YY1 helps to bring loose ends together: Figure 1.

Calame, Kathryn; Atchison, Michael L.

doi:10.1101/gad.1559007

Cited by 37 publications

(34 citation statements)

References 72 publications

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“…39,42 It is also known that YY1 interacts with the TFs SP1 and BSAP. 46,47 These studies suggest that the other three TFs in this group interact with E2F1 directly or indirectly, which supports the functionality of this group of interacting TFs. The GO enrichment analysis shown that the target genes of this group of TFs significantly share a function, positive regulation of transcription factor activity (GO: 0051091, corrected p-value=2.6E-4).…”

Section: Chipmodule Identified Tfs and Their Cofactors In Experimentamentioning

confidence: 68%

Chipmodule: Systematic Discovery of Transcription Factors and Their Cofactors From Chip-Seq Data

et al. 2012

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We have developed a novel approach called ChIPModule to systematically discover transcription factors and their cofactors from ChIP-seq data. Given a ChIP-seq dataset and the binding patterns of a large number of transcription factors, ChIPModule can efficiently identify groups of transcription factors, whose binding sites significantly co-occur in the ChIP-seq peak regions. By testing ChIPModule on simulated data and experimental data, we have shown that ChIPModule identifies known cofactors of transcription factors, and predicts new cofactors that are supported by literature. ChIPModule provides a useful tool for studying gene transcriptional regulation.

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Section: Chipmodule Identified Tfs and Their Cofactors In Experimentamentioning

confidence: 68%

Chipmodule: Systematic Discovery of Transcription Factors and Their Cofactors From Chip-Seq Data

et al. 2012

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“…Cell Culture and Irradiation-A549 and U2OS cells were cultured in Eagle's minimum essential medium (MEM) or DMEM (Invitrogen), respectively, supplemented with 10% FCS, L-glutamine, penicillin, and streptomycin (Invitrogen) at 37°C in a humidified 95% air and 5% CO 2 5 of U2OS cells were co-transfected with 0.25 g of VN173-and VC155-derived plasmids using a NanoJuice Transfection Reagent kit (Novagen). 24 h post-transfection cells were fixed with 3% (w/v) paraformaldehyde, permeabilized with 0.5% Triton X-100, and mounted with Vectashield containing 4Ј,6-diamidino-2-phenylindole (DAPI; Vector Laboratories Ltd).…”

Section: Methodsmentioning

confidence: 99%

“…YY1 is ubiquitously expressed in many tissues and participates in replication, differentiation, proliferation, embryogenesis, and development (1)(2)(3)(4). YY1 overexpression in some tumors correlates with recurrences and bad prognosis, and YY1 has been proposed as a marker for cancer progression (5).…”

Section: Yin Yang 1 (Yy1)mentioning

confidence: 99%

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

López-Perrote

Alatwi

Torreira

et al. 2014

Journal of Biological Chemistry

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Background: Oligomerization of transcription factor YY1 is not well understood. Results: YY1 assembles homo-oligomers that bind DNAs without the consensus sequence, whose structure is studied by electron microscopy. Conclusion: RuvBL1-RuvBL2 enhances YY1 binding to DNAs without the consensus sequence for the transcription factor. Significance: YY1-RuvBL1-RuvBL2 complexes could contribute to functions beyond transcription, and we find this occurs during homologous recombination.

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“…YY1 is a zinc-finger containing protein, that has remained conserved throughout invertebrate and vertebrate evolution. It is ubiquitously expressed but since it interacts with elements present in the Ig enhancers, it has been suggested to play critical roles in immunoglobulin gene regulation [45,46,47]. Recent data have shown that B cell development in YY1-deficient mice is blocked prior to the onset of Igh V(D)J gene rearrangement [21].…”

Section: Nuclear Location Compaction Looping and Antigen Receptor Gmentioning

confidence: 99%

Epigenetics of antigen-receptor gene assembly

Murre

2007

Current Opinion in Genetics & Development

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IntroductionIt is established that the temporal and lineage specificity of V(D)J rearrangement is controlled at multiple levels [1,2]. These include germ-line transcription, chromatin remodeling, histone acetylation and DNA methylation. It is, however, unknown how a region spanning large genomic distances allows the assembly of antigen receptor genes. Recent data have suggested that an underlying structural order must exist that facilitates the association of DNA elements separated by large genomic distances. B cell development and ordered immunoglobulin gene rearrangementThe developmental progression of B cells has been characterized on the basis of antigen receptor gene rearrangements and on the dynamic expression patterns of cell surface proteins, which have served as maturation markers [3]. The Igh locus is comprised of distinct DNA elements encoding the variable (V), diversity (D), joining (J), and constant (C) regions. Eight Igh constant regions encode for distinct isotypes that include C μ , C δ , C γ1 C γ2a , C γ2b , C γ3 , C α and C ε . Upstream of the IgM constant region are located twelve D H and four J H segments. Fifteen partially dispersed V region families are present that span approximately 2 Mbp of genomic sequence. The IgK and L light chain loci are also organized into distinct DNA elements, encoding V H , J H and C H segments. Ig V H , D H and J H elements are flanked by recombination signal sequences that interact with the RAG1 and RAG2 gene products.In pro-B cells, Igh D H J H joining precedes that of V H (D H )J H gene rearrangement [4]. Once a V(D)J gene rearrangement leads to a productive joint, pre-BCR signaling acts to inhibit RAG1 and RAG2 gene expression and to promote the survival, expansion and developmental progression of large pre-B cells [5.6]. The expansion phase is followed by cell cycle arrest, during which RAG gene expression is reactivated to initiate the rearrangement of the Ig light chain genes. In the presence of self-reactivity, continued rearrangements will replace primary IgK VJ joints, generating receptors with novel specificities. Once a BCR is expressed which lacks auto-reactivity, tonic signaling mediated by the BCR will permanently suppress RAG1 and RAG2 gene expression. Tonic BCR signaling will also trigger the migration of B cells to the peripheral lymphoid organs where they, upon interacting with pathogens, will undergo class switching and somatic hypermutation. T-lineage development and T cell receptor gene rearrangementT-lineage cells also develop sequentially [7]. Two distinct T cell lineages develop from a common progenitor, named αβ and γδ T cells. The rearrangement of the TCRβ and γδ loci is Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production...

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YY1 helps to bring loose ends together: Figure 1.

Cited by 37 publications

References 72 publications

Chipmodule: Systematic Discovery of Transcription Factors and Their Cofactors From Chip-Seq Data

Chipmodule: Systematic Discovery of Transcription Factors and Their Cofactors From Chip-Seq Data

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

Epigenetics of antigen-receptor gene assembly

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