Autoubiquitylation of the V(D)J recombinase protein RAG1

V(D)J recombination, the rearrangement of gene segments to assemble Ig and T cell receptor coding regions, is vital to B and T lymphocyte development. Here, we demonstrate that the V(D)J recombinase protein RAG1 undergoes ubiquitylation in cells. In vitro, the RING finger domain of RAG1 acts as a ubiquitin ligase that mediates its own ubiquitylation at a highly conserved K residue in the RAG1 amino-terminal region. Ubiquitylation is best supported by a specific ubiquitin-conjugating enzyme, UbcH3/CDC34, and requires an intact RAG1 RING finger motif. Disruption of the RING finger and certain RAG1 N-terminal truncations are associated with immunodeficiency in human patients, suggesting that RAG1's ubiquitin ligase is required for its biological role in lymphocyte development.     

N-terminal truncated human RAG1 proteins can direct T-cell receptor but not immunoglobulin gene rearrangements

The proteins encoded by RAG1 and RAG2 can initiate gene recombination by site-specific cleavage of DNA in immunoglobulin and T-cell receptor (TCR) loci. We identified a new homozygous RAG1 gene mutation (631delT) that leads to a premature stop codon in the 5' part of the RAG1 gene. The patient carrying this 631delT RAG1 gene mutation died at the age of 5 weeks from an Omenn syndrome-like T(+)/B(- )severe combined immunodeficiency disease. The high number of blood T-lymphocytes (55 x 10(6)/mL) showed an almost polyclonal TCR gene rearrangement repertoire not of maternal origin. In contrast, B-lymphocytes and immunoglobulin gene rearrangements were hardly detectable. We showed that the 631delT RAG1 gene can give rise to an N-terminal truncated RAG1 protein, using an internal AUG codon as the translation start site. Consistent with the V(D)J recombination in T cells, this N-terminal truncated RAG1 protein was active in a plasmid V(D)J recombination assay. Apparently, the N-terminal truncated RAG1 protein can recombine TCR genes but not immunoglobulin genes. We conclude that the N-terminus of the RAG1 protein is specifically involved in immunoglobulin gene rearrangements.     

Aberrant V(D)J recombination is not required for rapid development of H2ax/p53-deficient thymic lymphomas with clonal translocations

Histone H2AX is required to maintain genomic stability in cells and to suppress malignant transformation of lymphocytes in mice. H2ax(-/-)p53(-/-) mice succumb predominantly to immature alphabeta T-cell lymphomas with translocations, deletions, and genomic amplifications that do not involve T-cell receptor (TCR). In addition, H2ax(-/-)p53(-/-) mice also develop at lower frequencies B and T lymphomas with antigen receptor locus translocations. V(D)J recombination is initiated through the programmed induction of DNA double-strand breaks (DSBs) by the RAG1/RAG2 endonuclease. Because promiscuous RAG1/RAG2 cutting outside of antigen receptor loci can promote genomic instability, H2ax(-/-)p53(-/-) T-lineage lymphomas might arise, at least in part, through erroneous V(D)J recombination. Here, we show that H2ax(-/-)p53(-/-)Rag2(-/-) mice exhibit a similar genetic predisposition as do H2ax(-/-)p53(-/-) mice to thymic lymphoma with translocations, deletions, and amplifications. We also found that H2ax(-/-)p53(-/-)Rag2(-/-) mice often develop thymic lymphomas with loss or deletion of the p53(+) locus. Our data show that aberrant V(D)J recombination is not required for rapid onset of H2ax/p53-deficient thymic lymphomas with genomic instability and that H2ax deficiency predisposes p53(-/-)Rag2(-/-) thymocytes to transformation associated with p53 inactivation. Thus, H2AX is essential for suppressing the transformation of developing thymocytes arising from the aberrant repair of spontaneous DSBs.     

