scholarly journals CTCF and cohesin promote focal detachment of DNA from the nuclear lamina

2021 ◽  
Author(s):  
Tom van Schaik ◽  
Ning Qing Liu ◽  
Stefano G. Manzo ◽  
Daan Peric-Hupkes ◽  
Elzo de Wit ◽  
...  
Keyword(s):  
Stem Cells ◽  
Histone Modifications ◽  
Binding Sites ◽  
Embryonic Stem ◽  
Nuclear Lamina ◽  
Fine Tuning ◽  
Ctcf Binding ◽  
Strongly Correlated ◽  
Sharp Transition ◽  
Genomic Regions

Lamina associated domains (LADs) are large genomic regions that are positioned at the nuclear lamina (NL). It has remained largely unclear what drives the positioning and demarcation of LADs. Because the insulator protein CTCF is enriched at LAD borders, it was postulated that CTCF binding could position a subset of LAD boundaries, possibly through its function in stalling cohesin and hence preventing cohesin to invade into the LAD. To test this, we mapped genome - NL interactions in mouse embryonic stem cells after rapid depletion of CTCF and other perturbations of cohesin dynamics. CTCF and cohesin contribute to a sharp transition in NL interactions at LAD borders, whilst LADs are maintained after depletion of these proteins, also at borders marked by CTCF. CTCF and cohesin may thus reinforce LAD borders, but do not position these. CTCF binding sites within LADs are locally detached from the NL and enriched for accessible DNA and active histone modifications. Remarkably, even though NL positioning is strongly correlated with genome inactivity, this DNA remains accessible after the local detachment is lost following CTCF depletion. At a chromosomal scale, cohesin depletion and cohesin stabilization (depletion of the unloading factor WAPL) quantitatively affect NL interactions, indicative of perturbed chromosomal positioning in the nucleus. Finally, while H3K27me3 is locally enriched at CTCF-marked LAD borders, we find no evidence for an interplay between CTCF and H3K27me3 on NL interactions. Combined, these findings illustrate that CTCF and cohesin do not shape LAD patterns. Rather, these proteins mediate fine-tuning of NL interactions.

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.

3076 – FINE-TUNING GENE EXPRESSION BY CRISPRA IN MOUSE EMBRYONIC STEM CELLS FOR SPECIFIC TISSUE INDUCTION

2020 ◽  
Vol 88 ◽  
pp. S62
Author(s):  
Luis Galán Palma ◽  
Roshana Thambyrajah ◽  
Antonella Fidanza ◽  
Lesley Forrester ◽  
Pablo Menéndez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Fine Tuning ◽  
Specific Tissue

CBIO-05. SOX2 CHROMATIN ARCHITECTURE AND ENHANCER ACTIVITY IN THE MAINTENANCE AND DEVELOPMENT OF NEURAL STEM CELLS

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi28-vi28
Author(s):  
Devin Bready ◽  
Aram Modrek ◽  
Joshua Frenster ◽  
Jane Skok ◽  
Dimitris Placantonakis
Keyword(s):  
Stem Cells ◽  
Neural Stem Cells ◽  
Developmental Process ◽  
Embryonic Stem ◽  
Stem Cell Differentiation ◽  
Ctcf Binding ◽  
Low Grade ◽  
Lower Grade ◽  
Cell Of Origin ◽  
Putative Enhancer

Abstract Gain of function mutations in isocitrate dehydrogenase I (IDH1) result in the formation of the oncometabolite 2-hydroxyglutarate (2HG) in adult lower grade gliomas. To gain insight into mechanisms of gliomagenesis, our lab previously created a tractable human cellular model of low grade astrocytoma (LGA) using the putative cell-of-origin, human neural stem cells (NSCs), engineered to express mutant IDH1 and knockdown constructs against TP53 and ATRX, the two other genetic changes that accompany the IDH mutation in these tumors. We found that transcription factor (sex determining region Y)-box 2 SOX2, which is essential to NSC multipotency, the ability to differentiate to neuroglial lineages, behaves as a tumor suppressor during glioma initiation. In this context, we showed SOX2 is transcriptionally downregulated to impair NSC multipotency, thus locking NSCs in an undifferentiated state to initiate gliomagenesis. This downregulation occurs secondary to dynamic reorganization of the topologically associating domain (TAD) of SOX2 and the loss of contact with several genomic loci with histone modifications and chromatin accessibility suggestive of being enhancers. Here we show that those putative enhancers acquire enhancer-like features simultaneous to tje TAD organizing in a way that facilitates interaction with the SOX2 promoter during the process of pluripotent stem cell differentiation into neuroectodermal lineages, suggesting a developmental role. Preliminary data suggests that disruption of the SOX2 TAD by preventing binding of the genome organizer CTCF downregulates SOX2 expression in NSCs. Targeted silencing of several regions of a putative enhancer with CRISPRi also downregulates SOX2. In human embryonic stem cells (hESCs), interfering with these CTCF binding sites biases their differentiation away from the neuroectoderm. We are currently performing CRISPRi screen against all putative enhancer loci, teratoma formation assays on hESCs lacking relevant CTCF binding, and CRISPR mediated deletion of putative enhancers. Understanding this developmental process may reveal underlying vulnerabilities in LGA.

