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Genetic Instability and Transcriptional Regulation

Ahmed Khamlichi

Group Leader

The main aim of our current work and projects is to understand 1) the molecular mechanisms that control, in vivo, the long-range interactions between promoters and master enhancers of the immunoglobulin heavy chain locus, 2) the co-transcriptional and epigenetic mechanisms involved in the recruitment of the RAG complex and AID during chromosomal translocations associated with V(D)J recombination and class switch recombination.

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Developing B lymphocytes have a remarkable capacity to somatically alter their genomes. Diversification of their immunoglobulin (Ig) loci through V(D)J recombination is initiated by the RAG1/2 complex which introduces double-strand breaks in recombination-signal sequences flanking Ig gene segments (V, D, and J segments).

Mature B cells have the unique ability to undergo an additional recombination process initiated by AID called class switch recombination (CSR) which targets the constant genes of the Ig heavy chain (IgH) locus. Both V(D)J recombination and CSR are controlled by remote regulatory elements and their deregulation is associated with various B cell tumors.

The main aim of our current work and projects is to understand; 1) the molecular mechanisms that control, in vivo, the long-range interactions between promoters and master enhancers during V(D) J recombination and CSR, 2) the co-transcriptional and epigenetic mechanisms involved in the recruitment of the RAG complex and AID during V(D)J recombination, CSR and associated chromosomal translocations, respectively. As a model, we use mouse lines in which different mutations were introduced at various sites of the IgH locus, and a combination of genetic, functional and mechanistic analyses. We focus on two long-range IgH regulatory elements: the Eμ enhancer located between the variable and the constant regions of the IgH locus and a locus control region made up of four enhancers (termed the 3’ regulatory region, 3’RR) located downstream of the locus.

Main publications

 

Santos JM et al. (2019) Two modes of cis-activation of switch transcription by the IgH superenhancer. PNAS 116: 14708-13.

· Oudinet C et al. (2019) Developmental regulation of DNA cytosine methylation at the immunoglobulin heavy chain constant locus. PLoS Genet 15(2): e1007930.

·  Jamrog L et al. (2018) PAX5-ELN oncoprotein promotes multistep B-cell acute lymphoblastic leukemia in mice. PNAS 115:10357-62.

·  Braikia FZ et al. (2017) Inducible CTCF insulator delays the IgH 3' regulatory region-mediated activation of germline promoters and alters class switching. PNAS 114:6092-97.

·  Braikia FZ et al. (2015) Developmental switch in the transcriptional activity of a long-range regulatory element. Mol Cell Biol 35: 3370-80.

 

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Scheme of a rearranged mouse IgH locus with the two major regulatory elements: Eμ enhancer and the 3’RR. V(D)J recombination, CSR and associated chromosomal translocations are catalyzed by the RAG complex and AID respectively.

 

 

Scientist

Amine Khamlichi

CNRS Research director

Research Assistant

Audrey Dauba

University of Toulouse Technician

Post-doctoral Fellow

Joana Santos

ANR-funded Post-doc

PhD Student

Chloé Oudinet

Fellow of the Ministry of Higher Education & Research

2019

  • Oudinet C, Braikia FZ, Dauba A, Santos JM, Khamlichi AA. Developmental regulation of DNA cytosine methylation at the immunoglobulin heavy chain constant locus. PLoS Genet. 2019. 15(2): e1007930.

2018

  • Khamlichi AA, Feil R Parallels between mammalian mechanisms of monoallelic gene expression. Trends Genet. 2018 34(12):954-971.
  • Jamrog L, Chemin G, Fregona V, Coster L, Pasquet M, Oudinet C, Rouquié N, Prade N, Lagarde S, Cresson C, Hébrard S, Nguyen Huu NS, Bousquet M, Quelen C, Brousset P, Mancini SJC, Delabesse E, Khamlichi AA, Gerby B, Broccardo C. PAX5-ELN oncoprotein promotes multistep B-cell acute lymphoblastic leukemia in mice. PNAS. 2018 115(41):10357-10362. ​​​​
  • Santos JM, Braikia FZ, Oudinet C, Haddad D, Conte C, Dauba A, Khamlichi AA. Duplication of a germline promoter downstream of the IgH 3' regulatory region impairs class switch recombination. Sci Rep. 2018 8(1):9164.

