Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells.
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Authors
Koohy, Hashem
Bolland, Daniel John
Stellato, Claudia
Dimond, Andrew
Várnai, Csilla
Chovanec, Peter
Denizot, Jeremy
Manzano Garcia, Raquel
Wingett, Steven W
Freire-Pritchett, Paula
Nagano, Takashi
Stephens, Leonard
Elderkin, Sarah
Spivakov, Mikhail
Fraser, Peter
Publication Date
2018-09-05Journal Title
Genome Biol
ISSN
1474-7596
Publisher
Springer Science and Business Media LLC
Volume
19
Issue
1
Pages
126
Language
eng
Type
Article
This Version
VoR
Physical Medium
Electronic
Metadata
Show full item recordCitation
Koohy, H., Bolland, D. J., Matheson, L. S., Schoenfelder, S., Stellato, C., Dimond, A., Várnai, C., et al. (2018). Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells.. Genome Biol, 19 (1), 126. https://doi.org/10.1186/s13059-018-1489-y
Abstract
BACKGROUND: Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expression and chromatin features genome-wide, including histone modifications and chromosome conformation, in bone marrow pro-B and pre-B cells from young and aged mice. RESULTS: Our analysis reveals that the expression levels of most genes are generally preserved in B cell precursors isolated from aged compared with young mice. Nonetheless, age-specific expression changes are observed at numerous genes, including microRNA encoding genes. Importantly, these changes are underpinned by multi-layered alterations in chromatin structure, including chromatin accessibility, histone modifications, long-range promoter interactions, and nuclear compartmentalization. Previous work has shown that differentiation is linked to changes in promoter-regulatory element interactions. We find that aging in B cell precursors is accompanied by rewiring of such interactions. We identify transcriptional downregulation of components of the insulin-like growth factor signaling pathway, in particular downregulation of Irs1 and upregulation of Let-7 microRNA expression, as a signature of the aged phenotype. These changes in expression are associated with specific alterations in H3K27me3 occupancy, suggesting that Polycomb-mediated repression plays a role in precursor B cell aging. CONCLUSIONS: Changes in chromatin and 3D genome organization play an important role in shaping the altered gene expression profile of aged precursor B cells. Components of the insulin-like growth factor signaling pathways are key targets of epigenetic regulation in aging in bone marrow B cell precursors.
Keywords
B-Lymphocytes, Chromatin, Stem Cells, Animals, Mice, Inbred C57BL, Somatomedins, Signal Transduction, Down-Regulation, Epigenesis, Genetic, Aging, Genome, Male, Transcriptome
Sponsorship
Biotechnology and Biological Sciences Research Council (BBS/E/B/000C0405)
Biotechnology and Biological Sciences Research Council (BBS/E/B/000C0404)
Identifiers
External DOI: https://doi.org/10.1186/s13059-018-1489-y
This record's URL: https://www.repository.cam.ac.uk/handle/1810/293936
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