Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming

Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood. Here we use transcription factor (TF)-mediated reprogramming to examine the interplay between genome architecture and transcriptional program...

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Vydané v:iScience Ročník 6; s. 232 - 246
Hlavní autori: Liu, Sijia, Chen, Haiming, Ronquist, Scott, Seaman, Laura, Ceglia, Nicholas, Meixner, Walter, Chen, Pin-Yu, Higgins, Gerald, Baldi, Pierre, Smale, Steve, Hero, Alfred, Muir, Lindsey A., Rajapakse, Indika
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States Elsevier Inc 31.08.2018
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Abstract Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood. Here we use transcription factor (TF)-mediated reprogramming to examine the interplay between genome architecture and transcriptional programs that transition cells into the myogenic identity. We recently developed new methods for evaluating the topological features of genome architecture based on network centrality. Through integrated analysis of these features of genome architecture and transcriptome dynamics during myogenic reprogramming of human fibroblasts we find that significant architectural reorganization precedes activation of a myogenic transcriptional program. This interplay sets the stage for a critical transition observed at several genomic scales reflecting definitive adoption of the myogenic phenotype. Subsequently, TFs within the myogenic transcriptional program participate in entrainment of biological rhythms. These findings reveal a role for topological features of genome architecture in the initiation of transcriptional programs during TF-mediated human cellular reprogramming. [Display omitted] •4D Nucleome analysis of direct human fibroblast to muscle reprogramming•A space-time bifurcation marks transit to a new cell identity•Chromatin reorganization precedes significant transcriptional changes•Myogenic master regulators have a role in entraining biological rhythms Molecular Structure; Integrative Aspects of Cell Biology; Systems Biology; Omics
AbstractList Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood. Here we use transcription factor (TF)-mediated reprogramming to examine the interplay between genome architecture and transcriptional programs that transition cells into the myogenic identity. We recently developed new methods for evaluating the topological features of genome architecture based on network centrality. Through integrated analysis of these features of genome architecture and transcriptome dynamics during myogenic reprogramming of human fibroblasts we find that significant architectural reorganization precedes activation of a myogenic transcriptional program. This interplay sets the stage for a critical transition observed at several genomic scales reflecting definitive adoption of the myogenic phenotype. Subsequently, TFs within the myogenic transcriptional program participate in entrainment of biological rhythms. These findings reveal a role for topological features of genome architecture in the initiation of transcriptional programs during TF-mediated human cellular reprogramming. : Molecular Structure; Integrative Aspects of Cell Biology; Systems Biology; Omics Subject Areas: Molecular Structure, Integrative Aspects of Cell Biology, Systems Biology, Omics
Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood. Here we use transcription factor (TF)-mediated reprogramming to examine the interplay between genome architecture and transcriptional programs that transition cells into the myogenic identity. We recently developed new methods for evaluating the topological features of genome architecture based on network centrality. Through integrated analysis of these features of genome architecture and transcriptome dynamics during myogenic reprogramming of human fibroblasts we find that significant architectural reorganization precedes activation of a myogenic transcriptional program. This interplay sets the stage for a critical transition observed at several genomic scales reflecting definitive adoption of the myogenic phenotype. Subsequently, TFs within the myogenic transcriptional program participate in entrainment of biological rhythms. These findings reveal a role for topological features of genome architecture in the initiation of transcriptional programs during TF-mediated human cellular reprogramming.
Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood. Here we use transcription factor (TF)-mediated reprogramming to examine the interplay between genome architecture and transcriptional programs that transition cells into the myogenic identity. We recently developed new methods for evaluating the topological features of genome architecture based on network centrality. Through integrated analysis of these features of genome architecture and transcriptome dynamics during myogenic reprogramming of human fibroblasts we find that significant architectural reorganization precedes activation of a myogenic transcriptional program. This interplay sets the stage for a critical transition observed at several genomic scales reflecting definitive adoption of the myogenic phenotype. Subsequently, TFs within the myogenic transcriptional program participate in entrainment of biological rhythms. These findings reveal a role for topological features of genome architecture in the initiation of transcriptional programs during TF-mediated human cellular reprogramming.Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood. Here we use transcription factor (TF)-mediated reprogramming to examine the interplay between genome architecture and transcriptional programs that transition cells into the myogenic identity. We recently developed new methods for evaluating the topological features of genome architecture based on network centrality. Through integrated analysis of these features of genome architecture and transcriptome dynamics during myogenic reprogramming of human fibroblasts we find that significant architectural reorganization precedes activation of a myogenic transcriptional program. This interplay sets the stage for a critical transition observed at several genomic scales reflecting definitive adoption of the myogenic phenotype. Subsequently, TFs within the myogenic transcriptional program participate in entrainment of biological rhythms. These findings reveal a role for topological features of genome architecture in the initiation of transcriptional programs during TF-mediated human cellular reprogramming.
Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood. Here we use transcription factor (TF)-mediated reprogramming to examine the interplay between genome architecture and transcriptional programs that transition cells into the myogenic identity. We recently developed new methods for evaluating the topological features of genome architecture based on network centrality. Through integrated analysis of these features of genome architecture and transcriptome dynamics during myogenic reprogramming of human fibroblasts we find that significant architectural reorganization precedes activation of a myogenic transcriptional program. This interplay sets the stage for a critical transition observed at several genomic scales reflecting definitive adoption of the myogenic phenotype. Subsequently, TFs within the myogenic transcriptional program participate in entrainment of biological rhythms. These findings reveal a role for topological features of genome architecture in the initiation of transcriptional programs during TF-mediated human cellular reprogramming. • 4D Nucleome analysis of direct human fibroblast to muscle reprogramming • A space-time bifurcation marks transit to a new cell identity • Chromatin reorganization precedes significant transcriptional changes • Myogenic master regulators have a role in entraining biological rhythms Molecular Structure; Integrative Aspects of Cell Biology; Systems Biology; Omics
Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood. Here we use transcription factor (TF)-mediated reprogramming to examine the interplay between genome architecture and transcriptional programs that transition cells into the myogenic identity. We recently developed new methods for evaluating the topological features of genome architecture based on network centrality. Through integrated analysis of these features of genome architecture and transcriptome dynamics during myogenic reprogramming of human fibroblasts we find that significant architectural reorganization precedes activation of a myogenic transcriptional program. This interplay sets the stage for a critical transition observed at several genomic scales reflecting definitive adoption of the myogenic phenotype. Subsequently, TFs within the myogenic transcriptional program participate in entrainment of biological rhythms. These findings reveal a role for topological features of genome architecture in the initiation of transcriptional programs during TF-mediated human cellular reprogramming. [Display omitted] •4D Nucleome analysis of direct human fibroblast to muscle reprogramming•A space-time bifurcation marks transit to a new cell identity•Chromatin reorganization precedes significant transcriptional changes•Myogenic master regulators have a role in entraining biological rhythms Molecular Structure; Integrative Aspects of Cell Biology; Systems Biology; Omics
Author Higgins, Gerald
Seaman, Laura
Smale, Steve
Rajapakse, Indika
Chen, Haiming
Meixner, Walter
Ronquist, Scott
Muir, Lindsey A.
Baldi, Pierre
Chen, Pin-Yu
Liu, Sijia
Ceglia, Nicholas
Hero, Alfred
AuthorAffiliation 3 Department of Computer Science, University of California-Irvine, Irvine, CA 92697, USA
1 Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
2 Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
5 Department of Mathematics, City University of Hong Kong, Hong Kong 999077, China
7 Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
4 AI Foundations, IBM T. J. Watson Research Center, Yorktown Heights, NY 10598, USA
6 Department of Mathematics, University of California, Berkeley, CA 94720, USA
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Keywords Molecular Structure
Systems Biology
Integrative Aspects of Cell Biology
Omics
Language English
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Snippet Genome architecture has emerged as a critical element of transcriptional regulation, although its role in the control of cell identity is not well understood....
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SubjectTerms Integrative Aspects of Cell Biology
Molecular Structure
Omics
Systems Biology
Title Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming
URI https://dx.doi.org/10.1016/j.isci.2018.08.002
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