause the disease to become more severe during life and in subsequent generations. Evidence is accumulating that trinucleotide repeat instability and disease progression involve aberrant chromatin dynamics. We explored the chromatin environment in relation to expanded CTG-repeat tracts in hearts from transgenic mice carrying the DM1 locus with different repeat lengths. Using bisulfite sequencing we detected abundant CpG methylation in the regions flanking the expanded CTG-repeat. CpG methylation was postulated to affect CTCF binding but we found that CTCF binding is not affected by CTG-repeat length in our transgenic mice. We detected significantly decreasedDMPKsense andSIX5transcript expression levels in mice with expanded CTG-repeats. Expression of the DM1 antisense transcript was barely affected by CTG-repeat expansion. In line with altered gene expression, ChIP studies revealed a locally less active chromatin conformation around the expanded CTG-repeat, namely, decreased enrichment of active histone mark H3K9/14Ac and increased H3K9Me3 enrichment (repressive chromatin mark). We also observed binding of PCNA around the repeats, a candidate that could launch chromatin remodelling cascades at expanded repeats, ultimately affecting gene transcription and repeat instability.

scholarly journals Contribution of CTCF binding to transcriptional activity at the HOXA locus in NPM1-mutant AML cells

2020 ◽  
Author(s):  
Reza Ghasemi ◽  
Heidi Struthers ◽  
Elisabeth R. Wilson ◽  
David H. Spencer
Keyword(s):  
Gene Expression ◽  
Transcriptional Activity ◽  
Three Dimensional ◽  
Ctcf Binding ◽  
Chromatin Domain ◽  
Intrinsic Factors ◽  
Chromatin Loops ◽  
Chromatin Interactions ◽  
The Common

AbstractTranscriptional regulation of the HOXA genes is thought to involve CTCF-mediated chromatin loops and the opposing actions of the COMPASS and Polycomb epigenetic complexes. We investigated the role of these mechanisms at the HOXA cluster in AML cells with the common NPM1c mutation, which express both HOXA and HOXB genes. CTCF binding at the HOXA locus is conserved across primary AML samples, regardless of HOXA gene expression, and defines a continuous chromatin domain marked by COMPASS-associated histone H3 trimethylation in NPM1-mutant primary AML samples. Profiling of the three-dimensional chromatin architecture of NPM1-mutant OCI-AML3 cells identified chromatin loops between the active HOXA9-HOXA11 genes and loci in the SNX10 gene and an intergenic region located 1.4Mbp upstream of the HOXA locus. Deletion of CTCF binding sites in OCI-AML3 cells reduced these interactions, but resulted in new, CTCF-independent loops with regions in the SKAP2 gene that were marked by enhancer-associated histone modifications in primary AML samples. HOXA gene expression was maintained in the CTCF deletion mutants, indicating that transcriptional activity at the HOXA locus in NPM1-mutant AML cells does not require long-range CTCF-mediated chromatin interactions, and instead may be driven by intrinsic factors within the HOXA gene cluster.

scholarly journals multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments

2019 ◽  
Vol 35 (17) ◽  
pp. 2916-2923 ◽  
Author(s):  
John C Stansfield ◽  
Kellen G Cresswell ◽  
Mikhail G Dozmorov
Keyword(s):  
Comparative Analysis ◽  
A Priori ◽  
Three Dimensional ◽  
R Package ◽  
Supplementary Information ◽  
Chromatin Interaction ◽  
Model Framework ◽  
Chromatin Interactions ◽  
Loess Regression ◽  
Sequencing Studies

Abstract Motivation With the development of chromatin conformation capture technology and its high-throughput derivative Hi-C sequencing, studies of the three-dimensional interactome of the genome that involve multiple Hi-C datasets are becoming available. To account for the technology-driven biases unique to each dataset, there is a distinct need for methods to jointly normalize multiple Hi-C datasets. Previous attempts at removing biases from Hi-C data have made use of techniques which normalize individual Hi-C datasets, or, at best, jointly normalize two datasets. Results Here, we present multiHiCcompare, a cyclic loess regression-based joint normalization technique for removing biases across multiple Hi-C datasets. In contrast to other normalization techniques, it properly handles the Hi-C-specific decay of chromatin interaction frequencies with the increasing distance between interacting regions. multiHiCcompare uses the general linear model framework for comparative analysis of multiple Hi-C datasets, adapted for the Hi-C-specific decay of chromatin interaction frequencies. multiHiCcompare outperforms other methods when detecting a priori known chromatin interaction differences from jointly normalized datasets. Applied to the analysis of auxin-treated versus untreated experiments, and CTCF depletion experiments, multiHiCcompare was able to recover the expected epigenetic and gene expression signatures of loss of chromatin interactions and reveal novel insights. Availability and implementation multiHiCcompare is freely available on GitHub and as a Bioconductor R package https://bioconductor.org/packages/multiHiCcompare. Supplementary information Supplementary data are available at Bioinformatics online.

