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Genomic-wide transcriptional profiling in primary myoblasts reveals Runx1-regulated genes in muscle regeneration.

Umansky KB, Feldmesser E, Groner Y - Genom Data (2015)

Bottom Line: In response to muscle damage the muscle adult stem cells are activated and differentiate into myoblasts that regenerate the damaged tissue.We employed Runx1-dependent gene expression, Chromatin Immunoprecipitation sequencing (ChIP-seq), Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and histone H3K4me1/H3K27ac modification analyses to identify a subset of Runx1-regulated genes that are co-occupied by the TFs MyoD and c-Jun and are involved in muscle regeneration (Umansky et al.).The data is available at the GEO database under the superseries accession number GSE56131.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel.

ABSTRACT
In response to muscle damage the muscle adult stem cells are activated and differentiate into myoblasts that regenerate the damaged tissue. We have recently showed that following myopathic damage the level of the Runx1 transcription factor (TF) is elevated and that during muscle regeneration this TF regulates the balance between myoblast proliferation and differentiation (Umansky et al.). We employed Runx1-dependent gene expression, Chromatin Immunoprecipitation sequencing (ChIP-seq), Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and histone H3K4me1/H3K27ac modification analyses to identify a subset of Runx1-regulated genes that are co-occupied by the TFs MyoD and c-Jun and are involved in muscle regeneration (Umansky et al.). The data is available at the GEO database under the superseries accession number GSE56131.

No MeSH data available.


Related in: MedlinePlus

Experimental design.Schematic representation of the selection procedures used to identify high-confidence Runx1-regulated genes (adapted from Umansky et al. [1]). Each cylinder represents a gene subset, with the gene number given in brackets. I — Runx1-responsive genes were derived from Runx1L/Lvs. Runx1f/f PM microarray expression data [1]. II — Runx1-regulated genes were derived by cross-analysis of the Runx1-responsive gene dataset and Runx1 ChIP-seq data. This gene subset represents Runx1-responsive genes that are also occupied by Runx1. III — RMJ-regulated genes are Runx1-responsive genes that are co-occupied by Runx1, MyoD and c-Jun. IV — High-confidence Runx1-regulated gene subset is RMJ-regulated genes that were also marked as having adjacent active regulatory elements by both anti-histone modifications (H3K4me1 & H3K27ac) ChIP-seq and ATAC-seq analysis.
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f0005: Experimental design.Schematic representation of the selection procedures used to identify high-confidence Runx1-regulated genes (adapted from Umansky et al. [1]). Each cylinder represents a gene subset, with the gene number given in brackets. I — Runx1-responsive genes were derived from Runx1L/Lvs. Runx1f/f PM microarray expression data [1]. II — Runx1-regulated genes were derived by cross-analysis of the Runx1-responsive gene dataset and Runx1 ChIP-seq data. This gene subset represents Runx1-responsive genes that are also occupied by Runx1. III — RMJ-regulated genes are Runx1-responsive genes that are co-occupied by Runx1, MyoD and c-Jun. IV — High-confidence Runx1-regulated gene subset is RMJ-regulated genes that were also marked as having adjacent active regulatory elements by both anti-histone modifications (H3K4me1 & H3K27ac) ChIP-seq and ATAC-seq analysis.

Mentions: To elucidate the Runx1-mediated myoblast transcriptional program during muscle regeneration, we employed genetically modified Runx1f/f and mdx/Runx1f/f mice [1]. The experimental design is schematically described in Fig. 1: First, we derived the Runx1-responsive genes by comparing the Runx1f/f PM transcriptome to that of Runx1L/L PMs. Next, we defined the Runx1-regulated gene subset by cross-analyzing the Runx1-responsive gene subset with genome-wide Runx1 ChIP-seq data in wild type PMs. To further characterize this Runx1-regulated gene subset we singled out Runx1-bound gene loci that were co-bound by Runx1 transcriptional collaborators MyoD and c-Jun (Fig. 1). Finally, we characterized the open/active chromatin by genome-wide mapping of active enhancer markers (H3K4me1, H3K27Ac) and ATAC-seq analyses. The combination of this comprehensive analysis generated a list of high-confidence Runx1-regulated genes. The expression profile of this high-confidence was validated in vivo using RNA-seq of RNA derived from muscles of mdx/Runx1f/fvs. mdx/Runx1L/L mice [1].


