scholarly journals Large-Scale Genomic Reorganizations of Topological Domains (TADs) at the HoxD Locus

2017 ◽  
Author(s):  
Pierre J. Fabre ◽  
Marion Leleu ◽  
Benjamin H. Mormann ◽  
Lucille Delisle ◽  
Daan Noordermeer ◽  
...  
Keyword(s):  
Long Range ◽  
Transcriptional Activation ◽  
Limb Development ◽  
Large Scale ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Sequence Specificity ◽  
Chromosome Conformation ◽  
Topological Domains ◽  
Genomic Deletions

ABSTRACTBackgroundThe transcriptional activation of Hoxd genes during mammalian limb development involves dynamic interactions with the two Topologically Associating Domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior Hoxd genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts. To assess the structure-function relationships underlying such interactions, we measured compaction levels and TAD discreteness using a combination of chromosome conformation capture (4C-seq) and DNA FISH.ResultsWe challenged the robustness of the TAD architecture by using a series of genomic deletions and inversions that impact the integrity of this chromatin domain and that remodel the long-range contacts. We report multi-partite associations between Hoxd genes and up to three enhancers and show that breaking the native chromatin topology leads to the remodelling of TAD structure.ConclusionsOur results reveal that the re-composition of TADs architectures after severe genomic re-arrangements depends on a boundary-selection mechanism that uses CTCF-mediated gating of long-range contacts in combination with genomic distance and, to a certain extent, sequence specificity.

scholarly journals Large-scale chromatin structure of inducible genes: transcription on a condensed, linear template

2009 ◽  
Vol 185 (1) ◽  
pp. 87-100 ◽  
Author(s):  
Yan Hu ◽  
Igor Kireev ◽  
Matt Plutz ◽  
Nazanin Ashourian ◽  
Andrew S. Belmont
Keyword(s):  
Chromatin Structure ◽  
Transcriptional Activation ◽  
Large Scale ◽  
Nuclear Speckles ◽  
Interphase Chromosome ◽  
Chromosome Conformation ◽  
Dynamic Events ◽  
Classical Models ◽  
Chromatin Fibers

The structure of interphase chromosomes, and in particular the changes in large-scale chromatin structure accompanying transcriptional activation, remain poorly characterized. Here we use light microscopy and in vivo immunogold labeling to directly visualize the interphase chromosome conformation of 1–2 Mbp chromatin domains formed by multi-copy BAC transgenes containing 130–220 kb of genomic DNA surrounding the DHFR, Hsp70, or MT gene loci. We demonstrate near-endogenous transcription levels in the context of large-scale chromatin fibers compacted nonuniformly well above the 30-nm chromatin fiber. An approximately 1.5–3-fold extension of these large-scale chromatin fibers accompanies transcriptional induction and active genes remain mobile. Heat shock–induced Hsp70 transgenes associate with the exterior of nuclear speckles, with Hsp70 transcripts accumulating within the speckle. Live-cell imaging reveals distinct dynamic events, with Hsp70 transgenes associating with adjacent speckles, nucleating new speckles, or moving to preexisting speckles. Our results call for reexamination of classical models of interphase chromosome organization.

scholarly journals Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

2021 ◽  
Author(s):  
Abrar Aljahani ◽  
Peng Hua ◽  
Magdalena A. Karpinska ◽  
Kimberly Quililan ◽  
James O. J. Davies ◽  
...  
Keyword(s):  
Large Scale ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Interaction Data ◽  
Chromosome Conformation ◽  
Regulatory Interactions ◽  
Nano Scale ◽  
Topologically Associating Domains ◽  
Scale Structures ◽  
Local Insulation

Enhancers and promoters predominantly interact within large-scale topologically associating domains (TADs), which are formed by loop extrusion mediated by cohesin and CTCF. However, it is unclear whether complex chromatin structures exist at sub-kilobase-scale and to what extent fine-scale regulatory interactions depend on loop extrusion. To address these questions, we present an MNase-based chromosome conformation capture (3C) approach, which has enabled us to generate the most detailed local interaction data to date and precisely investigate the effects of cohesin and CTCF depletion on chromatin architecture. Our data reveal that cis-regulatory elements have distinct internal nano-scale structures, within which local insulation is dependent on CTCF, but which are independent of cohesin. In contrast, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression.

scholarly journals A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
A. Marieke Oudelaar ◽  
Caroline L. Harrold ◽  
Lars L. P. Hanssen ◽  
Jelena M. Telenius ◽  
Douglas R. Higgs ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Gene Promoters ◽  
Multiple Promoters ◽  
Chromatin Interactions ◽  
Technological Advances ◽  
Single Complex ◽  
Membrane Bound