Recombinase activating gene enzymes of lymphocytes

Expression of T-cell receptor and surface immunoglobulins on T and B lymphocytes, respectively, is strictly dependent on the variable, (diversity) joining exon (V(D)J) recombination process, which is initiated by the lymphoid-specific recombinase activating gene proteins 1 and 2 (RAG1 and RAG2). Recent advances have highlighted the functional organization of the RAG1 and RAG2 proteins and have provided important information on the regulation of RAG gene expression. Depending on the severity of their effects on the V(D)J recombination process, mutations of the RAG genes account for a spectrum of combined immune deficiencies in humans.     

Oligoclonal expansion of T lymphocytes with multiple second-site mutations leads to Omenn syndrome in a patient with RAG1-deficient severe combined immunodeficiency

Omenn syndrome (OS) is a rare primary immunodeficiency characterized by the presence of activated/oligoclonal T cells, eosinophilia, and the absence of circulating B cells. OS patients carry leaky mutations of recombination activating genes (RAG1 or RAG2) resulting in partial V(D)J recombination activity, whereas null mutations cause severe combined immunodeficiency with absence of mature T and B cells (T-B- SCID). Here we describe somatic mosaicism due to multiple second-site mutations in a patient with RAG1 deficiency. We found that he is homozygous for a single base deletion in the RAG1 gene, which results in frameshift and likely abrogates the protein function. However, the patient showed typical OS features. Molecular analysis revealed that several second-site mutations, all of which restored the RAG1 reading frame and resulted in missense mutations, were demonstrated in his T cells. These findings suggest that his revertant T-cell mosaicism is responsible for OS phenotype switched from T-B- SCID.     

RAG-dependent peripheral T cell receptor diversification in CD8+ T lymphocytes

Rearrangement of T cell receptor (TCR) genes is driven by transient expression of V(D)J recombination-activating genes (RAGs) during lymphocyte development. Immunological dogma holds that T cells irreversibly terminate RAG expression before exiting the thymus, and that all of the progeny arising from mature T cells express the parental TCRs. When single pancreatic islet-derived, NRP-A7 peptide-reactive CD8(+) T cells from nonobese diabetic (NOD) mice were repeatedly stimulated with peptide-pulsed dendritic cells, daughter T cells reexpressed RAGs, lost their ability to bind to NRP-A7K(d) tetramers, ceased to transcribe tetramer-specific TCR genes, and, instead, expressed a vast array of other TCR rearrangements. Pancreatic lymph node (PLN) CD8(+) T cells from animals expressing a transgenic NRP-A7-reactive TCR transcribed and translated RAGs in vivo and displayed endogenous TCRs on their surface. RAG reexpression also occurred in the PLN CD8(+) T cells of wild-type NOD mice and could be induced in the peripheral CD8(+) T cells of nondiabetes-prone TCR-transgenic B10.H2(g7) mice by stimulation with peptide-pulsed dendritic cells. In contrast, reexpression of RAGs could not be induced in the CD8(+) T cells of B6 mice expressing an ovalbumin-specific, K(b)-restricted TCR, or in the CD8(+) T cells of NOD mice expressing a lymphocytic choriomeningitis virus-specific, D(b)-restricted TCR. Extra-thymic reexpression of the V(D)J recombination machinery in certain CD8(+) T cell subpopulations, therefore, enables further diversification of the peripheral T cell repertoire.     

Rch1, a protein that specifically interacts with the RAG-1 recombination-activating protein.

RAG1 and RAG2 are lymphoid-specific genes that together induce V(D)J recombinase activity in a variety of nonlymphoid cell types. While no other lymphoid-specific factors are required to induce recombination, other factors with more widespread expression patterns have been implicated in the reaction. However, none of these factors have been cloned, and their relationship to the RAG proteins is unclear. Using the yeast two-hybrid assay, we have identified RCH1, a gene encoding a protein of molecular weight 58,000 that interacts specifically with RAG-1. The predicted Rch1 protein sequence is 47% identical to yeast SRP1, a protein associated with the nuclear envelope. A truncated form of Rch1, which retains the ability to interact with RAG-1, reduces V(D)J recombination activity in HeLa cells.     

