PXD067536

PXD067536 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	SINE retrotransposons link replication timing with higher-order genome organization by recruiting H2Bub to gene body
Description	The mammalian genome is spatially segregated into euchromatin-associated A and heterochromatin-associated B compartments that replicate early, and late in S-phase respectively. The molecular links connecting higher-order genome organization with replication timing, however, remain unclear. Here, we show that H2Bub (histone H2B lysine 120 monoubiquitination), a transcription-coupled epigenetic mark enriched over the gene body, regulates early replication. Furthermore, enforced recruitment of H2Bub promotes early replication in cis. Consistent with these observations, genetic ablation of RNF20, an E3 ubiquitin ligase that mediates H2Bub deposition, leads to reduced firing of early replication origins and suppression of cellular and embryonic growth. We also find a role of H2Bub for promoting proximal chromatin contacts at the gene body, and in gene rich A compartments, indicating that H2Bub may connect replication timing with higher-order genome organization. Surprisingly, H2Bub-marked regions in the genome coincide with SINEs (short interspersed nuclear elements). SINE retrotransposon enrichment in transcribed gene bodies correlates with H2Bub levels, indicating that these elements may direct H2Bub deposition at chromatin. Indeed, ectopic insertion of SINEs promotes local recruitment H2Bub. Taken together, our results suggest an unexpected role for SINE retrotransposons in linking higher-order genome organization with replication timing via targeting of the transcription-coupled epigenetic mark H2Bub.
HostingRepository	jPOST
AnnounceDate	2025-08-27
AnnouncementXML	Submission_2025-08-26_17:21:45.440.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yong-Woon Han
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	S-carboxamidomethyl-L-cysteine; 2-pyrrolidone-5-carboxylic acid (Glu)
Instrument	TripleTOF 5600

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-21 02:35:34	ID requested
⏵ 1	2025-08-26 17:21:45	announced

Publication List

Dataset with its publication pending

Dataset with its publication pending

Keyword List

submitter keyword: DNA replication, SINE, H2B ubiquitination

submitter keyword: DNA replication, SINE, H2B ubiquitination

Contact List

Jafar Sharif
lab head
Yong-Woon Han
contact affiliation	Nagoya City University
dataset submitter

Full Dataset Link List

jPOST dataset URI
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jPOST dataset URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.jpostdb.org/JPST004019/