B lymphocytes recognize and destroy viruses and bacteria though antibodies. These molecules are secreted during the immune response, when B cells encounter and recognize foreign material on the surface of pathogens. How B cells are activated however is not entirely resolved. One key mechanism that controls this activation is transcription, the process whereby genes are expressed. Transcription during B cell development is orchestrated by promoter sequences and a variety of distal cis-regulatory elements. Key among these are enhancers, which associate with promoters to increase the transcriptional output of target genes in a tissue-specific manner. Enhancers are typically distinguished from non-regulatory DNA by their hypersensitivity to digestion with DNAses, and binding of specific proteins known as chromatin modifiers. Based on these parameters, 400,000 genomic sites displaying enhancer-like features were recently discovered, spanning nearly 10% of the human genome. Enhancers control cell identity by recruiting transcription factors, cofactors, and RNA Polymerase II, the enzyme that mediates transcription. All of these proteins mediate promoter-enhancer interactions by looping out of intervening sequences. In contrast to promoters and insulators, which vary little across cell types, the enhancer landscape changes considerably during development. This feature predicts that functional 3D connectivity in mammalian cells i) must display a high degree of tissue specificity and ii) should closely reflect transcriptome changes during cell differentiation. However, these ideas have not been fully explored because of the difficulty of mapping promoter-enhancer connections during development. In the absence of direct approaches, enhancers have been typically assigned to cognate promoters based on linear proximity or shared chromatin states. This strategy has limitations because enhancers do not always regulate nor share chromatin profiles with the nearest promoter. To overcome this challenge, this past year we applied a recently developed protocol (ChIA-PET) that permits visualization of promoter-enhancers interactions. In a manuscript published in Cell (Kieffer-Kwon et al, we mapped these interactions in mouse stem cells and B lymphocytes. We compared and contrasted these interactome maps and discovered several very interesting features: 1- We confirmed that enhancer usage varies widely across tissues. 2- Unexpectedly, we find that this feature extends not only to genes only expressed in stem cells or B cells, but also on those expressed ubiquitously (the so called housekeeping genes). 3- By means of genomic techniques we showed that these changing enhancers recruit cell-specific factors. These findings are important because they showed that organisms rely on a dynamic enhancer landscape to control basic cellular functions in a tissue-specific manner. Because mutations that cause diseases such as lupus and arthritis occur at enhancer elements, our techniques to map these domains and their interactions in a genome-wide manner will be highly valuable to those studying autoimmune and other disorders.

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Arthritis, Musculoskeletal, Skin Dis
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Juan, Aster H; Wang, Stan; Ko, Kyung Dae et al. (2017) Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells. Cell Rep 18:297
Kouzine, Fedor; Wojtowicz, Damian; Baranello, Laura et al. (2017) Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome. Cell Syst 4:344-356.e7
Kieffer-Kwon, Kyong-Rim; Nimura, Keisuke; Rao, Suhas S P et al. (2017) Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Mol Cell 67:566-578.e10
Wang, Qiao; Kieffer-Kwon, Kyong-Rim; Oliveira, Thiago Y et al. (2017) The cell cycle restricts activation-induced cytidine deaminase activity to early G1. J Exp Med 214:49-58
Canela, Andres; Maman, Yaakov; Jung, Seolkyoung et al. (2017) Genome Organization Drives Chromosome Fragility. Cell 170:507-521.e18
Zhang, Shaofei; Zhu, Iris; Deng, Tao et al. (2016) HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells. Nucleic Acids Res :
Casellas, Rafael; Basu, Uttiya; Yewdell, William T et al. (2016) Mutations, kataegis and translocations in B cells: understanding AID promiscuous activity. Nat Rev Immunol 16:164-76
Pratama, Alvin; Srivastava, Monika; Williams, Naomi J et al. (2015) MicroRNA-146a regulates ICOS-ICOSL signalling to limit accumulation of T follicular helper cells and germinal centres. Nat Commun 6:6436
Swaminathan, Srividya; Klemm, Lars; Park, Eugene et al. (2015) Mechanisms of clonal evolution in childhood acute lymphoblastic leukemia. Nat Immunol 16:766-774
Teng, Grace; Maman, Yaakov; Resch, Wolfgang et al. (2015) RAG Represents a Widespread Threat to the Lymphocyte Genome. Cell 162:751-65

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