Project description:Chip-chip from pro-T(DN) cells from Rag1KO mice for H3K27ac, P300 and FAIRE The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We have quantified Vβ usage in the pre-selection Tcrb repertoire and report relative contributions of 14 distinct features in shaping their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DβJβ targets, and quality of recombinase recognition elements. Computational analyses provide a unifying model, revealing a minimal set of eight parameters that are predictive of Vβusage, dominated by chromatin modifications associated with transcription, but largely independent of the precise spatial proximity to DβJβclusters. Rag1KO DN epigenetic landscape at Tcrb
Project description:The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We have quantified Vβ usage in the pre-selection Tcrb repertoire and report relative contributions of 14 distinct features in shaping their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DβJβ targets, and quality of recombinase recognition elements. Computational analyses provide a unifying model, revealing a minimal set of eight parameters that are predictive of Vβusage, dominated by chromatin modifications associated with transcription, but largely independent of the precise spatial proximity to DβJβclusters. Transcription profiles of mouse DN thymocytes from Rag1 KO mice were generated by deep sequencing, using Illumina Hi-Seq 2000.
Project description:Analysis of histone modifications in double negative thymocytes from RAG-/- mice For the ChIP-seq, input and immunoprecipitated DNA was given to The Scripps DNA Array Facility, where it was prepared for massively parallel sequencing on Illumina HiSeq 2000.
Project description:The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We have quantified Vβ usage in the pre-selection Tcrb repertoire and report relative contributions of 14 distinct features in shaping their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DβJβ targets, and quality of recombinase recognition elements. Computational analyses provide a unifying model, revealing a minimal set of eight parameters that are predictive of Vβusage, dominated by chromatin modifications associated with transcription, but largely independent of the precise spatial proximity to DβJβclusters.
Project description:Chip-chip from pro-T(DN) cells from Rag1KO mice for H3K27ac, P300 and FAIRE The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We have quantified Vβ usage in the pre-selection Tcrb repertoire and report relative contributions of 14 distinct features in shaping their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DβJβ targets, and quality of recombinase recognition elements. Computational analyses provide a unifying model, revealing a minimal set of eight parameters that are predictive of Vβusage, dominated by chromatin modifications associated with transcription, but largely independent of the precise spatial proximity to DβJβclusters.
Project description:The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We quantified V? use in the preselection Tcrb repertoire and report relative contributions of 13 distinct features that may shape their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their D?J? targets, and predicted quality of recombination signal sequences (RSSs). We show that, in contrast to functional V? gene segments, all pseudo-V? segments are sequestered in transcriptionally silent chromatin, which effectively suppresses wasteful recombination. Importantly, computational analyses provide a unifying model, revealing a minimum set of five parameters that are predictive of V? use, dominated by chromatin modifications associated with transcription, but largely independent of precise spatial proximity to D?J? clusters. This learned model-building strategy may be useful in predicting the relative contributions of epigenetic, spatial, and RSS features in shaping preselection V repertoires at other antigen receptor loci. Ultimately, such models may also predict how designed or naturally occurring alterations of these loci perturb the preselection use of variable gene segments.