Regulation of V(D)J recombination Salvatore Spicuglia, Don Marc Franchini and Pierre Ferrier Adaptive immunity is intimately linked to the expression of antigen-specific immunoglobulin and T cell receptor genes and their recombination assembly from germline V, D and J gene segments. This developmentally regulated process relies on the activity of the Rag1–Rag2 recombinase, on accessibility of target gene segments and on monoallelic gene activation. Recent studies have revealed new mechanisms that, along with recombinase activity and locus accessibility, are likely to contribute to the control of V(D)J recombination, including target-site bias by the recombinase, RNA processing and chromosome positioning. Addresses Centre d’Immunologie de Marseille-Luminy (CIML), Institut National de la Sante ´ et de la Recherche Me ´ dicale (INSERM); Centre National de la Recherche Scientifique (CNRS); Universite ´ de la Me ´ diterrane ´ e, Campus de Luminy, Case 906, 13288 Marseille Cedex 9, France Corresponding author: Ferrier, Pierre (ferrier@ciml.univ-mrs.fr) Current Opinion in Immunology 2006, 18:158–163 This review comes from a themed issue on Lymphocyte development Edited by Kristin Hogquist and Harinder Singh Available online 3rd February 2006 0952-7915/$ – see front matter # 2005 Elsevier Ltd. All rights reserved. DOI 10.1016/j.coi.2006.01.003 Introduction V(D)J recombination, the process that assembles the variable exon of immunoglobulin (Ig) and T cell receptor (TCR) genes, is exquisitely regulated with respect to lymphoid cell lineage and developmental stage specifi- cities [1]. Because the Rag1–Rag2 recombinase is expressed in all lymphoid B- and T-cell progenitors, V(D)J recombination is thought to be controlled primarily by modulating chromatin access to its target ‘recombina- tion signal sequences’ (RSSs) at given Ig and TCR gene segments and/or loci [2]. However, some regulatory aspects such as ordered and/or monoallelic rearrange- ments (i.e. allelic exclusion) cannot be fully explained by the ‘accessibility’ model. This review discusses recent advances in the understand- ing of the regulation of V(D)J recombination and the emerging concepts that RSS preference by the recombi- nase, RNA processing and/or chromosome positioning (and degree of compaction) might be integral parts of these controls. Locus accessibility: control by the Rag1–Rag2 recombinase and the RSSs In immune cells, V(D)J recombination depends on line- age- and cell stage-specific expression of the Rag1–Rag2 proteins and, with regard to Rag2, cell cycle-dependent degradation [1,3]. However, the Rag proteins themselves, through discrete domains outside the recombinase-core region, might have a regulatory function(s) at the chro- mosomal level [4,5]. Notably, the demonstration that Rag2 specifically interacts with core histones [6  ] is intri- guing in light of previous findings of nucleosome posi- tioning by the RSSs [7]. Numerous studies have shown that V(D)J recombination efficiency and specificity can be influenced by the geno- mic arrangement of the given gene segments and by nucleotide variability within the RSS and/or the coding flanks [5,8–10]. Normally, rearrangements involve pairs of gene segments carrying dissimilar RSSs (12 and 23 RSSs, respectively). However, RSSs at some loci represent an extreme situation because they preclude ‘12/23 compa- tible’ rearrangements, a supplemental restriction named ‘beyond 12/23’ [11,12]. At the TCRb locus, for example, beyond 12/23 restriction on Vb-to-Jb rearrangements makes it theoretically possible primarily to control locus recombination by modulating accessibility of intermedi- ate Db gene segments only. Regulation by cis-elements, trans-acting factors and chromatin regulators Gene-targeting studies have established the pivotal role of transcriptional cis-elements and cognate transcription fac- tors (TFs) in inducing V(D)J recombination [1,2]. A con- sensual view is that enhancers control chromatin accessibility at proximal (D)J regions by activating asso- ciated germline promoters. A recent example was provided by the TCRa locus, in which enhancer-mediated, hier- archical activation of two germline promoters orchestrates Ja rearrangements [13]. By contrast, the impact of enhan- cers on the control of V gene accessibility is presently unclear. Although the Ig heavy (H) and TCRb gene enhancers preferentially regulate accessibility within prox- imal 5 0 domains comprising D–J–C cluster(s) [14–16], the TCRa gene enhancer appears also to modulate histone acetylation and transcription of remote V gene segments [17]. V(D)J rearrangement at Ig loci requires the combined activity of various TFs, including Pax5, E2A, early-B-cell Current Opinion in Immunology 2006, 18:158–163 www.sciencedirect.com