High frequency of matrix attachment regions and cut-like protein x/CCAAT-displacement protein and B cell regulator of IgH transcription binding sites flanking Ig V region genes.
A major component in controlling V(D)J recombination is differential accessibility through localized changes in chromatin structure. Attachment of DNA to the nuclear matrix via matrix attachment region (MAR) sequences, and interaction with MAR-binding proteins have been shown to alter chromatin conformation, promote histone acetylation, and influence gene transcription. In this study, the flanking regions of several human and mouse Ig V(H) and Ig Vkappa genes were analyzed extensively for the presence of MARs by in vitro matrix-binding assay, and for interaction with the MAR-binding proteins cut-like protein x/CCAAT-displacement protein (Cux/CDP), B cell regulator of IgH transcription (Bright), and special AT-rich sequence-binding protein (SATB1) by EMSA. Cux/CDP and SATB1 are associated with repression, while Bright is an activator of Ig transcription. Binding sites were identified in the vicinity of all analyzed Ig V genes, and were also found flanking TCR Vbeta genes. We also show that the binding sites of the different factors do not always occur at MAR sequences. MAR sequences were also found within the Ig V loci at a much higher frequency than throughout the rest of the genome. Overall, the frequency and location of binding sites relative to the coding regions, and the strength of DNA-protein interaction showed much heterogeneity. Thus, variations in factor binding and MAR activity could potentially influence the extent of localized accessibility to V(D)J recombination and thus could play a role in unequal rearrangement of individual V genes. These sites could also contribute to effective transcription of Ig genes in mature and/or activated B cells, bringing both the promoter as well as the enhancer regions into close proximity at the nuclear matrix.
The Scripps Research Institute, La Jolla, CA 92037, USA.
Peter
P
Goebel
Alina
A
Montalbano
Neil
N
Ayers
Elizabeth
E
Kompfner
Liliane
L
Dickinson
Carol F
CF
Webb
Ann J
AJ
Feeney
D020121:5' Untranslated Regions / Q000235:genetics / Q000276:immunology / Q000378:metabolism*; D000225:Adenine / Q000378:metabolism; D000818:Animals; D001402:B-Lymphocytes / Q000276:immunology* / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics / Q000276:immunology; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D005091:Exons / Q000276:immunology; D015326:Gene Rearrangement, B-Lymphocyte, Heavy Chain; D005803:Genes, Immunoglobulin; D019674:Genes, T-Cell Receptor beta; D018398:Homeodomain Proteins; D006801:Humans; D007127:Immunoglobulin Constant Regions / Q000235:genetics / Q000378:metabolism; D007135:Immunoglobulin Variable Region / Q000235:genetics* / Q000378:metabolism; D007145:Immunoglobulin kappa-Chains / Q000235:genetics / Q000378:metabolism; D020084:Long Interspersed Nucleotide Elements / Q000276:immunology; D036961:Matrix Attachment Region Binding Proteins; D051379:Mice; D015530:Nuclear Matrix / Q000235:genetics / Q000378:metabolism*; D009687:Nuclear Proteins / Q000378:metabolism*; D009857:Oncogenes; D010446:Peptide Fragments / Q000276:immunology / Q000378:metabolism; D011485:Protein Binding / Q000235:genetics / Q000276:immunology; D012097:Repressor Proteins / Q000378:metabolism*; D013941:Thymine / Q000378:metabolism; D015534:Trans-Activators / Q000378:metabolism*; D014157:Transcription Factors; D014158:Transcription, Genetic / Q000276:immunology*; D014407:Tumor Cells, Cultured
D020121:5' Untranslated Regions; C490798:ARID3A protein, human; C097532:Arid3a protein, mouse; C080632:CUX1 protein, human; C000624101:Cux1 protein, mouse; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D007127:Immunoglobulin Constant Regions; D007135:Immunoglobulin Variable Region; D007145:Immunoglobulin kappa-Chains; D036961:Matrix Attachment Region Binding Proteins; D009687:Nuclear Proteins; D010446:Peptide Fragments; D012097:Repressor Proteins; C076189:SATB1 protein, human; D015534:Trans-Activators; D014157:Transcription Factors; D000225:Adenine; D013941:Thymine