scholarly journals KDM6A knockout in human iPSCs alters the genome-wide histone methylation profile at active and poised enhancers, activating expression of ectoderm gene expression pathways

2021 ◽  
Author(s):  
Shailendra S. Maurya ◽  
Wei Yang ◽  
Qiang Zhang ◽  
Petra Erdmann-Gilmore ◽  
Amelia Bystry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Histone Modification ◽  
Histone Modifications ◽  
Embryonic Stem ◽  
Specific Gene ◽  
Regulatory Domains ◽  
Genome Wide ◽  
Human Ipscs ◽  
Expression Pathways

AbstractKDM6A is a histone demethylase, known to remove methyl moieties at the lysine residues of histone 3-labeled (H3K27me3) poised enhancers and bivalent promoters, which regulates gene expression during the differentiation of embryonic stem cells and tissue-specific development. However, while tissue- and disease-specific analyses have been performed, little is known about the location and consequences on gene expression of these regulatory regions in human pluripotent cells. Poised enhancers and bivalent promoters function in a coordinated fashion during development, which requires timely and efficient histone modifications. Identification of KDM6A-specific gene-regulatory domains is important for understanding the developmental mechanisms controlled by these histone modifications in pluripotency. In this study, we compared genome-wide histone modification and gene expression differences in isogenic wild type and cas9-mediated KDM6A knockout human induced pluripotent stem cells (hiPSC) lines. Here, we report that the absence of KDM6A does not alter the pluripotent phenotype but does substantially alter the histone modification profile at poised and active enhancers, resulting in decreased expression of associated COMPASS complex genes KMT2C and KMT2D and subsequently increasing the expression of gene pathways involved in ectoderm differentiation.

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.

scholarly journals Epigenetic-scale comparison of human iPSCs generated by retrovirus, Sendai virus or episomal vectors

2018 ◽  
Author(s):  
Koichiro Nishino ◽  
Yoshikazu Arai ◽  
Ken Takasawa ◽  
Masashi Toyoda ◽  
Mayu Yamazaki-Inoue ◽  
...  
Keyword(s):  
Stem Cells ◽  
Gene Delivery ◽  
Sendai Virus ◽  
Embryonic Stem ◽  
Aberrant Methylation ◽  
Delivery Methods ◽  
Genome Wide ◽  
Human Ipscs ◽  
Episomal Vectors ◽  
Induced Pluripotent

AbstractHuman induced pluripotent stem cells (iPSCs) are established by introducing several reprogramming factors, such as OCT3/4, SOX2, KLF4, c-MYC. Because of their pluripotency and immortality, iPSCs are considered to be a powerful tool for regenerative medicine. To date, iPSCs have been established all over the world by various gene delivery methods. All methods induced high-quality iPSCs, but epigenetic analysis of abnormalities derived from differences in the gene delivery methods has not yet been performed. Here, we generated genetically matched human iPSCs from menstrual blood cells by using three kinds of vectors, i.e., retrovirus, Sendai virus, and episomal vectors, and compared genome-wide DNA methylation profiles among them. Although comparison of aberrant methylation revealed that iPSCs generated by Sendai virus vector have lowest number of aberrant methylation sites among the three vectors, the iPSCs generated by non-integrating methods did not show vector-specific aberrant methylation. However, the differences between the iPSC lines were determined to be the number of random aberrant hyper-methylated regions compared with embryonic stem cells. These random aberrant hyper-methylations might be a cause of the differences in the properties of each of the iPSC lines.

Distinct patterns of histone modifications at cardiac-specific gene promoters between cardiac stem cells and mesenchymal stem cells

2013 ◽  
Vol 304 (11) ◽  
pp. C1080-C1090 ◽  
Author(s):  
Meijing Wang ◽  
Qing Yu ◽  
Lina Wang ◽  
Hongmei Gu
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Histone Acetylation ◽  
Histone Modifications ◽  
Specific Gene ◽  
Cardiac Stem Cells ◽  
Gene Promoters ◽  
Promoter Regions ◽  
Specific Gene Expression

Mesenchymal stem cells (MSCs) and cardiac stem cells (CSCs) possess different potential to develop into cardiomyocytes. The mechanism underlying cardiomyogenic capacity of MSCs and CSCs remains elusive. It is well established that histone modifications correlate with gene expression and contribute to cell fate commitment. Here we hypothesize that specific histone modifications accompany cardiac-specific gene expression, thus determining the differentiation capacity of MSCs and CSCs toward heart cells. Our results indicate that, at the promoter regions of cardiac-specific genes ( Myh6, Myl2, Actc1, Tnni3, and Tnnt2), the levels of histone acetylation of H3 (acH3) and H4 (acH4), as a mark indicative of gene activation, were higher in CSCs (Sca-1+CD29+) than MSCs. Additionally, lower binding levels of histone deacetylase (HDAC) 1 and HDAC2 at promoter regions of cardiac-specific genes were noticed in CSCs than MSCs. Treatment with trichostatin A, an HDAC inhibitor, upregulated cardiac-specific gene expression in MSCs. Suppression of HDAC1 or HDAC2 expression by small interfering RNAs led to increased cardiac gene expression and was accompanied by enhanced acH3 and acH4 levels at gene loci. We conclude that greater levels of histone acetylation at cardiac-specific gene loci in CSCs than MSCs reflect a stronger potential for CSCs to develop into cardiomyocytes. These lineage-differential histone modifications are likely due to less HDAC recruitment at cardiac-specific gene promoters in CSCs than MSCs.

scholarly journals A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Phillip Wulfridge ◽  
Kavitha Sarma
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Genome Instability ◽  
Embryonic Stem ◽  
Gene Promoters ◽  
Detection Strategy ◽  
Genome Wide ◽  
Loop Detection ◽  
Nucleic Acid Structures ◽  
Nuclear Processes

R-loops are three-stranded nucleic acid structures with essential roles in many nuclear processes. However, their unchecked accumulation is associated with genome instability and is observed in neurodevelopmental diseases and cancers. Genome-wide profiling of R-loops in normal and diseased cells can help identify locations of pathogenic R-loops and advance efforts to attenuate them. We present an antibody-independent R-loop detection strategy, BisMapR, that combines nuclease-based R-loop isolation with non-denaturing bisulfite chemistry to produce genome-wide profiles that retain strand information. BisMapR achieves greater resolution and is faster than existing strand-specific R-loop profiling strategies. In mouse embryonic stem cells, we apply BisMapR to find that gene promoters form R-loops in both directions and uncover a subset of active enhancers that, despite being bidirectionally transcribed, form R-loops exclusively on one strand. BisMapR reveals a previously unnoticed feature of active enhancers and provides a tool to systematically examine their mechanisms in gene expression.

Sign in / Sign up

Export Citation Format

Share Document