The molecular details of how faithful DNA rearrangements are maintained in the context of the complex chromatin environment of the developing B lymphocyte is the focus of ongoing research in my lab. We have new data indicating that the IgH locus is regulated by the Ig locus and have identified the involvement of two Ig regulatory elements, the 3'E enhancer and Sis (silencer in the intervening sequence. Regulation is achieved through transient association of the two loci at the pro- to pre-B cell transition when the recombinase enzymes are targeted away from the IgH locus to the Ig locus.
We aim to elucidate the functional significance of association between the two loci and to understand in molecular detail how association is achieved. It is our hypothesis that association of the IgH and Ig loci plays a central role in enforcing allelic exclusion of the IgH locus, which is critical for maintaining the integrity of the recombination process and ensuring genome stability. Because de-regulation of recombination and allelic exclusion can result in immune deficiency, autoimmunity and translocations involving Ig loci, it is essential to understand the underlying mechanisms. In addition these studies have important implications for gene regulation as a whole. The ordered rearrangement of immunoglobulin (Ig) genes is a highly regulated process essential for adaptive immunity, orchestrating the expression of B and T lymphocyte receptors through allelic exclusion that ensures clonality, all the while protecting the genome from these inherently unstable recombination events. The molecular details of how faithful DNA rearrangements are maintained in the context of the complex chromatin environment of the developing B lymphocyte is the focus of ongoing research in my lab. Our recent studies indicate that the pericentric Ig? allele directs the unrearranged IgH allele towards a shared pericentromeric cluster. Association of the two loci in this repressive environment subsequently induces IgH locus decontraction on the non-functional allele. This identifies a novel mechanism for co-ordinating changes in accessibility and expression. The hypothesis to be tested is that association of IgH and Ig? loci plays a central role in enforcing allelic exclusion of the IgH locus, which is critical for maintaining the integrity of the recombination process and ensuring genome stability.
The aims i n this grant are designed to understand in molecular detail the mechanisms by which association of Ig loci contributes to allelic exclusion and genome stability. Understanding how changes at the two loci are co-ordinated and identifying the pathways involved is of fundamental importance in the field because de-regulation of recombination and allelic exclusion can result in immune deficiency, autoimmunity and translocations that involve Ig loci. These studies provide new detail to the basic mechanisms linking immunoglobulin gene transcription and rearrangement and paint a picture of a highly dynamic and ordered nuclear architecture that will have important implications for gene regulation in general.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM086852-05
Application #
8290421
Study Section
Cellular and Molecular Immunology - A Study Section (CMIA)
Program Officer
Marino, Pamela
Project Start
2008-09-11
Project End
2013-06-30
Budget Start
2012-07-01
Budget End
2013-06-30
Support Year
5
Fiscal Year
2012
Total Cost
$332,254
Indirect Cost
$136,234
Name
New York University
Department
Pathology
Type
Schools of Medicine
DUNS #
121911077
City
New York
State
NY
Country
United States
Zip Code
10016
Proudhon, Charlotte; Snetkova, Valentina; Raviram, Ramya et al. (2016) Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Rep 15:2159-69
Rocha, Pedro P; Raviram, Ramya; Fu, Yi et al. (2016) A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination. Cell Rep 16:48-55
Fu, Yi; Rocha, Pedro P; Luo, Vincent M et al. (2016) CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci. Nat Commun 7:11707
Thomas-Claudepierre, Anne-Sophie; Robert, Isabelle; Rocha, Pedro P et al. (2016) Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination. J Exp Med 213:303-12
Raviram, Ramya; Rocha, Pedro P; Müller, Christian L et al. (2016) 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. PLoS Comput Biol 12:e1004780
Narendra, Varun; Rocha, Pedro P; An, Disi et al. (2015) CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation. Science 347:1017-21
Blumenberg, Lili; Skok, Jane A (2015) RAG Off-Target Activity Is in the Loop. Trends Mol Med 21:733-5
Proudhon, Charlotte; Hao, Bingtao; Raviram, Ramya et al. (2015) Long-Range Regulation of V(D)J Recombination. Adv Immunol 128:123-82
Rocha, Pedro P; Raviram, Ramya; Bonneau, Richard et al. (2015) Breaking TADs: insights into hierarchical genome organization. Epigenomics 7:523-6
Dose, Marei; Emmanuel, Akinola Olumide; Chaumeil, Julie et al. (2014) *-Catenin induces T-cell transformation by promoting genomic instability. Proc Natl Acad Sci U S A 111:391-6

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