RAG2 is regulated differentially in B and T cells by elements 5′ of the promoter

To study RAG2 gene regulation in vivo, we developed a blastocyst complementation method in which RAG2-deficient embryonic stem cells were transfected with genomic clones containing RAG2 and then assessed for their ability to generate lymphocytes. A RAG2 genomic clone that contained only the RAG2 promoter sequences rescued V(D)J recombination in RAG2-deficient pro-B cell lines, but did not rescue development of RAG2-deficient lymphocytes in vivo. However, inclusion of varying lengths of sequences 5' of the RAG2 promoter generated constructs capable of rescuing only in vivo B cell development, as well as other constructs that rescued both B and T cell development. In particular, the 2-kb 5' region starting just upstream of the RAG2 promoter, as well as the region from 2-7 kb 5', could independently drive B cell development, but not efficient T cell development. Deletion of the 2-kb 5' region from the murine germ line demonstrated that this region was not required for RAG expression sufficient to generate normal B or T cell numbers, implying redundancy among 5' elements. We conclude that RAG2 expression in vivo requires elements beyond the core promoter, that such elements contribute to differential regulation in the B vs. T lineages, and that sequences sufficient to direct B cell expression are located in the promoter-proximal 5' region.     

V(D)J recombination activity in lymphoid cell lines is increased by agents that elevate cAMP.

V(D)J [variable--(diversity)--joining] recombination is regulated developmentally, being restricted to cells of the early B- and T-lymphocyte lineages. In this report we show that recombination activity can also be regulated in response to chemical effectors. Compounds that increase intracellular cAMP increase V(D)J recombination of extrachromosomal substrates in pre-B-cell lines as much as 10-fold. In contrast, V(D)J recombination is reduced 5- to 8-fold in response to phorbol 12-myristate 13-acetate or to the calcium ionophore A23187. The effect of cAMP agonists on recombination appears to reflect an increase in cellular recombination activity, as indicated by the caffeine-induced rise in the level of mRNA from the recombination-activating genes RAG1 and RAG2. Our data demonstrate that intracellular second messengers modulate recombination activity in lymphoid cell lines, implying that recombination activity can be regulated by these signals in developing B and T lymphocytes.     

Identical mutations in RAG1 or RAG2 genes leading to defective V(D)J recombinase activity can cause either T-B-severe combined immune deficiency or Omenn syndrome

Omenn syndrome (OS) is an inherited disorder characterized by an absence of circulating B cells and an infiltration of the skin and the intestine by activated oligoclonal T lymphocytes, indicating that a profound defect in the lymphoid developmental program could be accountable for this condition. Inherited mutations in either the recombination activating genes RAG1 or RAG2, resulting in partial V(D)J recombinase activity, were shown to be responsible for OS. This study reports on the characterization of new RAG1/2 gene mutations in a series of 9 patients with OS. Given the occurrence of the same mutations in patients with T-B-severe combined immune deficiency or OS on 3 separate occasions, the proposal is made that an additional factor may be required in certain circumstances for the development of the Omenn phenotype. The nature of this factor is discussed.     