Genomic-wide transcriptional profiling in primary myoblasts reveals Runx1-regulated genes in muscle regeneration.

Umansky KB, Feldmesser E, Groner Y - Genom Data (2015)

Experimental design.Schematic representation of the selection procedures used to identify high-confidence Runx1-regulated genes (adapted from Umansky et al. [1]). Each cylinder represents a gene subset, with the gene number given in brackets. I — Runx1-responsive genes were derived from Runx1L/Lvs. Runx1f/f PM microarray expression data [1]. II — Runx1-regulated genes were derived by cross-analysis of the Runx1-responsive gene dataset and Runx1 ChIP-seq data. This gene subset represents Runx1-responsive genes that are also occupied by Runx1. III — RMJ-regulated genes are Runx1-responsive genes that are co-occupied by Runx1, MyoD and c-Jun. IV — High-confidence Runx1-regulated gene subset is RMJ-regulated genes that were also marked as having adjacent active regulatory elements by both anti-histone modifications (H3K4me1 & H3K27ac) ChIP-seq and ATAC-seq analysis.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664707&req=5

f0005: Experimental design.Schematic representation of the selection procedures used to identify high-confidence Runx1-regulated genes (adapted from Umansky et al. [1]). Each cylinder represents a gene subset, with the gene number given in brackets. I — Runx1-responsive genes were derived from Runx1L/Lvs. Runx1f/f PM microarray expression data [1]. II — Runx1-regulated genes were derived by cross-analysis of the Runx1-responsive gene dataset and Runx1 ChIP-seq data. This gene subset represents Runx1-responsive genes that are also occupied by Runx1. III — RMJ-regulated genes are Runx1-responsive genes that are co-occupied by Runx1, MyoD and c-Jun. IV — High-confidence Runx1-regulated gene subset is RMJ-regulated genes that were also marked as having adjacent active regulatory elements by both anti-histone modifications (H3K4me1 & H3K27ac) ChIP-seq and ATAC-seq analysis.
Mentions: To elucidate the Runx1-mediated myoblast transcriptional program during muscle regeneration, we employed genetically modified Runx1f/f and mdx/Runx1f/f mice [1]. The experimental design is schematically described in Fig. 1: First, we derived the Runx1-responsive genes by comparing the Runx1f/f PM transcriptome to that of Runx1L/L PMs. Next, we defined the Runx1-regulated gene subset by cross-analyzing the Runx1-responsive gene subset with genome-wide Runx1 ChIP-seq data in wild type PMs. To further characterize this Runx1-regulated gene subset we singled out Runx1-bound gene loci that were co-bound by Runx1 transcriptional collaborators MyoD and c-Jun (Fig. 1). Finally, we characterized the open/active chromatin by genome-wide mapping of active enhancer markers (H3K4me1, H3K27Ac) and ATAC-seq analyses. The combination of this comprehensive analysis generated a list of high-confidence Runx1-regulated genes. The expression profile of this high-confidence was validated in vivo using RNA-seq of RNA derived from muscles of mdx/Runx1f/fvs. mdx/Runx1L/L mice [1].

Bottom Line: In response to muscle damage the muscle adult stem cells are activated and differentiate into myoblasts that regenerate the damaged tissue.We employed Runx1-dependent gene expression, Chromatin Immunoprecipitation sequencing (ChIP-seq), Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and histone H3K4me1/H3K27ac modification analyses to identify a subset of Runx1-regulated genes that are co-occupied by the TFs MyoD and c-Jun and are involved in muscle regeneration (Umansky et al.).The data is available at the GEO database under the superseries accession number GSE56131.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel.

ABSTRACT
In response to muscle damage the muscle adult stem cells are activated and differentiate into myoblasts that regenerate the damaged tissue. We have recently showed that following myopathic damage the level of the Runx1 transcription factor (TF) is elevated and that during muscle regeneration this TF regulates the balance between myoblast proliferation and differentiation (Umansky et al.). We employed Runx1-dependent gene expression, Chromatin Immunoprecipitation sequencing (ChIP-seq), Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and histone H3K4me1/H3K27ac modification analyses to identify a subset of Runx1-regulated genes that are co-occupied by the TFs MyoD and c-Jun and are involved in muscle regeneration (Umansky et al.). The data is available at the GEO database under the superseries accession number GSE56131.

No MeSH data available.


Related in: MedlinePlus