Identification of YY1 sequences necessary for association with the nuclear matrix and for transcriptional repression functions

Bushmeyer, Sarah; Atchison, Michael L.

doi:10.1002/(sici)1097-4644(19980315)68:4<484::aid-jcb8>3.0.co;2-m

Cited by 59 publications

(24 citation statements)

References 69 publications

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“…For example, evidence showing that YY1 can interact with both HDAC and HAT (74–80) led to a potential model proposing that YY1 can activate or repress transcription via changing the local chromatin environment (78). YY1 was also shown to be able to interact with components of nuclear matrix (81,82), which may also facilitate partitioning of active and repressive chromatin domains.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide prediction and analysis of human chromatin boundary elements

Wang

Lunyak

Jordan

2011

Nucleic Acids Research

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Boundary elements partition eukaryotic chromatin into active and repressive domains, and can also block regulatory interactions between domains. Boundary elements act via diverse mechanisms making accurate feature-based computational predictions difficult. Therefore, we developed an unbiased algorithm that predicts the locations of human boundary elements based on the genomic distributions of chromatin and transcriptional states, as opposed to any intrinsic characteristics that they may possess. Application of our algorithm to ChIP-seq data for histone modifications and RNA Pol II-binding data in human CD4+ T cells resulted in the prediction of 2542 putative chromatin boundary elements genome wide. Predicted boundary elements display two distinct features: first, position-specific open chromatin and histone acetylation that is coincident with the recruitment of sequence-specific DNA-binding factors such as CTCF, EVI1 and YYI, and second, a directional and gradual increase in histone lysine methylation across predicted boundaries coincident with a gain of expression of non-coding RNAs, including examples of boundaries encoded by tRNA and other non-coding RNA genes. Accordingly, a number of the predicted human boundaries may function via the synergistic action of sequence-specific recruitment of transcription factors leading to non-coding RNA transcriptional interference and the blocking of facultative heterochromatin propagation by transcription-associated chromatin remodeling complexes.

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Section: Resultsmentioning

confidence: 99%

Genome-wide prediction and analysis of human chromatin boundary elements

Wang

Lunyak

Jordan

2011

Nucleic Acids Research

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“…A role for YY1 in the regulation of imprinted genes has been postulated for the imprinted PEG3 locus where YY1 appears to act as an insulator-binding protein (40). YY1 is also reported to associate with the nuclear matrix (41), suggesting a possible role for the CAS in tethering this region of the paternally inherited SNRPN locus to the matrix.…”

Section: Discussionmentioning

confidence: 99%

Characterization of cis- and trans-acting elements in the imprinted human SNURF-SNRPN locus

Rodriguez-Jato

Nicholls²,

Driscoll³

et al. 2005

Nucleic Acids Research

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The imprinted SNRPN locus is a complex transcriptional unit that encodes the SNURF and SmN polypeptides as well as multiple non-coding RNAs. SNRPN is located within the Prader-Willi and Angelman syndrome (PWS/AS) region that contains multiple imprinted genes, which are coordinately regulated by a bipartite imprinting center (IC). The SNRPN 5′ region co-localizes with the PWS-IC and contains two DNase I hypersensitive sites, DHS1 at the SNRPN promoter, and DHS2 within intron 1, exclusively on the paternally inherited chromosome. We have examined DHS1 and DHS2 to identify cis- and trans-acting regulatory elements within the endogenous SNRPN 5′ region. Analysis of DHS1 by in vivo footprinting and chromatin immunoprecipitation identified allele-specific interaction with multiple regulatory proteins, including NRF-1, which regulates genes involved in mitochondrial and metabolic functions. DHS2 acted as an enhancer of the SNRPN promoter and contained a highly conserved region that showed allele-specific interaction with unphosphorylated RNA polymerase II, YY1, Sp1 and NRF-1, further suggesting a key role for NRF-1 in regulation of the SNRPN locus. We propose that one or more of the regulatory elements identified in this study may also contribute to PWS-IC function.

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“…the sensitivity of some transcriptional regulatory domains to their attached DBD or to their DNA-binding state, is emerging as a significant governing mechanism in gene expression (46 -48). Like Nmp4, the nuclear matrix transcription factors YY1 and Osf2/Cbfa1 both contain separable activation domains that function differently when tethered to a heterologous promoter by the GAL4-DBD as opposed to binding to their native consensus elements (25,49). The three activation domains of Osf2/Cbfa1, AD1, AD2, and AD3, all contributed to transcriptional activation in the context of the native DBD.…”

Section: The N Terminus Of Nmp4/21h Exhibits Strong Trans-activation mentioning

confidence: 99%

DNA Binding and Gene Activation Properties of the Nmp4 Nuclear Matrix Transcription Factors

Torrungruang

Alvarez

Shah

et al. 2002

Journal of Biological Chemistry

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Splice variants of the Nmp4 gene include nuclear matrix transcription factors that regulate the type I collagen ␣1(I) polypeptide chain (COL1A1) promoter and several matrix metalloproteinase (MMP) genes. To date, these are the only Cys 2 His 2 zinc finger proteins known to bind within the minor groove of homopolymeric (dA⅐dT) DNA. Nmp4 isoforms contain from 5 to 8 Cys 2 His 2 zinc fingers, an SH3-binding domain that overlaps with a putative AT-hook and a polyglutamine-alanine repeat (poly(QA)). To determine the mechanistic significance of Cys 2 His 2 zinc finger association with this unusual consensus DNA binding element, we identified the Nmp4 DNA-binding and transcriptional activation domains. Zinc fingers 2, 3, and 6 mediated association with the homopolymeric (dA⅐dT) COL1A1/MMP DNA consensus element. The N terminus of the Nmp4 protein exhibited a strong trans-activation capacity when fused to the GAL4 DNA-binding domain, but this activity was masked within the context of the full-length Nmp4-GAL4 DNA-binding domain chimera. However, upon binding to the COL1A1/MMP homopolymeric (dA⅐dT) element, the native Nmp4 protein up-regulated transcription, and the poly(QA) domain acquired a significant role in trans-activation. We propose that allosteric effects induced upon zinc finger association with the homopolymeric (dA⅐dT) minor groove confer context-specific functionality to this unusual family of Cys 2 His 2 transcription factors.

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Identification of YY1 sequences necessary for association with the nuclear matrix and for transcriptional repression functions

Cited by 59 publications

References 69 publications

Genome-wide prediction and analysis of human chromatin boundary elements

Genome-wide prediction and analysis of human chromatin boundary elements

Characterization of cis- and trans-acting elements in the imprinted human SNURF-SNRPN locus

DNA Binding and Gene Activation Properties of the Nmp4 Nuclear Matrix Transcription Factors

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