Role of RAG1 autoubiquitination in V(D)J recombination

The variable domains of Ig and T-cell receptor genes in vertebrates are assembled from gene fragments by the V(D)J recombination process. The RAG1–RAG2 recombinase (RAG1/2) initiates this recombination by cutting DNA at the borders of recombination signal sequences (RSS) and their neighboring gene segments. The RAG1 protein is also known to contain a ubiquitin E3 ligase activity, located in an N-terminal region that is not strictly required for the basic recombination reaction but helps to regulate recombination. The isolated E3 ligase domain was earlier shown to ubiquitinate one site in a neighboring RAG1 sequence. Here we show that autoubiquitination of full-length RAG1 at this specific residue (K233) results in a large increase of DNA cleavage by RAG1/2. A mutational block of the ubiquitination site abolishes this effect and inhibits recombination of a test substrate in mouse cells. Thus, ubiquitination of RAG1, which can be promoted by RAG1’s own ubiquitin ligase activity, plays a significant role in governing the level of V(D)J recombination activity.V(D)J recombination plays a central role in the production of antigen receptors by recombining V, D, and J gene segments from their genomic clusters to give rise to the highly varied populations of immunoglobulins and T-cell receptors (1). Recombination starts with the introduction of double-strand breaks by the RAG1/RAG2 protein complex at a pair of recombination signal sequences (RSS) (2, 3), distinguished by the length of the spacer DNA separating their conserved heptamer and nonamer elements. Recombination requires one RSS with a 12-base pair spacer and another with a 23-base pair spacer. Each pair of breaks is then processed by the nonhomologous DNA end-joining group of proteins to produce a junction of two segments of coding sequence (a coding joint) and a junction of the two RSSs (a signal joint) (4). The purified RAG1/2 protein complex displays the correct specificity for pairs of RSSs (5, 6), and has thus been used as a model for the initiation of V(D)J recombination. Until recently, the RAG proteins used for these studies have generally been minimal “core” regions of RAG1 and RAG2 (amino acids 384–1,008 of 1,040 in mouse RAG1 and 1–387 of 527 in RAG2), which are sufficient for specific binding and cleavage activity in a purified cell-free system. Ectopic expression of these truncated proteins supports V(D)J recombination in suitable cell lines, although with differences from the full-length proteins that will be discussed here.A complex composed of core RAG1 and RAG2 is more active than its full-length counterpart in cleavage of extrachromosomal substrates in a hamster cell line, but overall recombination is reported to be lower (7), indicating a defect in the stages of recombination subsequent to DNA cleavage. Similarly, mice or pre-B cells missing the RAG2 C-terminal noncore region are defective in the V to DJ recombination step of Ig heavy chain joining, although the earlier D to J joining step is normal (8). The mice also display an increased prevalence of lymphomas (9). A plant homeo domain (PHD) within the RAG2 C terminus is known to bind to chromatin, and specifically to histone 3 trimethylated on lysine 4 (H3K4me3), which is presumably an important step in directing RAG1/2 to loci bearing this “activating” modification (10). The lack of this domain may largely explain the defective functions of the RAG2 core protein. Similarly, although core RAG1 can support D to J rearrangement at the Ig heavy chain locus in RAG1^−/− pro-B cells, the level is reduced compared with that of full-length RAG1 (FLRAG1) (11), and deletions of certain smaller regions within the RAG1 N terminus have even greater effects (11). Some naturally occurring truncations of the RAG1 N terminus lead to human immunodeficiency (12). The functions of the parts of RAG1 and RAG2 outside of the catalytically essential cores have been reviewed (13). There is also evidence that the RAG1 and RAG2 C termini interact: DNA cleavage by RAG1/2 combinations containing both regions was greatly reduced but was restored upon addition of an H3K4me3-containing peptide (14). Relief of this autoinhibition may synergize with the chromatin-binding effect of the PHD domain to target recombination to the appropriate loci.The significant modulation of recombination in cells, and/or of DNA cleavage in vitro, by these “dispensable” regions of both RAG1 and RAG2 is further modified by covalent modifications of the proteins, which affect their stability or activity. RAG2 becomes phosphorylated at a specific site in its C terminus (T490) at the G1/S stage of the cell cycle, and is then ubiquitinated by the Skp2-SCF ubiquitin ligase, a central regulator of cell cycle progression, leading to its degradation in S phase (15, 16). Phosphorylation of RAG1 at residue S528 by the AMP-dependent protein kinase has also been described (17), in this case leading to increased activity of RAG1/2 both for cell-free DNA cleavage and for recombination in cells.The N terminus of RAG1 contains a Zn-binding motif (amino acids 264–389) that includes a C₃HC₄ RING (really interesting new gene) finger motif closely associated with an adjacent C₂H₂ Zn finger. This domain was shown to have ubiquitin ligase (E3) activity (18, 19), a common feature of RING finger domains, when combined with ubiquitin, the ubiquitin-activating (E1) enzyme, and an appropriate ubiquitin-conjugating (E2) enzyme. A naturally occurring human mutation in this RING finger motif (C328Y) was found to cause the primary immunodeficiency disease Omenn’s syndrome (20). A study of the equivalent mutation in mouse RAG1 (C325Y) showed that it greatly reduced recombination of an extrachromosomal plasmid, as did mutation of the neighboring residue (P326G) (21). Other RING finger residues critical for ubiquitin ligase activity appeared to contribute to robust recombination of extrachromosomal substrates (22). In biochemical experiments carried out with an N-terminal fragment of RAG1 (residues 218–389), the principal site of autoubiquitination was found to be a residue neighboring the RING finger, K233; mutation of this residue (K233M) essentially abolished autoubiquitination of the fragment (18).In this article, we assess the site or sites and extent of autoubiquitination of RAG1, the consequences of this modification for RAG1/RAG2 activity in a cell-free system and in cells, and the functional relationship between this modification and the histone-recognizing PHD domain of RAG2. We prepare FLRAG1 in complex with either full-length RAG2 (FLRAG2) or core RAG2 and find that FLRAG1 undergoes autoubiquitination specifically at K233. The ubiquitination of RAG1 protein enhances coupled cleavage by the RAG1/RAG2 complex of a 12/23 RSS pair by about fivefold. RAG1 autoubiquitination also ap-pears to be important for supporting V(D)J recombination in cells.     

