Direct Single-Molecule Observation of Sequential DNA Bending Transitions by the Sox2 HMG Box

Moosa, Mahdi Muhammad; Tsoi, Phoebe S.; Choi, Kyoung‐Jae; Ferreon, Allan Chris M.; Ferreon, Josephine C.

doi:10.3390/ijms19123865

Cited by 8 publications

(10 citation statements)

References 61 publications

(70 reference statements)

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“…for the high-affinity transition (Fig. 1a, b), which is well within the range of prior measurements (0.4 nM 37 to 15 nM 38,39 ). As evidence for site-specific DNA binding, Sox2 binds poorly to single-stranded DNA containing the consensus site and DNA lacking the consensus site.…”

Section: Resultssupporting

confidence: 88%

The Sox2 transcription factor binds RNA

et al. 2020

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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.

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Section: Resultssupporting

confidence: 88%

The Sox2 transcription factor binds RNA

et al. 2020

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“…KLF4 DBD can bridge two DNA duplexes. We tested this hypothesis using single molecule Förster resonance energy transfer (smFRET) [44][45][46] . In DBD:NANK models where ZnF1 is excluded from either KLFA or KLFB (Fig.…”

Section: Klf4 Forms Nuclear Condensates At Modest Expression Levelsmentioning

confidence: 99%

Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization

et al. 2021

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Expression of a few master transcription factors can reprogram the epigenetic landscape and three-dimensional chromatin topology of differentiated cells and achieve pluripotency. During reprogramming, thousands of long-range chromatin contacts are altered, and changes in promoter association with enhancers dramatically influence transcription. Molecular participants at these sites have been identified, but how this re-organization might be orchestrated is not known. Biomolecular condensation is implicated in subcellular organization, including the recruitment of RNA polymerase in transcriptional activation. Here, we show that reprogramming factor KLF4 undergoes biomolecular condensation even in the absence of its intrinsically disordered region. Liquid–liquid condensation of the isolated KLF4 DNA binding domain with a DNA fragment from the NANOG proximal promoter is enhanced by CpG methylation of a KLF4 cognate binding site. We propose KLF4-mediated condensation as one mechanism for selectively organizing and re-organizing the genome based on the local sequence and epigenetic state.

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“…All of the HMGB domains bound the consensus dsDNA ligand with affinities ranging from 0.6 to 72 nM (Table ), consistent with reports for those previously tested (Table S2). ,,,− Almost all were in the 1 nM range, with only those of two family members (Sox6 and Sox30) being significantly weaker. In the consensus dsDNA FA titrations, two distinct transitions were observed that correspond to 1:1 and 2:1 protein–dsDNA complexes.…”

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confidence: 99%

“…This was established by correlating each transition observed by FA to a protein-induced shift in an EMSA (Figure 2B and Figure S4); this behavior has been previously observed. 9,59 The first transition corresponds to high-affinity binding to the core consensus sequence and is the K D,app reported in Table 1 for all HMGB domains. The second transition likely results from a lower-affinity binding event corresponding to a second protein binding with K D2,app values given in Table S3.…”

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confidence: 99%

The DNA-Binding High-Mobility Group Box Domain of Sox Family Proteins Directly Interacts with RNA In Vitro

et al. 2022

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There is a growing body of evidence that a substantial number of protein domains identified as DNA-binding also interact with RNA to regulate biological processes. Several recent studies have revealed that the Sox2 transcription factor binds RNA through its high-mobility group box (HMGB) domain in vitro and in vivo. A high degree of conservation of this domain among members of the Sox family of transcription factors suggests that RNA-binding activity may be a general feature of these proteins. To address this hypothesis, we examined a subset of HMGB domains from human Sox family of proteins for their ability to bind both DNA and RNA in vitro. We observed selective, high-affinity interactions between Sox family HMGB domains and various model RNA elements, including a four-way junction RNA, a hairpin RNA with an internal bulge, G-quadruplex RNA, and a fragment of long noncoding RNA ES2, which is known to directly interact with Sox2. Importantly, the HMGB domains bind these RNA ligands significantly tighter than nonconsensus dsDNA and in some cases with affinities rivaling those of their consensus dsDNA sequences. These data suggest that RNA binding is a conserved feature of the Sox family of transcription factors with the potential to modulate unappreciated biological functions.

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Direct Single-Molecule Observation of Sequential DNA Bending Transitions by the Sox2 HMG Box

Cited by 8 publications

References 61 publications

The Sox2 transcription factor binds RNA

The Sox2 transcription factor binds RNA

Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization

The DNA-Binding High-Mobility Group Box Domain of Sox Family Proteins Directly Interacts with RNA In Vitro

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