The role of High Mobility Group A1 protein in transcriptional regulation of cellular senescence

Cellular senescence is characterised by the irreversible arrest of the cell cycle, triggered by diverse stress, such as oncogenic stress. The chromatin structure of senescent cells changes dramatically, exemplified by the formation of senescence-associated heterochromatic foci (SAHF). Moreover, senescent cells secrete a series of functional molecules, which are collectively called senescence-associated secretory phenotype (SASP). These molecules can be beneficial or detrimental depending on the biological context. High mobility group A (HMGA) proteins are DNA binding proteins that are known to be highly expressed in embryonic, senescent and cancer cells. HMGA1 is a key structural component for SAHF formation. In contrast, it has been suggested that HMGA proteins are involved in gene activation potentially through structurally altering regulatory elements. However, comprehensive understanding of how HMGA modulates gene expression is missing largely due to a lack of genome-wide characterisation. To address this, we leveraged the distinct phenotype, namely senescence, and mapped HMGA1-dependent gene regulation through a genome-wide approach. Here we find that HMGA1 negatively regulates inflammatory SASP, potentially through direct binding to the genes. We found that numerous SASP genes are further up-regulated if HMGA1 is depleted during senescence. Next, we conducted HMGA1 chromatin immunoprecipitation (ChIP-seq). As expected, HMGA1 was highly enriched in heterochromatin regions, but a substantial fraction of peaks were found on genes. Among these were the aforementioned SASP genes suggesting a direct regulatory role of HMGA1 in ‘buffering’ their expression. To uncover the mechanism by which HMGA1 directly controls transcription, we employed a combination of RNAPol2 ChIP-seq and nascent RNA-seq. We found that RNAPol2 binding increased on the genes in shHMGA1 condition, suggesting that the modulation occurs at least in part at a (co-)transcriptional stage; whereas our nascent RNA-seq also showed qualitative increase in shHMGA1 for some targets, but more quantitative analysis is required. Furthermore, we used proteomics approaches to identify HMGA1-binding partners and among the candidates, we singled out the linker histone variant H1.0, which appears to be functionally linked to HMGA1 regulating SASP pro-inflammatory genes. In conclusion, our comprehensive analysis of HMGA1 expands our knowledge of the role of HMGA1 on transcriptional regulation.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2021

Author dc:creator

• Ando Kuri, Masami

Advisor dc:contributor.advisor

• Narita, Masashi

• Cellular senescence

Licence

• https://www.rioxx.net/licenses/all-rights-reserved/

Language dc:language

eng

Author Identifier

0000-0002-7594-3359

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/335470