The immunophenotypic and immunogenotypic B-cell differentiation arrest in bone marrow of RAG-deficient SCID patients corresponds to residual recombination activities of mutated RAG proteins

The protein products of the recombination activating genes (RAG1 and RAG2) initiate the formation of immunoglobulin (Ig) and T-cell receptors, which are essential for B- and T-cell development, respectively. Mutations in the RAG genes result in severe combined immunodeficiency disease (SCID), generally characterized by the absence of mature B and T lymphocytes, but presence of natural killer (NK) cells. Biochemically, mutations in the RAG genes result either in nonfunctional proteins or in proteins with partial recombination activity. The mutated RAG genes of 9 patients from 7 families were analyzed for their recombination activity using extrachromosomal recombination substrates, rearrangement of endogenous Ig loci in RAG gene-transfected nonlymphoid cells, or the presence of Ig gene rearrangements in bone marrow (BM). Recombination activity was virtually absent in all 6 patients with mutations in the RAG core domains, but partial activity was present in the other 3 RAG-deficient patients, 2 of them having Omenn syndrome with oligoclonal T lymphocytes. Using 4-color flow cytometry, we could define the exact stage at which B-cell differentiation was arrested in the BM of 5 RAG-deficient SCID patients. In 4 of 5 patients, the absence of recombination activity was associated with a complete B-cell differentiation arrest at the transition from cytoplasmic (Cy) Igmu(-) pre-B-I cells to CyIgmu(+) pre-B-II cells. However, the fifth patient showed low frequencies of precursor B cells with CyIgmu and surface membrane IgM, in line with the partial recombination activity of the patient's mutated RAG gene and the detection of in-frame Ig gene rearrangements in BM.     

