scholarly journals CHD4 Conceals Aberrant CTCF-Binding Sites at TAD Interiors by Regulating Chromatin Accessibility in Mouse Embryonic Stem Cells

2021 ◽  
Author(s):  
Sungwook Han ◽  
Hosuk Lee ◽  
Andrew J. Lee ◽  
Seung-Kyoon Kim ◽  
Inkyung Jung ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Binding Sites ◽  
Embryonic Stem ◽  
Chromatin Accessibility ◽  
Mouse Embryonic Stem Cells ◽  
Ctcf Binding

scholarly journals CHD4 conceals aberrant CTCF-binding sites at TAD interiors by regulating chromatin accessibility in mESCs

2021 ◽  
Author(s):  
Sungwook Han ◽  
Hosuk Lee ◽  
Andrew J. Lee ◽  
Seung-Kyoon Kim ◽  
Inkyung Jung ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Binding Sites ◽  
Rna Binding ◽  
Critical Role ◽  
Embryonic Stem ◽  
Chromatin Accessibility ◽  
Ctcf Binding ◽  
Detailed Mechanism ◽  
Intrinsically Disordered

CTCF plays a critical role in the 3D chromatin organization by determining the TAD borders. Although CTCF primarily binds at the TAD borders, there also exist putative CTCF-binding sites within TADs, which are spread throughout the genome by retrotransposition. However, the detailed mechanism responsible for masking these putative CTCF-binding sites remains elusive. Here, we show that the ATP-dependent chromatin remodeler, CHD4, regulates chromatin accessibility to conceal aberrant CTCF-binding sites embedded in H3K9me3-enriched heterochromatic B2 SINEs in mouse embryonic stem cells (mESCs). Upon CHD4 depletion, these aberrant CTCF-binding sites become accessible, and aberrant CTCF recruitment occurs at the TAD interiors, resulting in disorganization of the local TADs. Furthermore, RNA-binding intrinsically disordered domains of CHD4 is required to prevent the aberrant CTCF bindings. Lastly, CHD4 is required for the repression of B2 SINE transcripts. These results highlight the CHD4-mediated mechanism that safeguards the appropriate CTCF bindings and associated TAD organizations in mESCs.

scholarly journals Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

2011 ◽  
Vol 18 (2) ◽  
pp. 237-244 ◽  
Author(s):  
Anthony K L Leung ◽  
Amanda G Young ◽  
Arjun Bhutkar ◽  
Grace X Zheng ◽  
Andrew D Bosson ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Binding Sites ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Genome Wide ◽  
Mature Micrornas

scholarly journals Regulation of Cyclin E by transcription factors of the naïve pluripotency network in mouse embryonic stem cells

2019 ◽  
Author(s):  
Fabrice Gonnot ◽  
Diana Langer ◽  
Pierre-Yves Bourillot ◽  
Nathalie Doerflinger ◽  
Pierre Savatier
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Embryonic Stem Cells ◽  
Binding Sites ◽  
Cyclin E ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Negative Regulator ◽  
Expression Level ◽  
Luciferase Assay

AbstractContinuous, non-cell cycle-dependent expression of cyclin E is a characteristic feature of mouse embryonic stem cells (ESCs). We studied the 5’ regulatory region of Cyclin E, also known as Ccne1, and identified binding sites for transcription factors of the naïve pluripotency network, including Esrrb, Klf4, and Tfcp2l1 within 1 kilobase upstream of the transcription start site. Luciferase assay and chromatin immunoprecipitation-quantitative polymerase chain reaction (ChiP–qPCR) study highlighted one binding site for Esrrb that is essential to transcriptional activity of the promoter region, and three binding sites for Klf4 and Tfcp2l1. Knockdown of Esrrb, Klf4, and Tfcp2l1 reduced Cyclin E expression whereas overexpression of Esrrb and Klf4 increased it, indicating a strong correlation between the expression level of these factors and that of cyclin E. We observed that cyclin E overexpression delays differentiation induced by Esrrb depletion, suggesting that cyclin E is an important target of Esrrb for differentiation blockade. We observed that mESCs express a low level of miR-15a and that transfection of a miR-15a mimic decreases Cyclin E mRNA level. These results lead to the conclusion that the high expression level of Cyclin E in mESCs can be attributed to transcriptional activation by Esrrb as well as to the absence of its negative regulator, miR-15a.

scholarly journals ARGONAUTE proteins regulate a specific network of genes through KLF4 in mouse embryonic stem cells

2021 ◽  
Author(s):  
Madlen Mueller ◽  
Moritz Schaefer ◽  
Tara Faeh ◽  
Daniel Spies ◽  
Rodrigo Peña-Hernández ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Chromatin Accessibility ◽  
Mouse Embryonic Stem Cells ◽  
Mirna Biogenesis ◽  
Transcriptional Gene Silencing ◽  
Argonaute Proteins ◽  
Mutant Cells

The Argonaute proteins (AGO) are well-known for their essential role in post-transcriptional gene silencing in the microRNA (miRNA) pathway. Only two AGOs are expressed in mouse embryonic stem cells (mESCs). The transcriptome of Ago mutant mESCs revealed a large and specific set of differentially expressed genes (DEGs), compared to other miRNA biogenesis factor mutant cells, suggesting additional functions for AGOs. Integration of Ago DEGs with ENCODE histone modification data of WT mESCs revealed a correlation with H3K27me3 chromatin mark. We validated experimentally this result and observed a global loss of H3K27me3, which was only partially explaining the DEGs observed in Ago mutant cells. By integrating chromatin accessibility data in conjunction with the prediction of transcription factor (TF) binding sites, we identified differential binding for five TFs, including KLF4 as a key modulator of more than half of the specific DEGs in the absence of AGO proteins. Our findings illustrate that in addition to chromatin state, information about transcription factor binding is more revelatory in understanding the multi-layered mechanism adopted by cells to regulate gene expression.

