Structure of Yin Yang 1 Oligomers That Cooperate with RuvBL1-RuvBL2 ATPases

López-Perrote, Andrés; Alatwi, Hanan E.; Torreira, Eva; Ismail, Amani; Ayora, Silvia; Downs, Jessica A.; Llorca, Óscar

doi:10.1074/jbc.m114.567040

Cited by 43 publications

(51 citation statements)

References 48 publications

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“…To confirm that YY1 dimerization occurs, FLAG-tagged and HA-tagged versions of YY1 protein were expressed in cells, nuclei were isolated and the tagged YY1 proteins in nuclear extracts were immunoprecipitated with either anti-FLAG or anti-HA antibodies. The results show that the FLAG-tagged and HA-tagged YY1 proteins interact (Figures 1G, 1H, S1I, and S1J), consistent with prior reports that YY1 proteins oligomerize (López-Perrote et al, 2014). Other highly expressed nuclear proteins such as OCT4 did not co-precipitate, indicating that the assay was specific (Figure S1J).…”

Section: Resultssupporting

confidence: 91%

“…Of 26 transcription factors that occupy both enhancers and promoters (Figure 1A), four (CTCF, YY1, NRF1, and ZBTB11) are essential based on a CRISPR cell-essentiality screen (Figure 1B) (Wang et al, 2015) and two (CTCF, YY1) are expressed in >90% of tissues examined (Figure 1C). YY1 and CTCF share additional features: like CTCF, YY1 is a zinc-finger transcription factor (Klenova et al, 1993; Shi et al, 1991), essential for embryonic and adult cell viability (Donohoe et al, 1999; Heath et al, 2008) and capable of forming homodimers (López-Perrote et al, 2014; Saldaña-Meyer et al, 2014) (Table S1). YY1, however, tends to occupy active enhancers and promoters, as well as some insulators, whereas CTCF preferentially occupies insulator elements (Figures 1D and S1A–S1C).…”

Section: Resultsmentioning

confidence: 99%

“…Previous studies have reported that YY1 can form dimers (López-Perrote et al, 2014). To confirm that YY1 dimerization occurs, FLAG-tagged and HA-tagged versions of YY1 protein were expressed in cells, nuclei were isolated and the tagged YY1 proteins in nuclear extracts were immunoprecipitated with either anti-FLAG or anti-HA antibodies.…”

Section: Resultsmentioning

confidence: 99%

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YY1 Is a Structural Regulator of Enhancer-Promoter Loops

Weintraub

Zamudio

et al. 2017

Cell

833

808

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SUMMARY There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not employ this structural protein. Here, we show that the ubiquitously expressed transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements and forms dimers that facilitate the interaction of these DNA elements. Deletion of YY1 binding sites or depletion of YY1 protein disrupts enhancer-promoter looping and gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.

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Section: Resultssupporting

confidence: 91%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

YY1 Is a Structural Regulator of Enhancer-Promoter Loops

Weintraub

Zamudio

et al. 2017

Cell

833

808

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“…The affinity of the YY1 ZFs in our EMSAs does appear to be somewhat lower than in EMSAs of the full-length protein to RNA sequences of comparable length (23). Additionally, it has been suggested that full-length YY1 forms a homo-oligomer, allowing YY1 to bind DNA sequences lacking the cognate recognition site (42), and it is possible that YY1 oligomerisation also influences RNA specificity.…”

Section: Discussionmentioning

confidence: 99%

The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity

et al. 2016

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Classical zinc fingers (ZFs) are traditionally considered to act as sequence-specific DNA-binding domains. More recently, classical ZFs have been recognised as potential RNA-binding modules, raising the intriguing possibility that classical-ZF transcription factors are involved in post-transcriptional gene regulation via direct RNA binding. To date, however, only one classical ZF-RNA complex, that involving TFIIIA, has been structurally characterised. Yin Yang-1 (YY1) is a multi-functional transcription factor involved in many regulatory processes, and binds DNA via four classical ZFs. Recent evidence suggests that YY1 also interacts with RNA, but the molecular nature of the interaction remains unknown. In the present work, we directly assess the ability of YY1 to bind RNA using in vitro assays. Systematic Evolution of Ligands by EXponential enrichment (SELEX) was used to identify preferred RNA sequences bound by the YY1 ZFs from a randomised library over multiple rounds of selection. However, a strong motif was not consistently recovered, suggesting that the RNA sequence selectivity of these domains is modest. YY1 ZF residues involved in binding to single-stranded RNA were identified by NMR spectroscopy and found to be largely distinct from the set of residues involved in DNA binding, suggesting that interactions between YY1 and ssRNA constitute a separate mode of nucleic acid binding. Our data are consistent with recent reports that YY1 can bind to RNA in a low-specificity, yet physiologically relevant manner.

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“…Assembly of INO80 and TIP60 has been shown to be dependent on the RUVBLs [46], [47]. In addition, RUVBLs enhance the DNA binding ability of YY1, a transcription factor that canonically associates with INO80 [48]. This evidence suggests that the RUVBL proteins are required members of remodeler assemblies that exist to enhance binding efficiency and specification at epigenetic docking sites, similar to BAF53A.…”

Section: Accessory Subunits In Remodeler Activitiesmentioning

confidence: 99%

Epigenetic Regulation by ATP-Dependent Chromatin-Remodeling Enzymes

Runge

Raab

Magnuson

2016

Current Topics in Developmental Biology

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Cells utilize precise mechanisms to access genomic DNA with spatiotemporal accuracy. ATP-Dependent Chromatin Remodeling Enzymes (also known simply as “remodelers”) comprise a specialized class of enzymes that is intimately involved in genomic organization and accessibility. Remodelers selectively position nucleosomes to either alleviate chromatin compaction or achieve genomic condensation locally, based on a multitude of cellular signals. By dictating nucleosome position, remodelers control local euchromatic and heterochromatic states. These activities govern the accessibility of regulatory regions like promoters and enhancers to transcription factors, RNA polymerases, and co-activators or -repressors. As studies unravel the complexities of epigenetic topography, evidence points to a chromatin-based interactome where regulators interact competitively, cooperatively, and/or co-dependently through physical and functional means. These types of interactions, or crosstalk, between remodelers raise important questions for tissue development. Here, we briefly review the evidence for remodeler interactions and argue for additional studies examining crosstalk.

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Structure of Yin Yang 1 Oligomers That Cooperate with RuvBL1-RuvBL2 ATPases

Cited by 43 publications

References 48 publications

YY1 Is a Structural Regulator of Enhancer-Promoter Loops

YY1 Is a Structural Regulator of Enhancer-Promoter Loops

The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity

Epigenetic Regulation by ATP-Dependent Chromatin-Remodeling Enzymes

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