Risk of non-Hodgkin lymphoma (NHL) in relation to germline variation in DNA repair and related genes

Chromosomal translocations, insertions, and deletions are common early events in non-Hodgkin lymphoma (NHL) carcinogenesis, and implicated in their formation are endogenous processes involved in antigen-receptor diversification, such as V(D)J recombination. DNA repair genes respond to the double- and single-strand breaks induced by these processes and may influence NHL etiology. We examined 34 genetic variants in 19 genes within or related to 5 DNA repair pathways among 1172 cases and 982 matched controls who participated in a population-based NHL study in Los Angeles, Seattle, Detroit, and Iowa from 1998 to 2000. Cases were more likely than controls to have the RAG1 820 R/R (odds ratio [OR] = 2.7; 95% confidence interval [CI] = 1.4 to 5.0) than Lys/Lys genotypes, with evidence of a gene dosage effect (P trend < .001), and less likely to have the LIG4 (DNA ligase IV) 9 Ile/Ile (OR = 0.5; 95% CI = 0.3 to 0.9) than T/T genotype (P trend = .03) in the nonhomologous end joining (NHEJ)/V(D)J pathway. These NHEJ/V(D)J-related gene variants represent promising candidates for further studies of NHL etiology and require replication in other studies.     

An amphioxus RAG1-like DNA fragment encodes a functional central domain of vertebrate core RAG1

The highly diversified repertoire of antigen receptors in the vertebrate immune system is generated via proteins encoded by the recombination activating genes (RAGs) RAG1 and RAG2 by a process known as variable, diversity, and joining [V(D)J] gene recombination. Based on the study of vertebrate RAG proteins, many hypotheses have been proposed regarding the origin and evolution of RAG. This issue remains unresolved, leaving a significant gap in our understanding of the evolution of adaptive immunity. Here, we show that the amphioxus genome contains an ancient RAG1-like DNA fragment (bfRAG1L) that encodes a virus-related protein that is much shorter than vertebrate RAG1 and harbors a region homologous to the central domain of core RAG1 (cRAG1). bfRAG1L also contains an unexpected retroviral type II nuclease active site motif, DX_N(D/E)XK, and is capable of degrading both DNA and RNA. Moreover, bfRAG1L shares important functional properties with the central domain of cRAG1, including interaction with RAG2 and localization to the nucleus. Remarkably, the reconstitution of bfRAG1L into a cRAG1-like protein yielded an enzyme capable of recognizing recombination signal sequences and performing V(D)J recombination in the presence of mouse RAG2. Moreover, this reconstituted cRAG1-like protein could mediate the assembly of antigen receptor genes in RAG1-deficient mice. Together, our results demonstrate that amphioxus bfRAG1L encodes a protein that is functionally equivalent to the central domain of cRAG1 and is well prepared for further evolution to mediate V(D)J recombination. Thus, our findings provide unique insights into the evolutionary origin of RAG1.The adaptive immune system, with the high degree of antigen receptor diversity, gives the host the potential to recognize and evade any invader. Antigen receptor genes are assembled from variable (V), diversity (D), and joining (J) gene segments in a somatic DNA rearrangement reaction termed V(D)J recombination (1, 2), a process mediated by the recombination signal sequences (RSSs) and the proteins encoded by the recombination activating genes (RAGs) RAG1 and RAG2. RSSs that flank the V, D, and J gene segments consist of well conserved heptamer and nonamer sequences that are separated by relatively nonconserved spacer region of 12 or 23 base pairs (12-RSS or 23-RSS, respectively) (3), whereas RAG1 and RAG2 (thereafter referred to as RAG) proteins are responsible for sequence-specific DNA recognition and DNA cleavage. During V(D)J recombination, RAG1 binds to nonamer through its nonamer binding domain (NBD) and RAG2 acts as a regulator for the formation of RSS/RAG complex. Double-strand breaks are then introduced at the heptamer-coding flank border by the RAG1 enzymatic activity, generating covalently sealed hairpin coding ends and blunt 5′-phosphorylated signal ends. Finally, the signal and coding ends are repaired by nonhomologous end joining (NHEJ) machinery (4, 5).RAG-mediated V(D)J recombination is the main mechanism for generating antigen receptor diversity and is the hallmark of jawed vertebrate-specific adaptive immunity (6). Although SpRAG1L and SpRAG2L, a pair of RAG-like genes from the invertebrate purple sea urchin (Strongylocentrotus purpuratus), have been shown to represent ancient homologs of vertebrate RAG1 and RAG2 (7), the earliest known RAG-mediated adaptive immune system was demonstrated in cartilaginous fish, e.g., the horned shark (8). Thus far, no evidence has been provided that supports the existence of functional RAG in either invertebrates or jawless vertebrates.It has been reported that the hypothetical gene bfRAG1L, from the invertebrate amphioxus (Branchiostoma floridae), is a vertebrate RAG1-like DNA fragment (9). Here, we combined bioinformatic and experimental approaches to explore the relationship between bfRAG1L and vertebrate mouse RAG1 from basic structure to recombination function. We showed that bfRAG1L contains a retroviral type II nuclease active site motif, DX_N(D/E)XK, and is capable of degrading both DNA and RNA. Moreover, bfRAG1L shares important functional properties with the central domain of cRAG1, and the reconstitution of bfRAG1L into a cRAG1-like protein yielded an enzyme capable of recognizing RSSs and performing V(D)J recombination together with mouse RAG2. Moreover, this reconstituted cRAG1-like protein could mediate antigen receptor gene assembly in RAG1-deficient mice. Our findings suggest that the bfRAG1L DNA fragment is likely an ancient predecessor of vertebrate RAG1 and, thus, provide unique insights into the evolutionary origin of RAG1.     