AbstractSpecific communication between gene promoters and enhancers is critical for accurate regulation of gene expression. However, it remains unclear how specific interactions between multiple regulatory elements contained within a single chromatin domain are coordinated. Recent technological advances which can detect multi-way chromatin interactions at single alleles can provide insights into how multiple regulatory elements cooperate or compete for transcriptional activation. Here, we use such an approach to investigate how interactions of the α-globin enhancers are distributed between multiple promoters in a mouse model in which the α-globin domain is extended to include several additional genes. Our data show that gene promoters do not form mutually exclusive interactions with enhancers, but all interact simultaneously in a single complex. These findings suggest that promoters do not structurally compete for interactions with enhancers, but form a regulatory hub structure, which is consistent with recent models of transcriptional activation occurring in non-membrane bound nuclear compartments.

scholarly journals Allele-specific alternative splicing in human tissues

2020 ◽  
Author(s):  
Kofi Amoah ◽  
Yun-Hua Esther Hsiao ◽  
Jae Hoon Bahn ◽  
Yiwei Sun ◽  
Christina Burghard ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Genetic Variants ◽  
Large Scale ◽  
Phenotypic Diversity ◽  
Regulatory Elements ◽  
Similar Degree ◽  
Human Tissues ◽  
Sequence Specificity ◽  
Functional Variants ◽  
Allele Specific

AbstractAlternative splicing is an RNA processing mechanism that affects most genes in human, contributing to disease mechanisms and phenotypic diversity. The regulation of splicing involves an intricate network of cis-regulatory elements and trans-acting factors. Due to their high sequence specificity, cis-regulation of splicing can be altered by genetic variants, significantly affecting splicing outcomes. Recently, multiple methods have been applied to understanding the regulatory effects of genetic variants on splicing. However, it is still challenging to go beyond apparent association to pinpoint functional variants. To fill in this gap, we utilized large-scale datasets of the Genotype-Tissue Expression (GTEx) project to study genetically-modulated alternative splicing (GMAS) via identification of allele-specific splicing events. We demonstrate that GMAS events are shared across tissues and individuals more often than expected by chance, consistent with their genetically driven nature. Moreover, although the allelic bias of GMAS exons varies across samples, the degree of variation is similar across tissues vs. individuals. Thus, genetic background drives the GMAS pattern to a similar degree as tissue-specific splicing mechanisms. Leveraging the genetically driven nature of GMAS, we developed a new method to predict functional splicing-altering variants, built upon a genotype-phenotype concordance model across samples. Complemented by experimental validations, this method predicted >1000 functional variants, many of which may alter RNA-protein interactions. Lastly, 72% of GMAS-associated SNPs were in linkage disequilibrium with GWAS-reported SNPs, and such association was enriched in tissues of relevance for specific traits/diseases. Our study enables a comprehensive view of genetically driven splicing variations in human tissues.

scholarly journals Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness

2021 ◽  
pp. gr.275901.121
Author(s):  
Alexandre Laverre ◽  
Eric Tannier ◽  
Anamaria Necsulea
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Large Scale ◽  
Target Genes ◽  
Expression Profiles ◽  
Regulatory Element ◽  
Gene Expression Profiles ◽  
Evolutionary Conservation ◽  
Regulatory Elements ◽  
Regulatory Landscapes

Gene expression is regulated through complex molecular interactions, involving cis-acting elements that can be situated far away from their target genes. Data on long-range contacts between promoters and regulatory elements is rapidly accumulating. However, it remains unclear how these regulatory relationships evolve and how they contribute to the establishment of robust gene expression profiles. Here, we address these questions by comparing genome-wide maps of promoter-centered chromatin contacts in mouse and human. We show that there is significant evolutionary conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve not only regulatory element sequences but also their chromatin contacts with target genes. The extent of evolutionary conservation is remarkable for long-range promoter-enhancer contacts, illustrating how the structure of regulatory landscapes constrains large-scale genome evolution. We show that the evolution of cis-regulatory landscapes, measured in terms of distal element sequences, synteny or contacts with target genes, is significantly associated with gene expression evolution.

