scholarly journals Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

Nature ◽  
2011 ◽  
Vol 473 (7347) ◽  
pp. 394-397 ◽  
Author(s):  
William A. Pastor ◽  
Utz J. Pape ◽  
Yun Huang ◽  
Hope R. Henderson ◽  
Ryan Lister ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Genome Wide

scholarly journals Genome-Wide Definition of Promoter and Enhancer Usage during Neural Induction of Human Embryonic Stem Cells

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0126590 ◽  
Author(s):  
Valentina Poletti ◽  
Alessia Delli Carri ◽  
Guidantonio Malagoli Tagliazucchi ◽  
Andrea Faedo ◽  
Luca Petiti ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Neural Induction ◽  
Genome Wide ◽  
Wide Definition ◽  
Definition Of

scholarly journals Induction of Recurrent Break Cluster Genes in Neural Progenitor Cells Differentiated from Embryonic Stem Cells In Culture

2019 ◽  
Author(s):  
Aseda Tena ◽  
Yuxiang Zhang ◽  
Nia Kyritsis ◽  
Anne Devorak ◽  
Jeffrey Zurita ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Progenitor Cells ◽  
Es Cells ◽  
Embryonic Stem ◽  
Neural Progenitors ◽  
Neural Genes ◽  
Genome Wide ◽  
Primary Mouse

ABSTRACTMild replication stress enhances appearance of dozens of robust recurrent genomic break clusters, termed RDCs, in cultured primary mouse neural stem and progenitor cells (NSPCs). Robust RDCs occur within genes (“RDC-genes”) that are long and have roles in neural cell communications and/or have been implicated in neuropsychiatric diseases or cancer. We sought to develop an in vitro approach to determine whether specific RDC formation is associated with neural development. For this purpose, we adapted a system to induce neural progenitor cell (NPC) development from mouse embryonic stem cell (ESC) lines deficient for XRCC4 plus p53, a genotype that enhances DNA double-strand break (DSB) persistence to enhance detection. We tested for RDCs by our genome wide DSB identification approach that captures DSBs genome-wide via their ability to join to specific genomic Cas9/sgRNA-generated bait DSBs. In XRCC4/p53-deficient ES cells, we detected 7 RDCs, which were in genes, with two RDCs being robust. In contrast, in NPCs derived from these ES cell lines, we detected 29 RDCs, a large fraction of which were robust and associated with long, transcribed neural genes that were also robust RDC-genes in primary NSPCs. These studies suggest that many RDCs present in NSPCs are developmentally influenced to occur in this cell type and indicate that induced development of NPCs from ES cells provides an approach to rapidly elucidate mechanistic aspects of NPC RDC formation.SIGNIFICANCE STATEMENTWe previously discovered a set of long neural genes susceptible to frequent DNA breaks in primary mouse brain progenitor cells. We termed these genes RDC-genes. RDC-gene breakage during brain development might alter neural gene function and contribute to neurological diseases and brain cancer. To provide an approach to characterize the unknown mechanism of neural RDC-gene breakage, we asked whether RDC-genes appear in neural progenitors differentiated from embryonic stem cells in culture. Indeed, robust RDC-genes appeared in neural progenitors differentiated in culture and many overlapped with robust RDC-genes in primary brain progenitors. These studies indicate that in vitro development of neural progenitors provides a model system for elucidating how RDC-genes are formed.

scholarly journals A genome-wide RNAi screen in mouse embryonic stem cells identifies Mp1 as a key mediator of differentiation

2011 ◽  
Vol 195 (6) ◽  
pp. i9-i9 ◽  
Author(s):  
Bart A. Westerman ◽  
A. Koen Braat ◽  
Nicole Taub ◽  
Marko Potman ◽  
Joseph H.A. Vissers ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Rnai Screen ◽  
Genome Wide ◽  
A Genome

scholarly journals NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Susan L. Kloet ◽  
Ino D. Karemaker ◽  
Lisa van Voorthuijsen ◽  
Rik G. H. Lindeboom ◽  
Marijke P. Baltissen ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Interacting Protein ◽  
Genome Wide

scholarly journals Genome-Wide Reprogramming in Hybrids of Somatic Cells and Embryonic Stem Cells

Stem Cells ◽  
2007 ◽  
Vol 25 (5) ◽  
pp. 1104-1113 ◽  
Author(s):  
Dominic J. Ambrosi ◽  
Borko Tanasijevic ◽  
Anupinder Kaur ◽  
Craig Obergfell ◽  
Rachel J. O'Neill ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Somatic Cells ◽  
Embryonic Stem ◽  
Genome Wide

scholarly journals Genome-Wide Identification of Targets and Function of Individual MicroRNAs in Mouse Embryonic Stem Cells

PLoS Genetics ◽  
2010 ◽  
Vol 6 (10) ◽  
pp. e1001163 ◽  
Author(s):  
Sophie A. Hanina ◽  
William Mifsud ◽  
Thomas A. Down ◽  
Katsuhiko Hayashi ◽  
Dónal O'Carroll ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Genome Wide ◽  
And Function

scholarly journals Gene trapping: An antibody-dependent approach for verifying integration in your favorite gene

2008 ◽  
Vol 13 (4) ◽  
Author(s):  
Anna Gorelik ◽  
Tamar Sapir ◽  
Orly Reiner
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Fusion Proteins ◽  
Integration Site ◽  
Embryonic Stem ◽  
Protein Product ◽  
Terminal Portion ◽  
Gene Trapping ◽  
Genome Wide ◽  
Identity Based

AbstractGene trapping is used to introduce genome-wide insertional mutations in embryonic stem cells. Determining the integration site is based on highthroughput PCR, which has inevitable possibilities for mistakes, thus necessitating clone verification prior to the generation of mutant mice. Here, we propose a rapid method to validate gene identity based on the fact that many high throughput gene-trapping integrations result in fusion proteins encompassing the N-terminal portion of the gene of interest and LacZ being expressed in embryonic stem cells. Our method utilizes an immunoprecipitation assay using a specific N-terminal-directed antibody to the protein product of the gene of interest followed by a color LacZ assay of the immunoprecipitate, strongly supporting the formation of a fusion protein when the color develops.

scholarly journals Genome-wide identification and characterisation of HOT regions in the human genome

2016 ◽  
Author(s):  
Hao Li ◽  
Feng Liu ◽  
Chao Ren ◽  
Xiaochen Bo ◽  
Wenjie Shu
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Embryonic Stem Cells ◽  
Epigenetic Regulation ◽  
Human Cell ◽  
Embryonic Stem ◽  
Cell Types ◽  
Genome Wide ◽  
Development And Differentiation ◽  
Epigenetic Analysis

AbstractHOT (high-occupancy target) regions, which are bound by a surprisingly large number of transcription factors, are considered to be among the most intriguing findings of recent years. An improved understanding of the roles that HOT regions play in biology would be afforded by knowing the constellation of factors that constitute these domains and by identifying HOT regions across the spectrum of human cell types. We characterised and validated HOT regions in embryonic stem cells (ESCs) and produced a catalogue of HOT regions in a broad range of human cell types. We found that HOT regions are associated with genes that control and define the developmental processes of the respective cell and tissue types. We also showed evidence of the developmental persistence of HOT regions at primitive enhancers and demonstrate unique signatures of HOT regions that distinguish them from typical enhancers and super-enhancers. Finally, we performed an epigenetic analysis to reveal the dynamic epigenetic regulation of HOT regions upon H1 differentiation. Taken together, our results provide a resource for the functional exploration of HOT regions and extend our understanding of the key roles of HOT regions in development and differentiation.

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