CDK11 safeguards the identity of human embryonic stem cells via fine‐tuning signaling pathways

2019 ◽  
Vol 235 (5) ◽  
pp. 4279-4290
Author(s):  
Jianyi Ding ◽  
Zhuoqing Fang ◽  
Xinyuan Liu ◽  
Zhexin Zhu ◽  
Chunsheng Wen ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Signaling Pathways ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Fine Tuning

scholarly journals Dynamics of gene expression with positive feedback to histone modifications at bivalent domains

2018 ◽  
Vol 32 (07) ◽  
pp. 1850075
Author(s):  
Rongsheng Huang ◽  
Jinzhi Lei
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Histone Modification ◽  
Histone Modifications ◽  
Positive Feedback ◽  
State Transition ◽  
Embryonic Stem ◽  
Cell Cycles ◽  
Histone Marks

Experiments have shown that in embryonic stem cells, the promoters of many lineage-control genes contain “bivalent domains”, within which the nucleosomes possess both active (H3K4me3) and repressive (H3K27me3) marks. Such bivalent modifications play important roles in maintaining pluripotency in embryonic stem cells. Here, to investigate gene expression dynamics when there are regulations in bivalent histone modifications and random partition in cell divisions, we study how positive feedback to histone methylation/demethylation controls the transition dynamics of the histone modification patterns along with cell cycles. We constructed a computational model that includes dynamics of histone marks, three-stage chromatin state transitions, transcription and translation, feedbacks from protein product to enzymes to regulate the addition and removal of histone marks, and the inheritance of nucleosome state between cell cycles. The model reveals how dynamics of both nucleosome state transition and gene expression are dependent on the enzyme activities and feedback regulations. Results show that the combination of stochastic histone modification at each cell division and the deterministic feedback regulation work together to adjust the dynamics of chromatin state transition in stem cell regenerations.

Characterization of Histone Modifications on Lineage-Affiliated Genes During Hematopoietic Stem Cell Differentiation

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 4784-4784
Author(s):  
Chen Fangping ◽  
Huarong Tang
Keyword(s):  
Stem Cells ◽  
Hematopoietic Stem Cells ◽  
Histone Modifications ◽  
Conflicts Of Interest ◽  
Embryonic Stem ◽  
Stem Cell Differentiation ◽  
Differentiation Potential ◽  
Hematopoietic Stem ◽  
Low Level ◽  
Lineage Specific Genes

Abstract Abstract 4784 Hematopoietic stem cells (HSCs) are multipotent stem cells capable of self-renewal and multi-lineage differentiation. Though it has been shown that multiple factors take part in the maintenance of HSCs’ multipotency and differentiation potential, the mechanisms are unclear. Recent studies showed that histone modifications play an important role in maintenance of embryonic stem cells pluripotency and differentiation. To characterize the histone modification patterns of different lineages, HSCs were collected from umbilical cord blood and induced to differentiate to granulocytic, erythroid, and megakarytic in vitro. genes during HSC differentiation. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) technology was adopted to investigate the dynamic changes of histone modifications on lineage specific transcription factors and lineage–affiliated genes. Our results showed a certain level of H4 acetylation and H3 acetylation together with high level of H3K4me2 and low level of H3K4me3, H3K9me3 and H3K27me3 were present in lineage specific genes in CD34+CD38- HSCs. As CD34+CD38- cells differentiated, the modification level of acH3, acH4, H3K4me2, H3K9me3 and H3K27me3 on lineage specific genes remained the same, while H3K4me3 level increased greatly. In non-lineage specific genes, the acH3 and acH4 levels decreased, and H3K4me3 level remain at low level, while H3K9me3 and H3K27me3 levels increased. Thus, our data suggested that histone modifications played an important role in maintenaning the multipotency and differentiation capability of hematopoietic stem cells. Disclosures: No relevant conflicts of interest to declare.

Human embryonic stem cells are characterized by distinct patterns of histone modifications in comparison with cells of feeder layer

2008 ◽  
Vol 2008 (Spring) ◽  
Author(s):  
Eva Bartova ◽  
Abdrea Harnicarova ◽  
Jana Krejci ◽  
Gabriela Galiova ◽  
Stanislav Kozubek
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Histone Modifications ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Feeder Layer
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