The role of CTCF in coordinating the expression of single gene loci

2011 ◽  
Vol 89 (5) ◽  
pp. 489-494 ◽  
Author(s):  
Austin E Gillen ◽  
Ann Harris
Keyword(s):  
Gene Expression ◽  
Mhc Class Ii ◽  
Noncoding Rna ◽  
Single Gene ◽  
Functional Model ◽  
Gene Clusters ◽  
Ctcf Binding ◽  
Chromatin Interactions ◽  
Insulator Elements

The CCCTC-binding factor (CTCF), which binds insulator elements in vertebrates, also facilitates coordinated gene expression at several gene clusters, including the β-globin, Igf2/H19 (insulin like growth factor 2/H19 noncoding RNA), and major histocompatibility complex (MHC) class II loci. CTCF controls expression of these genes both by enabling insulator function and facilitating higher order chromatin interactions. While the role of CTCF in gene regulation is best studied at these multi-gene loci, there is also evidence that CTCF contributes to the regulated expression of single genes. Here, we discuss how CTCF participates in coordinating gene expression at the CFTR (cystic fibrosis transmembrane conductance regulator) and IFNG (interferon-gamma) loci. We consider the structural similarities between the loci with regard to CTCF-binding elements, the possible interaction between nuclear receptors and CTCF, and the role of CTCF in chromatin looping at these genes. These comparisons reveal a functional model that may be applicable to other single-gene loci that require CTCF for coordinated gene expression.

scholarly journals Expanded CAG/CTG repeats resist gene silencing mediated by targeted Epigenome editing

2021 ◽  
Author(s):  
Bin Yang ◽  
Alicia C Borgeaud ◽  
Marcela Buřičová ◽  
Lorène Aeschbach ◽  
Oscar Rodríguez-Lima ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Dna Methyltransferase ◽  
Rational Design ◽  
Repeat Instability ◽  
Efficient Treatment ◽  
Ctg Repeats ◽  
Epigenome Editing ◽  
Molecule Inhibitor ◽  
Gfp Reporter ◽  
Ctg Repeat

Abstract Expanded CAG/CTG repeat disorders affect over 1 in 2500 individuals worldwide. Potential therapeutic avenues include gene silencing and modulation of repeat instability. However, there are major mechanistic gaps in our understanding of these processes, which prevent the rational design of an efficient treatment. To address this, we developed a novel system, ParB/ANCHOR-mediated Inducible Targeting (PInT), in which any protein can be recruited at will to a GFP reporter containing an expanded CAG/CTG repeat. Previous studies have implicated the histone deacetylase HDAC5 and the DNA methyltransferase DNMT1 as modulators of repeat instability via mechanisms that are not fully understood. Using PInT, we found no evidence that HDAC5 or DNMT1 modulate repeat instability upon targeting to the expanded repeat, suggesting that their effect is independent of local chromatin structure. Unexpectedly, we found that expanded CAG/CTG repeats reduce the effectiveness of gene silencing mediated by targeting HDAC5 and DNMT1. The repeat-length effect in gene silencing by HDAC5 was abolished by a small molecule inhibitor of HDAC3. Our results have important implications on the design of epigenome editing approaches for expanded CAG/CTG repeat disorders. PInT is a versatile synthetic system to study the effect of any sequence of interest on epigenome editing.

scholarly journals H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells

Development ◽  
2020 ◽  
Vol 147 (23) ◽  
pp. dev188516
Author(s):  
Jiji T. Kurup ◽  
Zhijun Han ◽  
Wenfei Jin ◽  
Benjamin L. Kidder
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Es Cells ◽  
Three Dimensional ◽  
Embryonic Stem ◽  
Pericentric Heterochromatin ◽  
Es Cell ◽  
Chromatin Interactions ◽  
Repressive Histone Modification ◽  
Dna Elements

