scholarly journals Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells

2018 ◽  
Vol 28 (10) ◽  
pp. 1543-1554 ◽  
Author(s):  
Anish Dattani ◽  
Damian Kao ◽  
Yuliana Mihaylova ◽  
Prasad Abnave ◽  
Samantha Hughes ◽  
...  
Keyword(s):  
Stem Cells ◽  
Histone Modifications

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 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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