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The Sox2 transcription factor binds RNA

ABSTRACT: The Sox2 transcription factor binds RNA

PROVIDER: PRJNA595571 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10691047_1.fastq.gz	Fastqsanger.gz
	SRR10691047_2.fastq.gz	Fastqsanger.gz
	SRR10691048_1.fastq.gz	Fastqsanger.gz
	SRR10691048_2.fastq.gz	Fastqsanger.gz
	SRR10691049_1.fastq.gz	Fastqsanger.gz

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The Sox2 transcription factor binds RNA

Project description:A subset of transcription factors is proposed to form functional interactions with RNA to facilitate proper regulation of gene expression. Sox2, a critical transcription factor for maintenance of pluripotency and neurogenesis, is found associated with several lncRNAs, although it is unknown whether these interactions are direct or via other proteins. We demonstrate that human Sox2 interacts directly with one of these lncRNAs with high affinity through its HMG DNA-binding domain. Furthermore, rather than interacting with a single high affinity site, Sox2 binds regions of dsRNA in a non-sequence specific fashion. RNA binding is competitive with dsDNA, yet interaction with RNA is primarily electrostatically driven using a partially overlapping set of amino acids as that used for DNA binding. Finally, we use two distinct crosslinking techniques, formaldehyde and UV, with RNA immunoprecipitation (respectively, “fRIP” and “UVRIP”) of Sox2 in mouse embryonic stem cells to identify >1000 potential Sox2-RNA interacting partners with ~75% overlap between the two techniques. Together, these data reveal that Sox2 productively binds dsRNA with affinities rivaling ChIP-validated promoter DNA sites, suggesting that the transcriptome plays a significant role in regulation of gene expression by Sox2.

2020-03-16 | GSE142013 | GEO

Transcription factor GATA4 binds to RNA [eCLIP-seq]

Project description:Transcription factor GATA4 binds to RNA [eCLIP-seq]

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The Sox2 transcription factor binds RNA.

Project description: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.

| S-EPMC7156710 | biostudies-literature

Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

Project description:Embryonic stem cell (ESCs) identity is orchestrated by co-operativity between the transcription factors (TFs) Sox2 and the class V POU-TF, Oct4 at composite Sox/Oct motifs. Neural stem cells (NSCs) lack Oct4 but express Sox2 and class III POU-TFs. This raises the question of how Sox2 interacts with POU-TFs to transcriptionally specify ESCs or NSCs. Here we show that Oct4 alone binds the Sox/Oct motif and the octamer-containing palindromic MORE equally well. Sox2 binding selectively increases the affinity of Oct4 for the Sox/Oct motif. In contrast, Oct6 binds preferentially to the MORE, and is unaffected by Sox2. ChIP-seq in NSCs shows the MORE to be the most enriched motif for class III POU-TFs, with MORE sub-types apparent, but no Sox/Oct motif enrichment. These results suggest that in NSCs, co-operativity between Sox2 and class III POU-TFs may not occur and that POU-TF driven transcription uses predominantly the MORE cis architecture. Thus, distinct interactions between Sox2 and POU-TF subclasses distinguish pluripotent ESCs from multipotent NSCs, providing molecular insight into how Oct4 alone can convert NSCs to pluripotency.

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Pupylation sites on protein Sox2

Project description:As a test for the effectiveness of SPIDER with RNA-protein pairs, We used Sox2 and specific biotin-DNA and biotin-RNA to validate the efficiency of SPIDER capturing protein-nucleic acid interaction. Pupylation sites on Sox2 after SPIDER assay was identified by LC-MS/MS analysis, by searching for an additional mass of ~243 Da, which represents the three C-terminal residues of Pup, i. e., GGE, that covalently binds to adjacent lysine by pupylation. ）

2021-06-04 | PXD026517 |

HSP70 binds RNA and regulates transcription by RNA Polymerase III [RNA-seq]

Project description:HSP70 binds RNA and regulates transcription by RNA Polymerase III [RNA-seq]

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Nucleosome binding by the pioneer transcription factor OCT4

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Project description:The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II

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HSP70 binds RNA and regulates transcription by RNA Polymerase III [ChIP-seq]

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HSP70 binds RNA and regulates transcription by RNA Polymerase III [FLASH-seq]

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