Physical linkage of mouse lambda genes by pulsed-field gel electrophoresis suggests that the rearrangement process favors proximate target sequences.

Abstract

The first complete map of a mammalian immunoglobulin gene locus is presented. Mouse A genes were mapped by pulsed-field gel electrophoresis. The gene order is V2-Vx-C2-C4-Vl-C3-Cl. The distance between V2 or Vx and the C2-C4 cluster is 74 or 55 kilobases (kb), respectively, whereas that between Vl and C3-C1 is only 19 kb; V2 and C3-Cl are at least 190 kb apart. Thus, the distances between the A subloci are inversely proportional to their frequencies of rearrangement. The related gene A5 is not within the 500 kb of the A locus mapped here.Mouse A genes have been found in four separate clusters of DNA clones which so far were physically unlinked: a cluster of clones containing the JC3 and JC1 genes, one of JC2 and the pseudogene JC4, and separate groups of clones for Vl and V2 (2, 31). Interestingly, the lambda genes rearrange in restricted combinations, VA1 only with CX1 or CX3 and VX2 almost exclusively with CX2 but very rarely with CA1 or CX3 (7). The newly discovered VXx gene has so far been seen rearranged only with CX2 (6,28). Recently, the order and orientation of A genes, except for Vx, were determined by deletion mapping with unique probes (18). The genes were all found to be in the same transcriptional orientation, and the order was determined to be V2-C2-C4-Vl-C3-Cl (18). This organization explains why V1-C2 rearrangements were not found but gives no clues about why rearrangements of Vl are about 5 to 10 times more frequent than rearrangements of V2. Furthermore, the location of Vx in this scheme was unknown. Since the sequence of Vx is as related to VK as to VX1-VX2 (6), its evolutionary association with the A locus presumably occurred in a way different from that of V1-V2 and thus its location and orientation may be unusual.We have cloned, in phage and cosmids, approximately 140 kilobases (kb) of DNA making up the VA and CA genes and their flanking regions. However, it was impossible to link up the A genes by chromosomal walking because of the paucity of unique sequences in this locus (18). We therefore used pulsed-field gel electrophoresis (PFGE) (3,30,33) transferred into lysis buffer (0.5 M EDTA, pH 9.5, 1% N-lauryl sarcosine, 0.25 mg of proteinase K per ml). The agarose inserts were incubated for 48 h at 50°C, washed extensively for 48 h in 10 mM Tris (pH 7.2)-i mM EDTA (TE) at 4°C, and stored at 4°C in TE. DNA inserts were digested in the restriction enzyme buffer specified by the manufacturer (New England BioLabs, Inc.) containing 4 mM spermidine. Each 40-,lI insert was incubated in 40 ,ul of 2x reaction mixture with 60 U of enzyme at 37°C overnight; on the next morning, a further 40 U of enzyme, 4 ,umol of spermidine, and sufficient lOx buffer and bovine serum albumin to bring these reagents to lx were added. Incubation was continued for 4 to 6 h at 37°C, and the inserts were rinsed with 3 ml of electrophoresis buffer (0.25x TAE [16]) for 30 min on ice and electrophoresed as indicated in the figure legends.5-Azacytidine treatment. 5-Azacytidine treatment was for 32 h in culture (9, 12); cel...

Complete Sequence Assembly and Characterization of the C57BL/6 Mouse Ig Heavy Chain V Region

“…Despite the lack of complete locus sequence, many factors affecting recombination have been studied in small V gene families, in which the number and relative position of genes could be predicted reasonably accurately by Southern blotting and deletion mapping, and for which sequence was available. These include the recombination signal sequence (RSS), heptamer, nonamer (13,14), and spacer sequences (15); relative V gene promoter strength (16 -18); distance between rearranging elements (19); requirement for additional regulatory elements (18). However, with notable exceptions (20), these studies have relied on sequences of the genes themselves, or at most a small amount of flanking sequence, and have not been able to assess the role of chromatin context, provided by the relatively large tracts of intervening sequence (2-50 kb) between the relatively small (500 bp) V genes.…”

The basis for the mechanistic bias for deletional over inversional V(D)J recombination.

“…Although the second hypothesis seems at odds with the notion that V(D)J recombination is a random exon assembly system, work from several laboratories has been cited in favor of some form of tracking. First, the joining at the murine ~ locus markedly favors proximal over distal segments (Storb et al 1989). Second, at the TCR ~/ locus, the temporal onset of V~/2, VV3, and V~/4 rearrangement correlates with distance.…”

Two conserved essential motifs of the murine immunoglobulin lambda enhancers bind B-cell-specific factors.

“…The murine k locus is bipartite, presumably a result of an evolutionary gene duplication: two clusters of k Ig constant genes (CA3CA1 and CX2CX4) are spaced over 100 kb apart on chromosome 16 (11,65). Two highly homologous B-cellspecific enhancer elements map to 35 kb downstream of CA3CA1 (EA3-1) and 15.5 kb downstream of CA2CA4 (EA2-4) (27).…”