A Runx1 Interactome Identifies Novel Hematopoietic Enhancers

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 726-726
Author(s):  
Judith Marsman ◽  
Amarni L Thomas ◽  
Motomi Osato ◽  
Justin M O'Sullivan ◽  
Julia A Horsfield
Keyword(s):  
Transcription Factor ◽  
Long Range ◽  
Conflicts Of Interest ◽  
K562 Cells ◽  
Regulatory Elements ◽  
Hematopoietic Progenitor Cell ◽  
Circular Chromosome ◽  
Chromosome Conformation ◽  
Dna Elements ◽  
Runx1 Expression

Abstract The transcription factor Runx1 is essential for definitive hematopoiesis, and human RUNX1 is frequently translocated or mutated in leukaemia. Runx1 expression from its two promoters, the proximal P1 and distal P2, must be tightly regulated for normal hematopoiesis to occur. The mechanism(s) of promoter-specific Runx1 expression during development and differentiation of hematopoietic progenitors is poorly understood. Gene regulatory elements located in non-coding DNA, such as the previously identified +24 enhancer (Ng et al, Stem Cells 2010), are likely to be important for Runx1 transcription. Here, we identify novel cis-regulatory DNA elements that are competent to drive hematopoietic expression in zebrafish, and that interact long-range with the Runx1 gene. Circular chromosome conformation capture sequencing (4C-seq) was used to identify long-range interactions of DNA elements with the promoters of Runx1 in the mouse hematopoietic progenitor cell line, HPC7. We used the P1 and P2 promoters and the +24 enhancer (located 24 kb downstream from the P1 promoter) as anchor points from which to view cis-interactions on mouse chromosome 16. 4C-seq reveals that high levels of chromatin interactions at Runx1 are contained within a 1 megabase domain, spanning from the upstream Setd4 gene to the downstream Clic6 gene. A comparison with HiC data in K562 cells shows that the same domain is conserved in humans. HPC7 cells express Runx1 almost exclusively from the P1 promoter, such that DNA elements interacting with P1 are likely to activate gene expression. The active P1 promoter interacts with multiple non-coding regions both upstream and downstream of Runx1-P1. Interacting regions were overlapped with DNAse hypersensitivity peaks and transcription factor binding sites (available in the USCS genome browser) to identify putative enhancers for Runx1. The majority of putative enhancer regions function as blood specific enhancers in zebrafish (Table). Interestingly, the previously identified +24 enhancer interacted promiscuously within and outside of the 1 megabase Runx1 domain, indicating it may regulate the expression of many additional genes. Overall, our study of the Runx1 interactome identifies multiple novel hematopoietic enhancers that directly interact with the P1 promoter of Runx1, suggesting they are likely involved in regulating Runx1 expression. Table Table. Disclosures No relevant conflicts of interest to declare.

scholarly journals Chromosome looping at the human α-globin locus is mediated via the major upstream regulatory element (HS −40)

Blood ◽  
2009 ◽  
Vol 114 (19) ◽  
pp. 4253-4260 ◽  
Author(s):  
Douglas Vernimmen ◽  
Fatima Marques-Kranc ◽  
Jacqueline A. Sharpe ◽  
Jacqueline A. Sloane-Stanley ◽  
William G. Wood ◽  
...  
Keyword(s):  
Long Range ◽  
Regulatory Element ◽  
Globin Gene ◽  
Regulatory Elements ◽  
Chromosome Conformation ◽  
Long Range Interactions ◽  
Upstream Regulatory Element ◽  
Physical Interactions ◽  
Globin Promoter

Abstract Previous studies in the mouse have shown that high levels of α-globin gene expression in late erythropoiesis depend on long-range, physical interactions between remote upstream regulatory elements and the globin promoters. Using quantitative chromosome conformation capture (q3C), we have now analyzed all interactions between 4 such elements lying 10 to 50 kb upstream of the human α cluster and their interactions with the α-globin promoter. All of these elements interact with the α-globin gene in an erythroid-specific manner. These results were confirmed in a mouse model of human α globin expression in which the human cluster replaces the mouse cluster in situ (humanized mouse). We have also shown that expression and all of the long-range interactions depend largely on just one of these elements; removal of the previously characterized major regulatory element (called HS −40) results in loss of all the interactions and α-globin expression. Reinsertion of this element at an ectopic location restores both expression and the intralocus interactions. In contrast to other more complex systems involving multiple upstream elements and promoters, analysis of the human α-globin cluster during erythropoiesis provides a simple and tractable model to understand the mechanisms underlying long-range gene regulation.

scholarly journals Drosophila Nipped-B Protein Supports Sister Chromatid Cohesion and Opposes the Stromalin/Scc3 Cohesion Factor To Facilitate Long-Range Activation of the cut Gene

