Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen.
3D chromatin organization
CTCF
Endogenous retrovirus
Hi-C
Pig spleen
Transposable element
Journal
Computational and structural biotechnology journal
ISSN: 2001-0370
Titre abrégé: Comput Struct Biotechnol J
Pays: Netherlands
ID NLM: 101585369
Informations de publication
Date de publication:
2023
2023
Historique:
received:
07
08
2023
revised:
23
09
2023
accepted:
23
09
2023
medline:
4
10
2023
pubmed:
4
10
2023
entrez:
4
10
2023
Statut:
epublish
Résumé
Like other mammalian species, the pig genome is abundant with transposable elements (TEs). The importance of TEs for three-dimensional (3D) chromatin organization has been observed in species like human and mouse, yet current understanding about pig TEs is absent. Here, we investigated the contribution of TEs for the 3D chromatin organization in three pig tissues, focusing on spleen which is crucial for both adaptive and innate immunity. We identified dozens of TE families overrepresented with CTCF binding sites, including LTR22_SS, LTR15_SS and LTR16_SSc which are pig-specific families of endogenous retroviruses (ERVs). Interestingly, LTR22_SS elements harbor a CTCF motif and create hundreds of CTCF binding sites that are associated with adaptive immunity. We further applied Hi-C to profile the 3D chromatin structure in spleen and found that TE-derived CTCF binding sites correlate with chromatin insulation and frequently overlap TAD borders and loop anchors. Notably, one LTR22_SS-derived CTCF binding site demarcate a TAD boundary upstream of XCL1, which is a spleen-enriched chemokine gene important for lymphocyte trafficking and inflammation. Overall, this study represents a first step toward understanding the function of TEs on 3D chromatin organization regulation in pigs and expands our understanding about the functional importance of TEs in mammals.
Identifiants
pubmed: 37790243
doi: 10.1016/j.csbj.2023.09.029
pii: S2001-0370(23)00341-0
pmc: PMC10542605
doi:
Types de publication
Journal Article
Langues
eng
Pagination
4580-4588Informations de copyright
© 2023 The Authors.
Déclaration de conflit d'intérêts
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
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