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Mapping the Chromatin State Dynamics in Myoblasts

ABSTRACT: The chromatin state in developing body parts provides a zip code to cellular populations that direct their cell fates. We used antibodies for H3K4me3, H3K27me3 and Pol2, to identify the chromatin state signature of the Pitx2-null mouse forelimb during mid-gestation, at embryonic day 12. The families of genes marked included those related to transcription, transcriptional regulation, and embryonic organ development. Transcription factors specific for muscle development were characterized by bivalent chromatin, as E12 is a transition time point from embryonic to fetal myogenesis. The identified chromatin state of muscle specific genes was in strong correlation with their observed expression profile.

ORGANISM(S): Mus musculus

PROVIDER: GSE71128 | GEO | 2016/07/17

SECONDARY ACCESSION(S): PRJNA290430

REPOSITORIES: GEO

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Mapping the Chromatin State Dynamics in Myoblasts

Project description:The chromatin state in developing body parts provides a zip code to cellular populations that direct their cell fates. We used antibodies for H3K4me3, H3K27me3 and Pol2, to identify the chromatin state signature of the Pitx2-null mouse forelimb during mid-gestation, at embryonic day 12. The families of genes marked included those related to transcription, transcriptional regulation, and embryonic organ development. Transcription factors specific for muscle development were characterized by bivalent chromatin, as E12 is a transition time point from embryonic to fetal myogenesis. The identified chromatin state of muscle specific genes was in strong correlation with their observed expression profile. Examination of the histone marks H3K4me3, H3k27me3, and Pol2 in whole E12.5 forelimb tissues from Pitx2 null mice using the Illumina HiSeq 2000

2016-07-17 | E-GEOD-71128 | biostudies-arrayexpress

Genome-wide maps of chromatin state in E12.5 mouse forelimbs

Project description:The chromatin state in developing body parts provides a zip code to cellular populations that direct their cell fates. We used antibodies for H3K4me3, H3K27me3 and Pol2, to identify the chromatin state signature of the mouse forelimb during mid-gestation, at embryonic day 12. The families of genes marked included those related to transcription, transcriptional regulation, and embryonic organ development. Transcription factors specific for muscle development were characterized by bivalent chromatin, as E12 is a transition time point from embryonic to fetal myogenesis. The identified chromatin state of muscle specific genes was in strong correlation with their observed expression profile. Examination of the histone marks H3K4me3, H3k27me3, and Pol2 in whole E12.5 forelimnb tissues using the Illumina HiSeq 2000.

2015-02-20 | E-GEOD-49010 | biostudies-arrayexpress

Genome-wide maps of chromatin state in E12.5 mouse forelimbs

Project description:The chromatin state in developing body parts provides a zip code to cellular populations that direct their cell fates. We used antibodies for H3K4me3, H3K27me3 and Pol2, to identify the chromatin state signature of the mouse forelimb during mid-gestation, at embryonic day 12. The families of genes marked included those related to transcription, transcriptional regulation, and embryonic organ development. Transcription factors specific for muscle development were characterized by bivalent chromatin, as E12 is a transition time point from embryonic to fetal myogenesis. The identified chromatin state of muscle specific genes was in strong correlation with their observed expression profile.

2015-02-20 | GSE49010 | GEO

Expression data from Lbx1-EGFP+ flow sorted cells from Pitx2 WT, HT, Null forelimb tissue

Project description:Determing the gene network regulated by Pitx2 in during forelimb muscle development of mouse embryos at E12.5. Lbx1 is coexpressed in Pitx2+ cells during forelimb development, thus Pitx2-LacZ and Lbx1-EGFP+ mice were cross bred to allow us to purify Lbx1-EGFP+|Pitx2 -wildtype, het, or null cells by flow sorting We used microarray analysis to determine the genes misregulated in Pitx2 null mice compared to Pitx2 wildtype and heterozyogtes.

