scholarly journals SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease

2021 ◽  
Author(s):  
Andres Tapia del Fierro ◽  
Bianca den Hamer ◽  
Natasha Jansz ◽  
Kelan Chen ◽  
Tamara Beck ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Long Range ◽  
Normal Development ◽  
Gene Activation ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Hox Gene ◽  
Chromatin Architecture ◽  
Chromatin Interactions ◽  
Epigenetic Regulator ◽  
Different Levels

The interplay between 3D chromatin architecture and gene silencing is incompletely understood. Here, we report a novel point mutation in the non-canonical SMC protein SMCHD1 that enhances its silencing capacity at endogenous developmental targets and at the facioscapulohumeral muscular dystrophy associated macro-array, D4Z4. Heightened SMCHD1 silencing perturbs developmental Hox gene activation, causing a homeotic transformation in mice. Paradoxically, the mutant SMCHD1 appears to enhance insulation against another epigenetic regulator complex, PRC2, while depleting long range chromatin interactions akin to what is observed in the absence of SMCHD1. These data suggest that SMCHD1′s role in long range chromatin interactions is not directly linked to gene silencing or insulating the chromatin, refining the model for how the different levels of SMCHD1-mediated chromatin regulation interact to bring about gene silencing in normal development and disease.

scholarly journals CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells

2020 ◽  
Author(s):  
Naoki Kubo ◽  
Haruhiko Ishii ◽  
Xiong Xiong ◽  
Simona Bianco ◽  
Franz Meitinger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Expression Profiles ◽  
Gene Activation ◽  
Ctcf Binding ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Chromatin Architecture ◽  
Mouse Tissues ◽  
Lineage Specific Gene

AbstractTopologically associating domains (TAD) and insulated neighborhoods (INs) have been proposed to constrain enhancer-promoter communications to enable cell-type specific transcription programs, but recent studies show that disruption of TADs and INs resulted in relatively mild changes in gene expression profiles. To better understand the role of chromatin architecture in dynamic enhancer-promoter contacts and lineage-specific gene expression, we have utilized the auxin-inducible degron system to acutely deplete CTCF, a key factor involved in TADs and IN formation, in mouse embryonic stem cells (mESCs) and examined chromatin architecture and gene regulation during neural differentiation. We find that while CTCF depletion leads to global weakening of TAD boundaries and loss of INs, only a minor fraction of enhancer-promoter contacts are lost, affecting a small subset of genes. The CTCF-dependent enhancer-promoter contacts tend to be long-range, spanning hundreds of kilobases, and are established directly by CTCF binding to promoters. Disruption of CTCF binding at the promoter reduces enhancer-promoter contacts and transcription, while artificial tethering of CTCF to the promoter restores the enhancer-promoter contacts and gene activation. Genome-wide analysis of CTCF binding and gene expression across multiple mouse tissues suggests that CTCF-dependent promoter-enhancer contacts may regulate expression of additional mouse genes, particularly those expressed in the brain. Our results uncover both CTCF-dependent and independent enhancer-promoter contacts, and highlight a distinct role for CTCF in promoting enhancer-promoter contacts and gene activation in addition to its insulator function.

scholarly journals Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo

2021 ◽  
Author(s):  
Natalia Benetti ◽  
Quentin Gouil ◽  
Andres Tapia del Fierro ◽  
Tamara Beck ◽  
Kelsey Breslin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Maternal Effect ◽  
Normal Development ◽  
Preimplantation Embryo ◽  
Epigenetic Silencing ◽  
Hox Gene ◽  
Skeletal Patterning ◽  
Epigenetic Effects ◽  
Epigenetic Regulator ◽  
Maternal Effect Genes

AbstractParents transmit genetic and epigenetic information to their offspring. Maternal effect genes regulate the offspring epigenome to ensure normal development. Here we report that the epigenetic regulator SMCHD1 has a maternal effect on Hox gene expression and skeletal patterning. Maternal SMCHD1, present in the oocyte and preimplantation embryo, prevents precocious activation of Hox genes postimplantation. Without maternal SMCHD1, highly penetrant posterior homeotic transformations occur in the embryo. Hox genes are decorated with Polycomb marks H2AK119ub and H3K27me3 from the oocyte throughout early embryonic development; however, loss of maternal SMCHD1 does not alter these marks. Therefore, we propose maternal SMCHD1 acts downstream of Polycomb marks to establish a chromatin state necessary for persistent epigenetic silencing and appropriate Hox gene expression later in the developing embryo. This is a striking role for maternal SMCHD1 in long-lived epigenetic effects impacting offspring phenotype.

scholarly journals HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells

2021 ◽  
Vol 4 (3) ◽  
pp. 49
Author(s):  
Tomas Zelenka ◽  
Charalampos Spilianakis
Keyword(s):  
T Cells ◽  
Long Range ◽  
Three Dimensional ◽  
Cell Types ◽  
Range Interaction ◽  
Chromatin Interactions ◽  
Optimized Protocol ◽  
Long Range Interaction ◽  
Chromatin Compactness ◽  
Detailed Protocol