ABSTRACTHeterochromatin, a densely packed chromatin state that is transcriptionally silent, is a critical regulator of gene expression. However, it is unclear how the repressive histone modification H4K20me3 or the histone methyltransferase SUV420H2 regulates embryonic stem (ES) cell fate by patterning the epigenetic landscape. Here, we report that depletion of SUV420H2 leads to a near-complete loss of H4K20me3 genome wide, dysregulated gene expression and delayed ES cell differentiation. SUV420H2-bound regions are enriched with repetitive DNA elements, which are de-repressed in SUV420H2 knockout ES cells. Moreover, SUV420H2 regulation of H4K20me3-marked heterochromatin controls chromatin architecture, including fine-scale chromatin interactions in pluripotent ES cells. Our results indicate that SUV420H2 plays a crucial role in stabilizing the three-dimensional chromatin landscape of ES cells, as loss of SUV420H2 resulted in A/B compartment switching, perturbed chromatin insulation, and altered chromatin interactions of pericentric heterochromatin and surrounding regions, indicative of localized decondensation. In addition, depletion of SUV420H2 resulted in compromised interactions between H4K20me3 and gene-regulatory regions. Together, these findings describe a new role for SUV420H2 in regulating the chromatin landscape of ES cells.

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 Loop competition and extrusion model predicts CTCF interaction specificity

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Wang Xi ◽  
Michael A. Beer
Keyword(s):  
Binding Site ◽  
Critical Role ◽  
Three Dimensional ◽  
Ctcf Binding ◽  
Chromatin Interaction ◽  
Ctcf Binding Site ◽  
Loop Formation ◽  
Critical Determinant ◽  
Frequency Changes ◽  
Transcriptional Gene Regulation

AbstractThree-dimensional chromatin looping interactions play an important role in constraining enhancer–promoter interactions and mediating transcriptional gene regulation. CTCF is thought to play a critical role in the formation of these loops, but the specificity of which CTCF binding events form loops and which do not is difficult to predict. Loops often have convergent CTCF binding site motif orientation, but this constraint alone is only weakly predictive of genome-wide interaction data. Here we present an easily interpretable and simple mathematical model of CTCF mediated loop formation which is consistent with Cohesin extrusion and can predict ChIA-PET CTCF looping interaction measurements with high accuracy. Competition between overlapping loops is a critical determinant of loop specificity. We show that this model is consistent with observed chromatin interaction frequency changes induced by CTCF binding site deletion, inversion, and mutation, and is also consistent with observed constraints on validated enhancer–promoter interactions.

scholarly journals Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map

2020 ◽  
Author(s):  
Timothy Kunz ◽  
Lila Rieber ◽  
Shaun Mahony
Keyword(s):  
Genome Organization ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Interaction Space ◽  
The Self ◽  
Chromatin Interaction ◽  
High Dimensional ◽  
Self Organizing Map ◽  
Two Dimensional ◽  
Chromatin Interactions

ABSTRACTFew existing methods enable the visualization of relationships between regulatory genomic activities and genome organization as captured by Hi-C experimental data. Genome-wide Hi-C datasets are often displayed using “heatmap” matrices, but it is difficult to intuit from these heatmaps which biochemical activities are compartmentalized together. High-dimensional Hi-C data vectors can alternatively be projected onto three-dimensional space using dimensionality reduction techniques. The resulting three-dimensional structures can serve as scaffolds for projecting other forms of genomic information, thereby enabling the exploration of relationships between genome organization and various genome annotations. However, while three-dimensional models are contextually appropriate for chromatin interaction data, some analyses and visualizations may be more intuitively and conveniently performed in two-dimensional space.We present a novel approach to the visualization and analysis of chromatin organization based on the Self-Organizing Map (SOM). The SOM algorithm provides a two-dimensional manifold which adapts to represent the high dimensional chromatin interaction space. The resulting data structure can then be used to assess the relationships between regulatory genomic activities and chromatin interactions. For example, given a set of genomic coordinates corresponding to a given biochemical activity, the degree to which this activity is segregated or compartmentalized in chromatin interaction space can be intuitively visualized on the 2D SOM grid and quantified using Lorenz curve analysis. We demonstrate our approach for exploratory analysis of genome compartmentalization in a high-resolution Hi-C dataset from the human GM12878 cell line. Our SOM-based approach provides an intuitive visualization of the large-scale structure of Hi-C data and serves as a platform for integrative analyses of the relationships between various genomic activities and genome organization.

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