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Certain transcription factors are proposed to form functional interactions with RNA to facilitate proper regulation of gene expression. Sox2, a transcription factor critical for maintenance of pluripotency and neurogenesis, has been found associated with several lncRNAs, although it is unknown whether these interactions are direct or via other proteins. Here we demonstrate that human Sox2 interacts directly with one of these lncRNAs with high affinity through its HMG DNA-binding domain in vitro. These interactions are primarily with double-stranded RNA in a non-sequence specific fashion, mediated by a similar but not identical interaction surface. We further determined that Sox2 directly binds RNA in mouse embryonic stem cells by UV-cross-linked immunoprecipitation of Sox2 and more than a thousand Sox2-RNA interactions in vivo were identified using fRIP-seq. Together, these data reveal that Sox2 employs a high-affinity/low-specificity paradigm for RNA binding in vitro and in vivo.
Zachariah E Holmes, and
Desmond J Hamilton, and
Taeyoung Hwang, and
Nicholas V Parsonnet, and
John L Rinn, and
Deborah S Wuttke, and
Robert T Batey
November 2017,
Nucleic acids research,
Zachariah E Holmes, and
Desmond J Hamilton, and
Taeyoung Hwang, and
Nicholas V Parsonnet, and
John L Rinn, and
Deborah S Wuttke, and
Robert T Batey
July 2022,
Development (Cambridge, England),
Zachariah E Holmes, and
Desmond J Hamilton, and
Taeyoung Hwang, and
Nicholas V Parsonnet, and
John L Rinn, and
Deborah S Wuttke, and
Robert T Batey
May 1999,
The EMBO journal,
Zachariah E Holmes, and
Desmond J Hamilton, and
Taeyoung Hwang, and
Nicholas V Parsonnet, and
John L Rinn, and
Deborah S Wuttke, and
Robert T Batey
July 2014,
International journal of oncology,
Zachariah E Holmes, and
Desmond J Hamilton, and
Taeyoung Hwang, and
Nicholas V Parsonnet, and
John L Rinn, and
Deborah S Wuttke, and
Robert T Batey
February 1996,
Molecular and cellular biology,
Zachariah E Holmes, and
Desmond J Hamilton, and
Taeyoung Hwang, and
Nicholas V Parsonnet, and
John L Rinn, and
Deborah S Wuttke, and
Robert T Batey
May 1996,
The EMBO journal,
Zachariah E Holmes, and
Desmond J Hamilton, and
Taeyoung Hwang, and
Nicholas V Parsonnet, and
John L Rinn, and
Deborah S Wuttke, and
Robert T Batey
May 1996,
The Journal of biological chemistry,
Zachariah E Holmes, and
Desmond J Hamilton, and
Taeyoung Hwang, and
Nicholas V Parsonnet, and
John L Rinn, and
Deborah S Wuttke, and
Robert T Batey
June 2013,
Nucleic acids research,
Zachariah E Holmes, and
Desmond J Hamilton, and
Taeyoung Hwang, and
Nicholas V Parsonnet, and
John L Rinn, and
Deborah S Wuttke, and
Robert T Batey
August 2010,
Cell death and differentiation,
Zachariah E Holmes, and
Desmond J Hamilton, and
Taeyoung Hwang, and
Nicholas V Parsonnet, and
John L Rinn, and
Deborah S Wuttke, and
Robert T Batey
May 1994,
Molecular and cellular biology,