2017

  • Braikia FZ, Oudinet C, Haddad D, Oruc Z, Orlando D, Dauba A, Le Bert M,Khamlichi AA. Inducible CTCF insulator delays the IgH 3' regulatory

region-mediated activation of germline promoters and alters class switching. PNAS. 2017 114(23):6092–6097 

2015

  • Braikia FZ, Conte C, Moutahir M, Denizot Y, Cogné M, Khamlichi AA. Developmental switch in the transcriptional activity of a long-range regulatory element. Mol Cell Biol 2015 35(19):3370-80
  • Puget N, Leduc C, Oruc Z, Moutahir M, Le Bert M, Khamlichi AA. Complete cis-exclusion upon duplication of Eμ enhancer at the immunoglobulin heavy chain locus. Mol Cell Biol 2015 35(13):2231-41
  • Puget N, Hirasawa R, Hu NS, Laviolette-Malirat N, Feil R, Khamlichi AA. Insertion of an imprinted insulator into the IgH locus reveals developmentally regulated, transcription-dependent control of V(D)J recombination. Mol Cell Biol 2015 35(3):529-43

2014

  • Braikia FZ, Chemin G, Moutahir M, Khamlichi AA. Quantification of V(D)J recombination by real-time quantitative PCR. Immunol Lett 2014 162(1 Pt A):119-23
  • Leduc C, Chemin G, Puget N, Sawan C, Moutahir M, Herceg Z, Khamlichi AA. Tissue-specific inactivation of HAT cofactor TRRAP reveals its essential role in B cells. Cell Cycle 2014 (10):1583-9

2011

  • Haddad D, Puget N, Laviolette-Malirat N, Conte C and Khamlichi AA. Seeking sense of anti-sense switch transcripts Transcription 2(4):183-188
  • Haddad, Oruc, Puget, Laviolette-Malirat, Philippe, Le Bert, Khamlichi AA. Sense transcription through the S region is essential for immunoglobulin class switch recombination EMBO J 2011 30(8):1608-1620

 

2010

  • Leduc C, Haddad D, Laviolette-Malirat N, Nguyen Huu NS, Khamlichi AA. Combined deficiency of MSH2 and Sμ region abolishes class switch recombination. Eur J Immunol 2010 40(10):2925-31
  • Zhang T, Franklin A, Boboila C, McQuay A, Gallagher MP, Manis JP, Khamlichi AA, Alt FW. Downstream class switching leads to IgE antibody production by B lymphocytes lacking IgM switch regions. Proc Natl Acad Sci USA 2010 107(7):3040-5
  • Haddad D, Dougier HL, Laviolette N, Puget N, Khamlichi AA Replacement of Imu-Cmu intron by NeoR gene alters Imu germ-line expression but has no effect on V(D)J recombination. Mol Immunol 2010 47(5):961-71

2009

  • Rajagopal D, Maul RW, Ghosh A, Chakraborty T,Khamlichi AA, Sen R and Gearhart PJ. (2009) Immunoglobulin switch mu sequence causes RNA polymerase II accumulation and reduces dA hypermutation. J Exp Med 2009 206(6):1237-44
  • Wang L, Wuerffel R, Feldman S, Khamlichi AA and Kenter AL. (2009) S region sequence, RNA polymerase II and histone modifications create chromatin accessibility during class switch recombination. J Exp Med 2009 206(8):1817-30

2007

  • Oruc Z., Boumédiène A., Le Bert M. and Khamlichi A.A. Replacement of Igamma3 germline promoter by Igamma1 inhibits class switch recombination to IgG3. Proc Natl Acad Sci USA 2007 104(51):20484-9
  • Teissier J., Cuvillier A., Glaudet F. and Khamlichi A.A. Internalization and molecular interactions of human CD21 receptor. Mol Immunol 2007 44(9):2415-25
  • Huang F.T., Yu K., Balter B.B., Selsing E., Oruc Z., Khamlichi A.A., Hsieh C.L. and Lieber M.R. Sequence-Dependence of Chromosomal R-loops at the Immunoglobulin Heavy Chain Smu Class Switch Region. Mol Cell Biol 2007 27(16):5921-32

2006

  • Samara M., Oruc Z., Dougier H.L., Essawi T., Cogné M. and Khamlichi A.A. Germ line transcription in mice bearing neor gene downstream of Igamma3 exon in the Ig heavy chain locus. Int Immunol 2006 18(4):581-9

 

Collaborations

International Collaborations

  • F.W. Alt (HHMI, Boston, USA)
  • P.J. Gearhart (NIH, NIA, Baltimore, USA)
  • A.L. Kenter (U. of Illinois College of Medicine, Chicago, USA)
  • M.R. Lieber (PIBBS research faculty, U. of Southern California, Los Angeles, USA)

 

National Collaborations

  • M. Cogné/Yves Denizot (CNRS UMR 6101-Limoges)
  • R. Feil (CNRS UMR 5535-IGMM Montpellier)
  • Z. Herceg (IARC Lyon)
  • B. Reina San Martin (IGBMC-Strasbourg)

Networks