UMMS Affiliation
Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology
Publication Date
2019-07-09
Document Type
Article
Disciplines
Amino Acids, Peptides, and Proteins | Biochemistry | Cell and Developmental Biology | Cells | Cellular and Molecular Physiology | Embryonic Structures | Genetic Phenomena | Molecular Biology | Structural Biology
Abstract
The temporal order of DNA replication is regulated during development and is highly correlated with gene expression, histone modifications and 3D genome architecture. We tracked changes in replication timing, gene expression, and chromatin conformation capture (Hi-C) A/B compartments over the first two cell cycles during differentiation of human embryonic stem cells to definitive endoderm. Remarkably, transcriptional programs were irreversibly reprogrammed within the first cell cycle and were largely but not universally coordinated with replication timing changes. Moreover, changes in A/B compartment and several histone modifications that normally correlate strongly with replication timing showed weak correlation during the early cell cycles of differentiation but showed increased alignment in later differentiation stages and in terminally differentiated cell lines. Thus, epigenetic cell fate transitions during early differentiation can occur despite dynamic and discordant changes in otherwise highly correlated genomic properties.
Keywords
chromatin 3D architecture, chromatin 3D organization, chromatin structure, differentiation, gene expression, lineage commitment, replication timing
Rights and Permissions
Copyright 2019 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
DOI of Published Version
10.1016/j.stemcr.2019.05.021
Source
Stem Cell Reports. 2019 Jul 9;13(1):193-206. doi: 10.1016/j.stemcr.2019.05.021. Epub 2019 Jun 20. Link to article on publisher's site
Journal/Book/Conference Title
Stem cell reports
Related Resources
PubMed ID
31231024
Repository Citation
Dileep, Vishnu; McCord, Rachel Patton; Dekker, Job; and Gilbert, David M., "Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment" (2019). Open Access Articles. 3936.
https://escholarship.umassmed.edu/oapubs/3936
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
Included in
Amino Acids, Peptides, and Proteins Commons, Biochemistry Commons, Cell and Developmental Biology Commons, Cells Commons, Cellular and Molecular Physiology Commons, Embryonic Structures Commons, Genetic Phenomena Commons, Molecular Biology Commons, Structural Biology Commons
Comments
Full author list omitted for brevity. For the full list of authors, see article.