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Immunology and Microbial Science

Ann Feeney, Ph.D.

Professor
Department of Immunology and Microbiology
California Campus
Laboratory Website
feeney@scripps.edu
(858) 784-2979

Scripps Research Joint Appointments

Faculty, Graduate Program

Research Focus

Epigenetic, genetic and transcriptional control of B cell differentiation and B cell repertoire formation

A main focus of our lab is the molecular analysis of the epigenetic, genetic and transcriptional mechanisms which regulate accessibility of the V, D, and J immunoglobulin (Ig) gene segments for V(D)J recombination, and that regulate the differentiation of B cell progenitors. In our repertoire formation studies, we are elucidating the factors which influence the composition of the initial antibody repertoire. Although there are many V, D, and J genes at each locus, we have previously shown that different gene segments rearrange with quite different relative frequencies in pro-B cells in vivo. One of our goals is to understand the basis of this non-random gene utilization. Cutting edge technologies such as ChIP-seq, RNA-seq, deep sequencing of the antibody repertoire and CRISPR/Cas9 genome editing are utilized in our research. We are analyzing the chromatin modifications that accompany B cell differentiation in vivo in an effort to understand the mechanism of lineage-specific and stage-specific control of accessibility of Ig genes, as well as to understand the control of rearrangement on the level of individual genes. 3D-FISH and chromosome conformation capture (3C) and 4C are being used to study the changes in the 3-dimensional structure of the Igh and Igκ loci. A related study is to determine which transcription factors control the changes in the epigenetic profile and in the 3-dimensional structure of the receptor loci at the developmental stage at which they undergo rearrangement. Current studies are aimed at elucidating the mechanism by which transcription factors control V(D)J rearrangement and B cell differentiation. We have identified regions with the epigenetic marks of enhancers within the Vκ portion of the Igκ locus, and we are using CRISPR/Cas9 technology to delete these novel enhancer-like regulatory elements in a cell line that we can induce to undergo Igκ rearrangement. In addition, we are deleting other key transcription factor binding sites, including those of the long-range looping protein CTCF, to determine what proteins are important in the proper folding of the rearranging Igκ locus. We are also studying the epigenetic regulation of later steps in B cell differentiation.

Selected References

Kleiman, E., Jia, H., Loguercio, S., Su, A.I. and Feeney, A.J.  YY1 plays an essential role at all stages of B-cell differentiation. Proc Natl Acad Sci U S A 113:E3911-3920 (2016).

Gerasimova, T., Guo, C., Ghosh, A., Qiu, X., Montefiori, L., Verma-Gaur, J., Choi, N.M., Feeney, A.J. and Sen, R.  A structural hierarchy mediated by multiple nuclear factors establishes IgH locus conformation. Genes Dev. 29:1683-1695 (2015).

Predeus, A.V., Gopalakrishnan, S., Huang, Y., Tang, J., Feeney, A.J., Oltz, E.M. and Artyomov, M.N.  Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci. J. Immunol. 192:1064-1070 (2014).

Kumar, S., Wuerffel, R., Achour, I., Lajoie, B., Sen, R., Dekker, J., Feeney, A.J. and Kenter, A.L.  Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny. Genes Dev. 27:2439-2444 (2013).

Gopalakrishnan, S., Majumder, K., Predeus, A., Huang, Y., Koues, O.I., Verma-Gaur, J., Loguercio, S., Su, A.I., Feeney, A.J., Artyomov, M.N. and Oltz, E.M. Unifying model for molecular determinants of the preselection Vbeta repertoire. Proc Natl Acad Sci USA 110:E3206-3215 (2013).

Choi, N.M., Loguercio, S., Verma-Gaur, J., Degner, S.C., Torkamani, A., Su, A.I., Oltz, E.M., Artyomov, M. and Feeney, A.J. Deep sequencing of the murine Igh repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies. J. Immunol. 191:2393-2402 (2013).

Shih, H.-Y., Verma-Gaur, J., Torkamani, A., Feeney, A.J., Galjart, N. and Krangel, M.S. Tcra gene recombination is supported by a Tcra enhancer- and CTCF-dependent chromatin hub. Proc Natl Acad Sci USA 109:E3943-E3502 (2012).

Verma-Gaur, J., Torkamani, A., Schaffer, L., Head, S.R., Schork, N.J. and Feeney, A.J. Noncoding transcription within the Igh distal VH region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells. Proc Natl Acad Sci USA 109:17004-17009 (2012).

Volpi, S.A., Verma-Gaur, J., Hassan, R., Ju, Z., Roa, S., Chatterjee, S., Werling, U., Hou, H., Jr., Will, B., Steidl, U., Scharff, M., Edelman, W., Feeney, A.J. and Birshtein, B.K. Germline deletion of Igh 3' regulatory region elements hs 5, 6, 7 (hs5-7) affects B cell-specific regulation, rearrangement, and insulation of the Igh locus. J. Immunol. 188:2556-2566 (2012).

Feeney, A.J. and Verma-Gaur, J. CTCF-cohesin complex: architect of chromatin structure regulates V(D)J rearrangement. Cell Res. 22:280-282 (2012).

Degner, S.C., Verma-Gaur, J., Wong, T.P., Bossen, C., Iverson, G.M., Torkamani, A., Vettermann, C., Lin, Y.C., Ju, Z., Schulz, D., Murre, C.S., Birshtein, B.K., Schork, N.J., Schlissel, M.S., Riblet, R., Murre, C. and Feeney, A.J. CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells. Proc Natl Acad Sci USA 108:9566-9571 (2011).

Feeney, A.J. Epigenetic regulation of antigen receptor gene rearrangement. Curr. Opin. Immunol. 23:171-177 (2011).

Lukin, K., Fields, S., Lopez, D., Cherrier, M., Ternyak, K., Ramirez, J., Feeney, A.J. and Hagman, J. Compound haploinsufficiencies of Ebf1 and Runx1 genes impede B cell lineage progression. Proc Natl Acad Sci USA 107:7869-7874 (2010).

Xu, C.R. and Feeney, A.J. The epigenetic profile of Ig genes is dynamically regulated during B cell differentiation and is modulated by pre-B cell receptor signaling. J. Immunol. 182:1362-1369 (2009). Chosen as a featured article in "In This Issue".

Degner, S.C., Wong, T.P., Jankevicius, G. and Feeney, A.J. Cutting edge: developmental stage-specific recruitment of cohesin to CTCF sites throughout immunoglobulin loci during B lymphocyte development. J. Immunol. 182:44-48 (2009). Evaluated by the Faculty of 1000 Biology.

Carey, J.B., Moffatt-Blue, C.S., Watson, L.C., Gavin, A.L. and Feeney, A.J. Repertoire-based selection into the marginal zone compartment during B cell development. J. Exp. Med. 205:2043-2052 (2008). Evaluated by the Faculty of 1000 Biology.

Xu, C.R., Schaffer, L., Head, S.R. and Feeney, A.J. Reciprocal patterns of methylation of H3K36 and H3K27 on proximal vs. distal IgVH genes are modulated by IL-7 and Pax5. Proc Natl Acad Sci USA 105:8685-8690 (2008).