UMMS Affiliation
Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology
Publication Date
2019-01-03
Document Type
Article
Disciplines
Amino Acids, Peptides, and Proteins | Biochemistry | Computational Biology | Molecular Biology | Structural Biology | Systems Biology
Abstract
The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically associated domains (TADs), A/B compartments and formation of two mega-domains. Here we demonstrate that the non-canonical SMC family protein, SmcHD1, which is important for gene silencing on Xi, contributes to this unique chromosome architecture. Specifically, allelic mapping of the transcriptome and epigenome in SmcHD1 mutant cells reveals the appearance of sub-megabase domains defined by gene activation, CpG hypermethylation and depletion of Polycomb-mediated H3K27me3. These domains, which correlate with sites of SmcHD1 enrichment on Xi in wild-type cells, additionally adopt features of active X chromosome higher-order chromosome architecture, including A/B compartments and partial restoration of TAD boundaries. Xi chromosome architecture changes also occurred following SmcHD1 knockout in a somatic cell model, but in this case, independent of Xi gene derepression. We conclude that SmcHD1 is a key factor in defining the unique chromosome architecture of Xi.
Keywords
Chromatin structure, Chromosomes, Dosage compensation, Epigenetic memory
Rights and Permissions
© The Author(s) 2019. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
DOI of Published Version
10.1038/s41467-018-07907-2
Source
Nat Commun. 2019 Jan 3;10(1):30. doi: 10.1038/s41467-018-07907-2. Link to article on publisher's site
Journal/Book/Conference Title
Nature communications
Related Resources
PubMed ID
30604745
Repository Citation
Gdula, Michal R.; Nesterova, Tatyana B.; Pintacuda, Greta; Godwin, Jonathan; Zhan, Ye; Ozadam, Hakan; McClellan, Michael; Moralli, Daniella; Krueger, Felix; Green, Catherine M.; Reik, Wolf; Kriaucionis, Skirmantas; Heard, Edith; Dekker, Job; and Brockdorff, Neil, "The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome" (2019). Open Access Articles. 3713.
https://escholarship.umassmed.edu/oapubs/3713
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Amino Acids, Peptides, and Proteins Commons, Biochemistry Commons, Computational Biology Commons, Molecular Biology Commons, Structural Biology Commons, Systems Biology Commons