The boundaries of the distribution of somatic hypermutation of rearranged immunoglobulin variable genes

Abstract

Summary Available evidence about the mechanisms and distribution of somatic hypermutation (SHM) of rearranged immunoglobulin (IgV) genes is reviewed with particular emphasis on the 5 ′ boundary. In heavy (H) chain genes, the 5 ′ boundary of SHM is the transcription start site; in contrast to κ light (L) chain genes, it is located in the leader (L) intron. DNA-based models of SHM cannot account for this difference. However, an updated reverse transcriptase (RT)-based model invoking error-prone RT activity of DNA polymerase η copying IgV premRNA templates to produce cDNA of the transcribed strand (TS) of IgV DNA, which then replaces the corresponding section of the original TS, can explain the difference. This explanation incorporates recent knowledge of pre-mRNA processing, in particular, binding of the splicing-associated protein termed U2AF to a pyrimidine-rich tract in the L intron of pre-mRNA of κ L chains that may block RT progression further upstream to the end of the pre-mRNA template (transcription start site). Reasons why this block may not occur in H chains and other aspects of the updated RT-model are discussed.

On the molecular mechanism of somatic hypermutation of rearranged immunoglobulin genes

“…Finally, the RT‐model presents the only scientific explanation available for the 5′ boundary of SHM at Igκ loci. As recently described in detail elsewhere 21 , it is suggested that this boundary in DNA is influenced by processing events within the leader intron at the RNA level. Briefly, binding of small nuclear (sn)RNA and protein factors involved in splicing to sequences within the leader intron of Igκ pre‐mRNA prevents full‐length reverse transcription to the 5′ end of this template and hence locates the common terminus of the cDNA tracts synthesized to the leader intron.…”

“…As noted by the authors, this model requires the evolution of a defective transcription factor. Recently, one of us (RVB) independently noted that, as UNG2 and pol‐η co‐localize with proliferating cell nuclear antigen (PCNA) in replication foci 96 , 97 and active mismatch recognition by MSH2/MSH6 requires formation of a complex with PCNA 98 , the collision of replication and transcription complexes would thus bring all of the molecules required for phase II SHM potentiation into the vicinity of an Ig locus 21 . PCNA also stimulates the DNA‐dependent 99 and the RNA‐dependent (A. Franklin & R.V.…”

“…Recently, one of us (RVB) independently noted that, as UNG2 and pol-η co-localize with proliferating cell nuclear antigen (PCNA) in replication foci 96,97 and active mismatch recognition by MSH2/MSH6 requires formation of a complex with PCNA, 98 the collision of replication and transcription complexes would thus bring all of the molecules required for phase II SHM potentiation into the vicinity of an Ig locus. 21 PCNA also stimulates the DNAdependent 99 It is presently speculated that a replication complex, which originates 5′ of an Ig promoter, experiences multiple episodes of pausing as it encounters sites of DNA remodelling throughout the J-C intron, like those that are generated by the B lymphocyte regulator of IgH transcription, BrIgHt. 100,101 Translocating RNAP II complexes may subsequently collide into the rear of the paused replication fork, and each other, causing a pileup.…”

“…The 5′ boundaries of SHM are (i) the transcription start site (TSS) upstream of VDJ sequences at the IgH locus 16 , 18 and (ii) a site within the leader intron upstream of VJ sequences at the Igκ locus 19 . The latter has recently been identified as encoding a motif involved in splicing of pre‐mRNA 20 , 21 . The 5′ boundary at the Igκ locus is not absolute, with mutations occurring infrequently between the TSS and the designated 5′ margin of SHM in the L‐V intron.…”

“…19 The latter has recently been identified as encoding a motif involved in splicing of pre-mRNA. 20,21 The 5 ′ boundary at the Ig κ locus is not absolute, with mutations occurring infrequently between the TSS and the designated 5 ′ margin of SHM in the L-V intron. Furthermore, rare mutations have been detected upstream of the TSS at both IgH and Ig κ loci.…”