title: Influence of a CTCF-Dependent Insulator on Multiple Aspects of Enhancer-Mediated Chromatin Organization.
abstract: Developmental stage-specific enhancer-promoter-insulator interactions regulate the chromatin configuration necessary for transcription at various loci and additionally for VDJ recombination at antigen receptor loci that encode immunoglobulins and T-cell receptors. To investigate these regulatory interactions, we analyzed the epigenetic landscape of the murine T-cell receptor β (TCRβ) locus in the presence and absence of an ectopic CTCF-dependent enhancer-blocking insulator, H19-ICR, in genetically manipulated mice. Our analysis demonstrated the ability of the H19-ICR insulator to restrict several aspects of enhancer-based chromatin alterations that are observed during activation of the TCRβ locus for transcription and recombination. The H19-ICR insulator abrogated enhancer-promoter contact-dependent chromatin alterations and additionally prevented Eβ-mediated histone modifications that have been suggested to be independent of enhancer-promoter interaction. Observed enhancer-promoter-insulator interactions, in conjunction with the chromatin structure of the Eβ-regulated domain at the nucleosomal level, provide useful insights regarding the activity of the regulatory elements in addition to supporting the accessibility hypothesis of VDJ recombination. Analysis of H19-ICR in the heterologous context of the developmentally regulated TCRβ locus suggests that different mechanisms proposed for CTCF-dependent insulator action might be manifested simultaneously or selectively depending on the genomic context and the nature of enhancer activity being curtailed.
authors.affiliation: National Institute of Immunology, New Delhi, India.
authors.forename: Garima
authors.initials: G
authors.lastname: Varma
authors.affiliation: National Institute of Immunology, New Delhi, India.
authors.forename: Pratishtha
authors.initials: P
authors.lastname: Rawat
authors.affiliation: National Institute of Immunology, New Delhi, India.
authors.forename: Manisha
authors.initials: M
authors.lastname: Jalan
authors.affiliation: National Institute of Immunology, New Delhi, India.
authors.forename: Manjula
authors.initials: M
authors.lastname: Vinayak
authors.affiliation: National Institute of Immunology, New Delhi, India madhus@nii.res.in.
authors.forename: Madhulika
authors.initials: M
authors.lastname: Srivastava
mesh_terms: D000818:Animals; D000076246:CCCTC-Binding Factor; D002478:Cells, Cultured; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D019674:Genes, T-Cell Receptor beta; D006657:Histones; D008565:Membrane Proteins / Q000378:metabolism; D008822:Mice, Transgenic; D016254:Mutagenesis, Insertional; D010750:Phosphoproteins / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D011499:Protein Processing, Post-Translational; D012319:RNA Polymerase II / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics; D012097:Repressor Proteins / Q000502:physiology*; D060168:Thymocytes; D015533:Transcriptional Activation
chemical_list: D000076246:CCCTC-Binding Factor; D002843:Chromatin; C000619698:Ctcf protein, mouse; D004268:DNA-Binding Proteins; C094335:H19 long non-coding RNA; D006657:Histones; D008565:Membrane Proteins; C498709:Pag1 protein, mouse; D010750:Phosphoproteins; D062085:RNA, Long Noncoding; C499308:Rag2 protein, mouse; D012097:Repressor Proteins; D012319:RNA Polymerase II