Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro

Doynova, Malina; Markworth, James F.; Cameron‐Smith, David; Vickers, Mark H.; O’Sullivan, Justin M.

doi:10.1186/s13395-017-0122-1

Cited by 51 publications

(46 citation statements)

References 94 publications

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“…Unlike TADs, chromosomal A/B compartments have often been reported as highly variable between tissues or developmental stages, involving dynamic mechanisms of epigenetic control [51][52][53]. Here, we postulated that despite its plasticity, the structural organization in genome compartments for a given tissue could also be under selective pressure across a large phylogenetic spectrum.…”

Section: Comprehensive Maps Of Topological Domains and Genomic Comparmentioning

confidence: 87%

Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species

Foissac

Djebali

Munyard

et al. 2018

Preprint

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Background: Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aims at profiling the landscape of transcription (RNA-seq) and chromatin accessibility and conformation (ATAC-seq and Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Results: Standardized protocols were applied to produce transcriptome and chromatin datasets for the four species. RNA-seq assays considerably extended the available catalog of protein-coding and non-coding transcripts. Gene expression profiles were consistent with known metabolic/immune functions and revealed differentially expressed transcripts with unknown function, including new lncRNAs in syntenic regions. The majority of ATAC-seq peaks of chromatin accessibility mapped to putative regulatory regions, with an enrichment of predicted transcription factor binding sites in differentially accessible peaks. Hi-C provided the first set of genome-wide maps of three-dimensional interactions across livestock and showed consistency with results from gene expression and chromatin accessibility in topological compartments of the genomes. Conclusions: We report the first multi-species and multi-assay genome annotation results obtained by a FAANG pilot project. The global consistency between gene expression and chromatin structure data in these four livestock species confirms previous findings in model animals. Overall, these results emphasize the value of FAANG for research on domesticated animals and strengthen the importance of future meta-analyses of the reference datasets being generated by this community on different species.

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Section: Comprehensive Maps Of Topological Domains and Genomic Comparmentioning

confidence: 87%

Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species

Foissac

Djebali

Munyard

et al. 2018

Preprint

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“…Comprehensive gene expression analyses have also shown that myogenic differentiation ensues in a stepwise fashion, where sequential activation of a specific set of genes restructures the cells one step at a time toward the differentiated phenotype [48]. Nonetheless, at the early stage of the differentiation, thousands of genes are differentially expressed [14,49,50], mostly within 24 hours of differentiation. As a result, epigenetic changes reflecting the alteration of gene programs should occur.…”

Section: Discussionmentioning

confidence: 99%

Loci-specific histone acetylation profiles associated with transcriptional coactivator p300 during early myoblast differentiation

et al. 2018

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Molecular regulation of stem cell differentiation is exerted through both genetic and epigenetic determinants over distal regulatory or enhancer regions. Understanding the mechanistic action of active or poised enhancers is therefore imperative for control of stem cell differentiation. Based on the genome-wide co-occurrence of different epigenetic marks in committed proliferating myoblasts, we have previously generated a 14-state chromatin state model to profile rexinoid-responsive histone acetylation in early myoblast differentiation. Here, we delineate the functional mode of transcription regulators during early myogenic differentiation using genome-wide chromatin state association. We define a role of transcriptional coactivator p300, when recruited by muscle master regulator MyoD, in the establishment and regulation of myogenic loci at the onset of myoblast differentiation. In addition, we reveal an enrichment of loci-specific histone acetylation at p300 associated active or poised enhancers, particularly when enlisted by MyoD. We provide novel molecular insights into the regulation of myogenic enhancers by p300 in concert with MyoD. Our studies present a valuable aptitude for driving condition-specific chromatin state or enhancers pharmacologically to treat muscle-related diseases and for the identification of additional myogenic targets and molecular interactions for therapeutic development.Abbreviations: MRF: Muscle regulatory factor; HAT: Histone acetyltransferase; CBP: CREB-binding protein; ES: Embryonic stem; ATCC: American type culture collection; DM: Differentiation medium; DMEM: Dulbecco’s Modified Eagle Medium; GM: Growth medium; GO: Gene ontology; GREAT: Genomic regions enrichment of annotations tool; FPKM: Fragments per kilobase of transcript per million; GEO: Gene expression omnibus; MACS: Model-based analysis for ChIP-seq

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“…A recent low-resolution (400 kb) genome-wide analysis of chromatin interactions in myoblasts pre- and post-differentiation showed overall similarity in genome organization despite the change in differentiation state. The resolution achieved precluded identifying gene-specific interactions but nevertheless showed that differentiation did induce some compartment switching, indicating interconversion of specific regions of hetero- and euchromatin in myoblasts and myotubes (139). …”

Section: The Chromatin State At Active Myogenic Locimentioning

confidence: 99%

Temporal regulation of chromatin during myoblast differentiation

Harada

Ohkawa

2017

Seminars in Cell & Developmental Biology

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The commitment to and execution of differentiation programs involves a significant change in gene expression in the precursor cell to facilitate development of the mature cell type. In addition to being regulated by lineage-determining and auxiliary transcription factors that drive these changes, the structural status of the chromatin has a considerable impact on the transcriptional competence of differentiation-specific genes, which is clearly demonstrated by the large number of cofactors and the extraordinary complex mechanisms by which these genes become activated. The terminal differentiation of myoblasts to myotubes and mature skeletal muscle is an excellent system to illustrate these points. The MyoD family of closely related, lineage-determining transcription factors directs, largely through targeting to chromatin, a cascade of cooperating transcription factors and enzymes that incorporate or remove variant histones, post-translationally modify histones, and alter nucleosome structure and positioning via energy released by ATP hydrolysis. The coordinated action of these transcription factors and enzymes prevents expression of differentiation-specific genes in myoblasts and facilitates the transition of these genes from transcriptionally repressed to activated during the differentiation process. Regulation is achieved in both a temporal as well as spatial manner, as at least some of these factors and enzymes affect local chromatin structure at myogenic gene regulatory sequences as well as higher-order genome organization. Here we discuss the transition of genes that promote myoblast differentiation from the silenced to the activated state with an emphasis on the changes that occur to individual histones and the chromatin structure present at these loci.

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Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro

Cited by 51 publications

References 94 publications

Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species

Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species

Loci-specific histone acetylation profiles associated with transcriptional coactivator p300 during early myoblast differentiation

Temporal regulation of chromatin during myoblast differentiation

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