2013-06-11 | GSE31945 | GEO

Expression data from Lbx1-EGFP+ flow sorted cells from Pitx2 WT, HT, Null forelimb tissue

Project description:Determing the gene network regulated by Pitx2 in during forelimb muscle development of mouse embryos at E12.5. Lbx1 is coexpressed in Pitx2+ cells during forelimb development, thus Pitx2-LacZ and Lbx1-EGFP+ mice were cross bred to allow us to purify Lbx1-EGFP+|Pitx2 -wild type, het, or null cells by flow sorting We used microarray analysis to determine the genes misregulated in Pitx2 null mice compared to Pitx2 wild type and heterozygotes. Lbx1-EGFP+|Pitx2(+/+, LacZ/+, or LacZ/LacZ) cells were flow sorted, RNA extracted, labelled cDNA was hybridized to Affymetrix mouse genome 430 2.0 arrays

2013-06-11 | E-GEOD-31945 | biostudies-arrayexpress

A Pitx2-miRNA pathway modulates cell proliferation in myoblasts and skeletal-muscle satellite cells and promotes their commitment to a myogenic cell fate.

Project description:The acquisition of a proliferating cell status from a quiescent state as well as the shift between proliferation and differentiation are key developmental steps in skeletal-muscle stem cells (satellite cells) to provide proper muscle regeneration. However, how satellite-cell proliferation is regulated, though, is not fully understood. Here, we report that the c-isoform of the transcription factor Pitx2 increases cell proliferation in myoblasts by down-regulating the miRNAs miR-15b, miR-23b, miR-106b, and miR-503. This Pitx2c-miRNA pathway also regulates cell proliferation in early-activated satellite cells, enhancing the Myf5+ satellite cells and thereby promoting their commitment to a myogenic cell fate. This study reveals unknown functions of several miRNAs in myoblast and satellite-cell behaviour and thus may have future applications in regenerative medicine. mirVana microarrays (Ambion) were used to profile microRNA signature at different Pitx2 overexpression conditions, namely two different doses (4 and 8 µg CMV-Pitx2c plasmid, respectively) after 24 hours of transfection in SOL8 skeletal myogenic cells. 20 µg of total RNA was used to hybridize two distinct microRNA microarrays on each condition analyzed.

2015-06-10 | E-GEOD-53943 | biostudies-arrayexpress

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.

Project description:The regulatory elements that direct tissue-specific gene expression in the developing mammalian embryo remain largely unknown. Although chromatin profiling has proven to be a powerful method for mapping regulatory sequences in cultured cells, chromatin states characteristic of active developmental enhancers have not been directly identified in embryonic tissues. Here we use whole transcriptome analysis coupled with genome-wide profiling of H3K27ac and H3K27me3 to map chromatin states and enhancers in mouse embryonic forelimb and hindlimb. We show that gene expression differences between forelimb and hindlimb, and between limb and other embryonic cell types, are correlated with tissue-specific H3K27ac signatures at promoters and distal sites. Using H3K27ac profiles, we identified 28,377 putative enhancers, many of which are likely to be limb-specific based on strong enrichment near genes highly expressed in the limb and comparisons with tissue-specific p300 sites and known enhancers. We describe a chromatin state signature associated with active developmental enhancers, defined by high levels of H3K27ac marking, nucleosome displacement, hypersensitivity to sonication, and strong depletion of H3K27me3. We also find that developmental enhancers exhibit components of this signature, including hypersensitivity, H3K27ac enrichment and H3K27me3 depletion, at lower levels in tissues in which they are not active. Our results establish histone modification profiling as a tool for developmental enhancer discovery, and suggest that enhancers maintain an open chromatin state in multiple embryonic tissues independent of their activity level. Examination of genome wide H3K27ac and H3K27me3 histone modifications and gene expression in early mouse embryonic limb tissue.

2012-03-16 | E-GEOD-30641 | biostudies-arrayexpress

RING1B binding in the 11 dpc embryonic tissues

Project description:We report the distribution of RING1B (one of Polycomb group factors) within the genome of mouse embryonic tissues. We prepared the chromatin from 11 dpc embryonic forebrain, midbrain, and forelimb buds and made chromatin precipitation with antibody against RING1B (mouse monoclonal antibody). High-throughput sequencing applied for the ChIP analysis revealed the differential distribution of RING1B protein among embryonic tissues. ChIP analysis of mouse 11 dpc embryonic forebrain, midbrain and forelimb buds against anti-RING1B antibody.

2014-01-14 | E-GEOD-48464 | biostudies-arrayexpress

A Pitx2-miRNA pathway modulates cell proliferation in myoblasts and skeletal-muscle satellite cells and promotes their commitment to a myogenic cell fate

2015-06-10 | GSE53943 | GEO

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.

2012-03-16 | GSE30641 | GEO