scholarly journals The role of MORC3 in silencing transposable elements in mouse embryonic stem cells

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Varsha P. Desai ◽  
Jihed Chouaref ◽  
Haoyu Wu ◽  
William A. Pastor ◽  
Ryan L. Kan ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Transposable Elements ◽  
Embryonic Stem ◽  
Chromatin Accessibility ◽  
Mouse Embryonic Stem Cells ◽  
Endogenous Retroviruses ◽  
Direct Role ◽  
Developmental Abnormalities

Abstract Background Microrchidia proteins (MORCs) are involved in epigenetic gene silencing in a variety of eukaryotic organisms. Deletion of MORCs result in several developmental abnormalities and their dysregulation has been implicated in developmental disease and multiple cancers. Specifically, mammalian MORC3 mutations are associated with immune system defects and human cancers such as bladder, uterine, stomach, lung, and diffuse large B cell lymphomas. While previous studies have shown that MORC3 binds to H3K4me3 in vitro and overlaps with H3K4me3 ChIP-seq peaks in mouse embryonic stem cells, the mechanism by which MORC3 regulates gene expression is unknown. Results In this study, we identified that mutation in Morc3 results in a suppressor of variegation phenotype in a Modifiers of murine metastable epialleles Dominant (MommeD) screen. We also find that MORC3 functions as an epigenetic silencer of transposable elements (TEs) in mouse embryonic stem cells (mESCs). Loss of Morc3 results in upregulation of TEs, specifically those belonging to the LTR class of retrotransposons also referred to as endogenous retroviruses (ERVs). Using ChIP-seq we found that MORC3, in addition to its known localization at H3K4me3 sites, also binds to ERVs, suggesting a direct role in regulating their expression. Previous studies have shown that these ERVs are marked by the repressive histone mark H3K9me3 which plays a key role in their silencing. However, we found that levels of H3K9me3 showed only minor losses in Morc3 mutant mES cells. Instead, we found that loss of Morc3 resulted in increased chromatin accessibility at ERVs as measured by ATAC-seq. Conclusions Our results reveal MORC3 as a novel regulator of ERV silencing in mouse embryonic stem cells. The relatively minor changes of H3K9me3 in the Morc3 mutant suggests that MORC3 acts mainly downstream of, or in a parallel pathway with, the TRIM28/SETDB1 complex that deposits H3K9me3 at these loci. The increased chromatin accessibility of ERVs in the Morc3 mutant suggests that MORC3 may act at the level of chromatin compaction to effect TE silencing.

scholarly journals STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Tianran Peng ◽  
Yanan Zhai ◽  
Yaser Atlasi ◽  
Menno ter Huurne ◽  
Hendrik Marks ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Cell Fate ◽  
Control Cell ◽  
Embryonic Stem ◽  
Chromatin Accessibility ◽  
Mouse Embryonic Stem Cells ◽  
Chromatin Signature ◽  
Genome Wide ◽  
A Genome

Abstract Background Enhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the pluripotency network is maintained by the function of a complex network of enhancers, that are drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for identifying putative enhancers and for describing their activity levels and dynamics. Results Here, we applied STARR-seq, a genome-wide plasmid-based assay, as a read-out for the enhancer landscape in “ground-state” (2i+LIF; 2iL) and “metastable” (serum+LIF; SL) mESCs. This analysis reveals that active STARR-seq loci show modest overlap with enhancer locations derived from peak calling of ChIP-seq libraries for common enhancer marks. We unveil ZIC3-bound loci with significant STARR-seq activity in SL-ESCs. Knock-out of Zic3 removes STARR-seq activity only in SL-ESCs and increases their propensity to differentiate towards the endodermal fate. STARR-seq also reveals enhancers that are not accessible, masked by a repressive chromatin signature. We describe a class of dormant, p53 bound enhancers that gain H3K27ac under specific conditions, such as after treatment with Nocodazol, or transiently during reprogramming from fibroblasts to pluripotency. Conclusions In conclusion, loci identified as active by STARR-seq often overlap with those identified by chromatin accessibility and active epigenetic marking, yet a significant fraction is epigenetically repressed or display condition-specific enhancer activity.

scholarly journals Erratum: Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs

2011 ◽  
Vol 18 (9) ◽  
pp. 1084-1084
Author(s):  
Anthony K L Leung ◽  
Amanda G Young ◽  
Arjun Bhutkar ◽  
Grace X Zheng ◽  
Andrew D Bosson ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Binding Sites ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Genome Wide ◽  
Mature Micrornas

scholarly journals Myc and Max Genome-Wide Binding Sites Analysis Links the Myc Regulatory Network with the Polycomb and the Core Pluripotency Networks in Mouse Embryonic Stem Cells

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e88933 ◽  
Author(s):  
Anna Krepelova ◽  
Francesco Neri ◽  
Mara Maldotti ◽  
Stefania Rapelli ◽  
Salvatore Oliviero
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Binding Sites ◽  
Regulatory Network ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
The Core ◽  
Genome Wide
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