An anti-silencer– and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development

Hao, Bingtao; Naik, Abani Kanta; Watanabe, Akiko; Tanaka, Hirokazu; Chen, Liang; Richards, Hunter W.; Kondo, Motonari; Taniuchi, Ichiro; Kohwi, Yoshinori; Kohwi-Shigematsu, Terumi; Krangel, Michael S.

doi:10.1084/jem.20142207

Title: An anti-silencer– and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development

Journal Article · Mon Apr 06 00:00:00 EDT 2015 · Journal of Experimental Medicine

DOI:https://doi.org/10.1084/jem.20142207· OSTI ID:1625199

Hao, Bingtao ^[1]; Naik, Abani Kanta ^[1]; Watanabe, Akiko ^[1]; Tanaka, Hirokazu ^[2]; Chen, Liang ^[1]; Richards, Hunter W. ^[3]; Kondo, Motonari ^[1]; Taniuchi, Ichiro ^[2]; Kohwi, Yoshinori ^[3]; Kohwi-Shigematsu, Terumi ^[3]; Krangel, Michael S. ^[1]

Duke University, Durham, NC (United States)
RIKEN Center for Centre for Integrative Medical Sciences, Yokohama (Japan)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Rag1 and Rag2 gene expression in CD4⁺CD8⁺ double-positive (DP) thymocytes depends on the activity of a distant anti-silencer element (ASE) that counteracts the activity of an intergenic silencer. However, the mechanistic basis for ASE activity is unknown. Here, we show that the ASE physically interacts with the distant Rag1 and Rag2 gene promoters in DP thymocytes, bringing the two promoters together to form an active chromatin hub. Moreover, we show that the ASE functions as a classical enhancer that can potently activate these promoters in the absence of the silencer or other locus elements. In thymocytes lacking the chromatin organizer SATB1, we identified a partial defect in Tcra gene rearrangement that was associated with reduced expression of Rag1 and Rag2 at the DP stage. SATB1 binds to the ASE and Rag promoters, facilitating inclusion of Rag2 in the chromatin hub and the loading of RNA polymerase II to both the Rag1 and Rag2 promoters. Our results provide a novel framework for understanding ASE function and demonstrate a novel role for SATB1 as a regulator of Rag locus organization and gene expression in DP thymocytes.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH); Japan Society for the Promotion of Science (JSPS); Leukemia and Lymphoma Society Scholar Award

Grant/Contract Number:: AC02-05CH11231; R37 GM10452; R37 CA39681; KAKENHI 24390121

OSTI ID:: 1625199

Journal Information:: Journal of Experimental Medicine, Vol. 212, Issue 5; ISSN 0022-1007

Publisher:: Rockefeller University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Title: An anti-silencer– and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development

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