Many levels of control of V gene rearrangement frequency

Abstract

V, D, and J gene segments rearrange at very different frequencies. As with most biological systems, there are multiple levels of control of V gene recombination frequency, and here we review some of the work from our laboratory that addresses these various control mechanisms. One of the important factors that affect non-random V gene rearrangement frequency is the natural heterogeneity in recombination signal sequences (RSSs). Not only does variation in the heptamer and nonamer affect rearrangement, but variation in the spacer can also dramatically affect recombination. However, there are clearly other factors which control V gene rearrangement, as revealed by the fact that genes with identical RSSs can rearrange at different frequencies in vivo. Some of these other influences most likely affect the earliest stages of control--the change from an inaccessible state to an accessible state. Transcription factors can play a role in inducing these changes. Rearrangement of many VkappaI genes can be induced in a non-lymphoid cell line after ectopic expression of E2A, while neighboring VkappaII and VkappaIII genes do not rearrange, demonstrating that at least one level of control of induction of accessibility occurs at the level of the individual gene. Also, changes in chromatin structure can affect accessibility and might influence individual V gene rearrangement frequency.

The Extent of Histone Acetylation Correlates with the Differential Rearrangement Frequency of Individual VH Genes in Pro-B Cells

“…It has been shown by several groups, including our own, that V H genes rearrange at different frequencies (19). Natural variation in the composition of the recombination signal sequence (RSS) 3 is part of the reason for this differential rearrangement, but it does not explain all of the nonrandom rearrangement (19).…”

Leaky severe combined immunodeficiency and aberrant DNA rearrangements due to a hypomorphic RAG1 mutation

“…The products of RAG1/2 cleavage are blunt, 5Ј phosphorylated signal ends and covalently closed, hairpin coding ends. Sequence elements within the nonconserved 12 and 23 spacers 7 and coding flanks [8][9][10][11] contribute to RAG1/2 interaction with the recombining DNA and strongly influence coding segment utilization. 7 Hence, the efficiency of binding and cleavage of individual RSSs is significantly affected by interactions of the RAG1/2 endonuclease with the heptamer, nonamer, 12 or 23 spacer, and coding sequences.…”

“…Sequence elements within the nonconserved 12 and 23 spacers 7 and coding flanks [8][9][10][11] contribute to RAG1/2 interaction with the recombining DNA and strongly influence coding segment utilization. 7 Hence, the efficiency of binding and cleavage of individual RSSs is significantly affected by interactions of the RAG1/2 endonuclease with the heptamer, nonamer, 12 or 23 spacer, and coding sequences.In addition to an essential role in initiating V(D)J rearrangements, RAG1/2 has been proposed to have important functions subsequent to the generation of DSBs. In vitro biochemical and cellular transfection assays have provided evidence that upon cleavage of the RSSs, the RAG proteins remain associated with the DNA ends in postcleavage complexes.…”

Transposon Mutagenesis Identifies Sites Upstream of the Neisseria gonorrhoeae pilE Gene That Modulate Pilin Antigenic Variation

“…While it is possible that low levels of transcription of pilE are provided by cryptic promoter sequences, the fact that there is no change in the frequency of pilin Av when normal transcription is blocked by mutation of the Ϫ10 sequence (Table 2) shows that these processes are not linked. In other recombination systems, such as V(D)J rearrangement, recombination is not directly controlled by transcription but is modulated by the action of transcription factors and changes in chromatin structure mediated by histone modifications and chromatin remodeling (8). As a bacterium, N. gonorrhoeae is not thought to carry nucleosomes or other wellordered structures found in eukaryotic chromatin, but it does possess genes predicted to be involved in chromosome structure, including genes encoding a histone deacetylase-like protein (hda), the DNA binding protein HU-beta (dbhB), and the heterodimeric bacterial histone-like protein IHF (ihfA and ihfB) (58).…”