The functional implications of the three-dimensional genome organization are becoming increasingly recognized. The Hi-C and HiChIP research approaches belong among the most popular choices for probing long-range chromatin interactions. A few methodical protocols have been published so far, yet their reproducibility and efficiency may vary. Most importantly, the high frequency of the dangling ends may dramatically affect the number of usable reads mapped to valid interaction pairs. Additionally, more obstacles arise from the chromatin compactness of certain investigated cell types, such as primary T cells, which due to their small and compact nuclei, impede limitations for their use in various genomic approaches. Here we systematically optimized all the major steps of the HiChIP protocol in T cells. As a result, we reduced the number of dangling ends to nearly zero and increased the proportion of long-range interaction pairs. Moreover, using three different mouse genotypes and multiple biological replicates, we demonstrated the high reproducibility of the optimized protocol. Although our primary goal was to optimize HiChIP, we also successfully applied the optimized steps to Hi-C, given their significant protocol overlap. Overall, we describe the rationale behind every optimization step, followed by a detailed protocol for both HiChIP and Hi-C experiments.

scholarly journals Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

Cell Research ◽  
2014 ◽  
Vol 24 (5) ◽  
pp. 513-531 ◽  
Author(s):  
Jian-Feng Xiang ◽  
Qing-Fei Yin ◽  
Tian Chen ◽  
Yang Zhang ◽  
Xiao-Ou Zhang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Long Range ◽  
Human Colorectal Cancer ◽  
Chromatin Interactions

scholarly journals Locus Control Region Transcription Plays an Active Role in Long-Range Gene Activation

2006 ◽  
Vol 23 (4) ◽  
pp. 619
Author(s):  
Yugong Ho ◽  
Felice Elefant ◽  
Stephen A. Liebhaber ◽  
Nancy E. Cooke
Keyword(s):  
Long Range ◽  
Control Region ◽  
Gene Activation ◽  
Locus Control Region ◽  
Active Role

scholarly journals Human PRE-PIK3C2B exhibits long-range intra- and inter-chromosomal interactions with genomic regions enriched in repressive marks

2020 ◽  
Author(s):  
Jayant Maini ◽  
Ankit Kumar Pathak ◽  
Kausik Bhattacharyya ◽  
Narendra Kumar ◽  
Ankita Narang ◽  
...  
Keyword(s):  
Long Range ◽  
Meta Analysis ◽  
Range Interaction ◽  
Dual Nature ◽  
Polycomb Response Element ◽  
Chromatin Interactions ◽  
Long Range Interaction ◽  
Intergenic Regions ◽  
Genomic Regions ◽  
Transcriptional Start Sites

AbstractHuman PRE-PIK3C2B is a dual nature polycomb response element that interacts with both polycomb as well as trithorax members. In the current study, using 4C-Seq (Capturing Circular Chromosomal Conformation-Sequencing), we identified long-range chromatin interactions associated with PRE-PIK3C2B and validated them with 3C-PCR. We identified both intra-as well as inter-chromosomal interactions, a large proportion of which were found to be closely distributed around transcriptional start sites (TSS). A significant number of interactions were also found to be associated with heterochromatic regions. Meta-analysis of ENCODE ChIP-Seq data identified an overall enrichment of YY1, CTCF as well as histone modification such as H3K4me3 and H3K27me marks in different cell lines. Almost 90% interactions were derived from either intronic or intergenic regions. among which large proportions of intronic interactors were either unique sequences or LINE/SINE derived. In case of intergenic interactions, majority of the interaction were associated with LINE/SINE repeats. We further found that genes proximal to the interactor sequences were co-expressed, they showed reduced expression. To the best of our knowledge this is one of the early demonstrations of long-range interaction of PRE sequences in human genome.

scholarly journals SMCHD1’s ubiquitin-like domain is required for N-terminal dimerization and chromatin localization

2021 ◽  
Author(s):  
Alexandra D Gurzau ◽  
Christopher Horne ◽  
Yee-Foong Mok ◽  
Megan Iminitoff ◽  
Tracy A Willson ◽  
...  
Keyword(s):  
Facioscapulohumeral Muscular Dystrophy ◽  
Chromatin Interaction ◽  
Structural Studies ◽  
Functional Importance ◽  
Targeted Deletion ◽  
Epigenetic Regulator ◽  
Biophysical Techniques ◽  
Structural Maintenance Of Chromosomes ◽  
Hinge Domain

Structural Maintenance of Chromosomes flexible Hinge Domain-containing 1 (SMCHD1) is an epigenetic regulator that mediates gene expression silencing at targeted sites across the genome. Our current understanding of SMCHD1’s molecular mechanism, and how substitutions within SMCHD1 lead to the diseases, facioscapulohumeral muscular dystrophy (FSHD) and Bosma arhinia microphthalmia syndrome (BAMS), are only emerging. Recent structural studies of its two component domains – the N-terminal ATPase and C-terminal SMC hinge – suggest that dimerization of each domain plays a central role in SMCHD1 function. Here, using biophysical techniques, we demonstrate that the SMCHD1 ATPase undergoes dimerization in a process that is dependent on both the N-terminal UBL (Ubiquitin-like) domain and ATP binding. We show that neither the dimerization event, nor the presence of a C-terminal extension past the transducer domain, affect SMCHD1’s in vitro catalytic activity as the rate of ATP turnover remains comparable to the monomeric protein. We further examined the functional importance of the N-terminal UBL domain in cells, revealing that its targeted deletion disrupts the localization of full-length SMCHD1 to chromatin. These findings implicate UBL-mediated SMCHD1 dimerization as a crucial step for chromatin interaction, and thereby for promoting SMCHD1-mediated gene silencing.

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