scholarly journals Chromatin Immunoprecipitation-Based Analysis of Gene Regulatory Networks Operative in Human Embryonic Stem Cells

2012 ◽  
pp. 269-280
Author(s):  
Marc Jung ◽  
James Adjaye
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Gene Regulatory Networks ◽  
Chromatin Immunoprecipitation ◽  
Regulatory Networks ◽  
Embryonic Stem ◽  
Gene Regulatory

scholarly journals Ethanol Interferes with Gene Regulatory Networks of Embryonic Stem Cells

2011 ◽  
Vol 25 (S1) ◽  
Author(s):  
Rosa Sanchez‐Alvarez ◽  
Saurabh Gayen ◽  
Rajanikanth Vadigepalli ◽  
Helen Anni
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Embryonic Stem ◽  
Gene Regulatory

scholarly journals PCL2 modulates gene regulatory networks controlling self-renewal and commitment in embryonic stem cells

Cell Cycle ◽  
2011 ◽  
Vol 10 (1) ◽  
pp. 45-51 ◽  
Author(s):  
Emily Walker ◽  
Janet L. Manias ◽  
Wing Y. Chang ◽  
William L. Stanford
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Embryonic Stem ◽  
Self Renewal ◽  
Gene Regulatory

scholarly journals Derivation of notochordal cells from human embryonic stem cells reveals unique regulatory networks by single cell‐transcriptomics

2019 ◽  
Vol 235 (6) ◽  
pp. 5241-5255 ◽  
Author(s):  
Martha E. Diaz‐Hernandez ◽  
Nazir M. Khan ◽  
Camila M. Trochez ◽  
Tim Yoon ◽  
Peter Maye ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Single Cell ◽  
Human Embryonic Stem Cells ◽  
Regulatory Networks ◽  
Embryonic Stem ◽  
Notochordal Cells

scholarly journals Regulatory networks specifying cortical interneurons from human embryonic stem cells reveal roles for CHD2 in interneuron development

2017 ◽  
Vol 114 (52) ◽  
pp. E11180-E11189 ◽  
Author(s):  
Kesavan Meganathan ◽  
Emily M. A. Lewis ◽  
Paul Gontarz ◽  
Shaopeng Liu ◽  
Edouard G. Stanley ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Transcription Factor ◽  
Embryonic Stem Cells ◽  
Chromatin Remodeling ◽  
Human Embryonic Stem Cells ◽  
Regulatory Networks ◽  
Embryonic Stem ◽  
Molecular Networks ◽  
Cortical Interneurons

Cortical interneurons (cINs) modulate excitatory neuronal activity by providing local inhibition. During fetal development, several cIN subtypes derive from the medial ganglionic eminence (MGE), a transient ventral telencephalic structure. While altered cIN development contributes to neurodevelopmental disorders, the inaccessibility of human fetal brain tissue during development has hampered efforts to define molecular networks controlling this process. Here, we modified protocols for directed differentiation of human embryonic stem cells, obtaining efficient, accelerated production of MGE-like progenitors and MGE-derived cIN subtypes with the expected electrophysiological properties. We defined transcriptome changes accompanying this process and integrated these data with direct transcriptional targets of NKX2-1, a transcription factor controlling MGE specification. This analysis defined NKX2-1–associated genes with enriched expression during MGE specification and cIN differentiation, including known and previously unreported transcription factor targets with likely roles in MGE specification, and other target classes regulating cIN migration and function. NKX2-1–associated peaks were enriched for consensus binding motifs for NKX2-1, LHX, and SOX transcription factors, suggesting roles in coregulating MGE gene expression. Among the NKX2-1 direct target genes with cIN-enriched expression was CHD2, which encodes a chromatin remodeling protein mutated to cause human epilepsies. Accordingly, CHD2 deficiency impaired cIN specification and altered later electrophysiological function, while CHD2 coassociated with NKX2-1 at cis-regulatory elements and was required for their transactivation by NKX2-1 in MGE-like progenitors. This analysis identified several aspects of gene-regulatory networks underlying human MGE specification and suggested mechanisms by which NKX2-1 acts with chromatin remodeling activities to regulate gene expression programs underlying cIN development.

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