Enhancers are regulatory elements that orchestrate cell type specific gene expression patterns. They can be separated from their target genes by large distances and activate transcription by coming into physical proximity with promoters in three-dimensional nuclear space. Complex regulatory networks with multiple enhancers often cooperate to control the same target gene. Antigen receptor loci have proved to be a rich ground for understanding enhancer-mediated gene regulation. The loci undergo somatic recombination of their V, (D), J segments to create a diverse repertoire of antigen receptors that can counteract a wide range of foreign antigens. V(D)J recombination relies on the presence of proximal enhancers that activate the antigen receptor loci in a lineage and cell stage specific manner. Unexpectedly we find that both active and inactive antigen receptor loci enhancers cooperate to disseminate their effects in a localized and long-range mode. We demonstrate the importance of short-range contacts between active enhancers that constitute an Igk super-enhancer in B cells. Deletion of one element reduces the interaction frequency between other enhancers in the hub, which compromises the transcriptional output of each enhancer. We further establish that in T cells, the Igk enhancer MiEκ exerts a long-range effect on another antigen receptor locus Tcrb located 29MB away on chromosome 6. MiEκ deletion leads to inefficient Tcrb recombination resulting in a block in T cell development, an effect that is associated with a long-range contact and cooperation between the MiEκ and the Tcrb enhancer, Eβ. MiEκ deletion alters enrichment of the transcription factor CBFβ on Eβ in a manner that impacts Tcrb recombination. These findings underline the complexities of enhancer regulation and point to a role for localized and long-range enhancer sharing between active and inactive elements in lineage and stage specific control. Finally, we expand our assessment of enhancer cooperation to the entire chromosome 6. We detect nearly nine hundred putative regulatory elements that are active in either DP or pre-B cells with less than 20% common to the two cell types. We also demonstrate how long-range contacts between enhancers and promoters coincide with target gene expression status, and provide a resource for identifying the regulatory elements that control T and B cell specific gene expression patterns.
|Commitee:||Apostolou, Effie, Koralov, Sergei, Littman, Dan, Stadtfeld, Matthias|
|School:||New York University|
|Department:||Basic Medical Science|
|School Location:||United States -- New York|
|Source:||DAI-B 78/12(E), Dissertation Abstracts International|
|Subjects:||Biology, Molecular biology, Cellular biology|
|Keywords:||Antigen receptor loci, Chromatin conformation capture, Enhancer, Gene regulation, Nuclear organization|
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