Cis-regulatory elements and epigenetic changes control genomic rearrangements of the IgH locus

Abstract

Immunoglobulin variable region exons are assembled from discontinuous variable (V), diversity (D), and joining (J) segments by the process of V(D)J recombination. V(D)J rearrangements of the immunoglobulin heavy chain (IgH) locus are tightly controlled in a tissue-specific, ordered and allele-specific manner by regulating accessibility of V, D, and J segments to the recombination activating gene proteins which are the specific components of the V(D)J recombinase. In this review we discuss recent advances and established models brought forward to explain the mechanisms underlying accessibility control of V(D)J recombination, including research on germline transcripts, spatial organization, and chromatin modifications of the immunoglobulin heavy chain (IgH) locus. Furthermore, we review the functions of well-described and potential new cis-regulatory elements with regard to processes such as V(D)J recombination, allelic exclusion, and IgH class switch recombination.

FIGURE 1.1

Schematic depiction of the murine IgH locus. (A) V_H, D_H, J_H gene segments and C_H exons are shown as rectangles, known and potential regulatory elements as ovals. The V_H families V_HJ558, V_HS107, and V_H7183 are depicted as examples for distal, intermediate, and proximal V_H families, respectively. The cis-regulatory elements P_DQ52 (promoter of DQ52), Eμ (intronic enhancer), and IgH 3′RR (IgH 3′ regulatory region) are depicted. The potential regulatory elements 5′RR (5′ regulatory region) and VD RR (V_H–D_H intergenic regulatory region) are depicted with a question mark. Drawing not to scale. (B) The 3′ part of the IgH locus. An assembled V_HDJ_H exon is shown as a white rectangle, C_H genes as squares, Eμ and individual DNaseI hypersensitive sites within the IgH 3′RR are depicted as black ovals, switch regions as white circles. I promoters are located upstream of every switch region (Chaudhuri et al., 2007; Lennon and Perry, 1985; Lutzker and Alt, 1988), only μ and γ1 I promoters (IμP, Iγ1P) are depicted. Transcripts from I promoters get spliced and polyadenylated. Switch regions also get transcribed in the antisense orientation (Apel et al., 1992; Julius et al., 1988, Morrison et al., 1998; Perlot et al., 2008). Concomitant transcription from IμP and, for example, Iγ1P can target AID to μ and γ1 switch regions and thereby initiate CSR to Cγ1.

FIGURE 1.2

Transcripts within the IgH locus. V_H, D_H, J_H gene segments and C_H exons are shown as rectangles, enhancer and promoter elements as ovals. 12 bp and 23 bp RSSs are depicted as black and white triangles, respectively. Drawings not to scale. (A) The IgH locus in germline configuration is transcribed from the promoter of DQ52 (P_DQ52) to produce the μ0 transcript (Alessandrini and Desiderio, 1991), and from within the Eμ enhancer to generate the Iμ transcript (Lennon and Perry, 1985; Su and Kadesch, 1990), both of which are getting spliced and polyadenylated (Kottmann et al., 1994, Su and Kadesch, 1990). D_H and J_H elements are transcribed in the antisense orientation (Bolland et al., 2007; Chakraborty et al., 2007), suggested start sites (dashed arrows) are located around P_DQ52 (Chakraborty et al., 2007) and Eμ (Bolland et al., 2007). Sites of transcriptional termination of D_H–J_H antisense germline transcripts are unknown. (B) Unrearranged V_H segments are transcribed in the sense orientation from the individual V_H promoters (V_HP) (Yancopoulos and Alt, 1985). The intron between the leader (L) and the V_H exon (V_H) is spliced out, and the V_H sense germline transcript gets polyadenylated (Yancopoulos and Alt, 1985). The V_H segments and V_H intergenic regions can also get transcribed in the antisense orientation (Bolland et al., 2004). Start and termination sites of V_H antisense germline transcripts are unknown. Therefore, individual antisense transcripts could comprise one V_H segment and its adjacent regions or multiple V_H segments including intergenic regions, shown as short and long solid arrows, respectively. (C) Upon D to J_H recombination, the assembled DJ_H exon gets transcribed from the D_H promoter (P_DH) and spliced to the Cμ exons to generate the Dμ transcript (Alessandrini and Desiderio, 1991; Reth and Alt, 1984), which in one reading frame encodes for a short μHC molecule (Reth and Alt, 1984). D_H antisense germline transcription is present throughout the remaining unrearranged D_H segments (Chakraborty et al., 2007). Suggested origin of D_H antisense germline transcripts is the region around the promoter of the recombined D_H segment (depicted as P_DH) (Chakraborty et al., 2007), transcriptional termination sites are unknown. (D) Upon V_H to DJ_H recombination, the promoter of the rearranged V_H segment (depicted as V_HP) drives expression of mRNA encoding for the μHC. In addition to Iμ sense transcription, the Sμ switch region is also transcribed in the antisense orientation (Perlot et al., 2008) from promoters residing within Sμ (Apel et al., 1992; Morrison et al., 1998), the transcriptional termination site of the Sμ antisense transcript is unknown. The assembled V_HDJ_H exon and the adjacent J_H region are transcribed in the antisense orientation potentially from start sites within the J_H cluster (dashed arrow) (Perlot et al., 2008), the transcriptional termination site of the V_HDJ_H antisense transcript is unknown. Upstream unrearranged V_H segments are transcriptionally silenced upon assembly of a functional V_HDJ_H exon (Bolland et al., 2004; Yancopoulos and Alt, 1985).