2004 ◽  
Vol 24 (8) ◽  
pp. 3100-3111 ◽  
Author(s):  
Robert A. Rollins ◽  
Maria Korom ◽  
Nathalie Aulner ◽  
Andrew Martens ◽  
Dale Dorsett
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Drosophila Melanogaster ◽  
Long Range ◽  
Sister Chromatid ◽  
Transcriptional Activation ◽  
Domain Boundary ◽  
Sister Chromatid Cohesion ◽  
Chromatin Domain ◽  
Chromatid Cohesion ◽  
Evolutionarily Conserved

ABSTRACT The Drosophila melanogaster Nipped-B protein facilitates transcriptional activation of the cut and Ultrabithorax genes by remote enhancers. Sequence homologues of Nipped-B, Scc2 of Saccharomyces cerevisiae, and Mis4 of Schizosaccharomyces pombe are required for sister chromatid cohesion during mitosis. The evolutionarily conserved Cohesin protein complex mediates sister chromatid cohesion, and Scc2 and Mis4 are needed for Cohesin to associate with chromosomes. Here, we show that Nipped-B is also required for sister chromatid cohesion but that, opposite to the effect of Nipped-B, the stromalin/Scc3 component of Cohesin inhibits long-range activation of cut. To explain these findings, we propose a model based on the chromatin domain boundary activities of Cohesin in which Nipped-B facilitates cut activation by alleviating Cohesin-mediated blocking of enhancer-promoter communication.

scholarly journals Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness

2021 ◽  
Author(s):  
Alexandre Laverré ◽  
Eric Tannier ◽  
Anamaria Necsulea
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Large Scale ◽  
Target Genes ◽  
Expression Profiles ◽  
Regulatory Element ◽  
Gene Expression Profiles ◽  
Evolutionary Conservation ◽  
Regulatory Elements ◽  
Regulatory Landscapes

AbstractGene expression is regulated through complex molecular interactions, involving cis-acting elements that can be situated far away from their target genes. Data on long-range contacts between promoters and regulatory elements is rapidly accumulating. However, it remains unclear how these regulatory relationships evolve and how they contribute to the establishment of robust gene expression profiles. Here, we address these questions by comparing genome-wide maps of promoter-centered chromatin contacts in mouse and human. We show that there is significant evolutionary conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve regulatory element sequences and their interactions with target genes. The extent of evolutionary conservation is remarkable for long-range promoter-enhancer contacts, illustrating how the structure of regulatory interactions constrains large-scale genome evolution. Notably, we show that the evolution of cis-regulatory landscapes, measured in terms of distal element sequences, synteny or contacts with target genes, is tightly linked to gene expression evolution.

scholarly journals Local and global chromatin interactions are altered by large genomic deletions associated with human brain development

2017 ◽  
Author(s):  
Xianglong Zhang ◽  
Ying Zhang ◽  
Xiaowei Zhu ◽  
Carolin Purmann ◽  
Michael S Haney ◽  
...  
Keyword(s):  
Long Range ◽  
Copy Number Variants ◽  
Large Deletion ◽  
Interaction Patterns ◽  
Topological Domains ◽  
Histone Marks ◽  
Genomic Deletions ◽  
Chromosome 22Q ◽  
Genome Wide ◽  
Flanking Regions

AbstractBackgroundLarge copy number variants (CNVs) in the human genome are strongly associated with common neurodevelopmental, neuropsychiatric disorders such as schizophrenia and autism. Using Hi-C analysis of long-range chromosome interactions, including haplotype-specific Hi-C analysis, and ChIP-Seq analysis of regulatory histone marks, we studied the epigenomic effects of the prominent heterozygous large deletion CNV on chromosome 22q11.2 and also replicated a subset of the findings for the heterozygous large deletion CNV on chromosome 1q21.1.ResultsThere are local and global gene expression changes as well as pronounced and multilayered effects on chromatin states, chromosome folding and topological domains of the chromatin, that emanate from the large CNV locus. Regulatory histone marks are altered in the deletion flanking regions, and in opposing directions for activating and repressing marks. Histone marks are changed along chromosome 22q and genome wide. Chromosome interaction patterns are weakened within the deletion boundaries and strengthened between the deletion flanking regions. The long-range folding contacts between the telomeric end of chromosome 22q and the distal deletion-flanking region are increased. On the chromosome 22q with deletion the topological domain spanning the CNV boundaries is deleted in its entirety while neighboring domains interact more intensely with each other. Finally, there is a widespread and complex effect on chromosome interactions genome-wide, i.e. involving all other autosomes, with some of the effect directly tied to the deletion region on 22q11.2.ConclusionsThese findings suggest novel principles of how such large genomic deletions can alter nuclear organization and affect genomic molecular activity.

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