The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2

Recombination activating gene (RAG) 1 and RAG2 together catalyze V(D)J gene rearrangement in lymphocytes as the first step in the assembly and maturation of antigen receptors. RAG2 contains a plant homeodomain (PHD) near its C terminus (RAG2-PHD) that recognizes histone H3 methylated at lysine 4 (H3K4me) and influences V(D)J recombination. We report here crystal structures of RAG2-PHD alone and complexed with five modified H3 peptides. Two aspects of RAG2-PHD are unique. First, in the absence of the modified peptide, a peptide N-terminal to RAG2-PHD occupies the substrate-binding site, which may reflect an autoregulatory mechanism. Second, in contrast to other H3K4me3-binding PHD domains, RAG2-PHD substitutes a carboxylate that interacts with arginine 2 (R2) with a Tyr, resulting in binding to H3K4me3 that is enhanced rather than inhibited by dimethylation of R2. Five residues involved in histone H3 recognition were found mutated in severe combined immunodeficiency (SCID) patients. Disruption of the RAG2-PHD structure appears to lead to the absence of T and B lymphocytes, whereas failure to bind H3K4me3 is linked to Omenn Syndrome. This work provides a molecular basis for chromatin-dependent gene recombination and presents a single protein domain that simultaneously recognizes two distinct histone modifications, revealing added complexity in the read-out of combinatorial histone modifications.     

Radiosensitive SCID patients with Artemis gene mutations show a complete B-cell differentiation arrest at the pre-B-cell receptor checkpoint in bone marrow

Severe combined immunodeficiency disease (SCID) can be immunologically classified by the absence or presence of T, B, and natural killer (NK) cells. About 30% of T(-)B(-)NK(+) SCID patients carry mutations in the recombination activating genes (RAG). Some T(-)B(-)NK(+) SCID patients without RAG gene mutations are sensitive to ionizing radiation, and several of these radiosensitive (RS) SCID patients were recently shown to have large deletions or truncation mutations in the Artemis gene, implying a role for Artemis in DNA double-strand break (dsb) repair. We identified 5 RS-SCID patients without RAG gene mutations, 4 of them with Artemis gene mutations. One patient had a large genomic deletion, but the other 3 patients carried simple missense mutations in conserved amino acid residues in the SNM1 homology domain of the Artemis protein. Extrachromosomal V(D)J recombination assays showed normal and precise signal joint formation, but inefficient coding joint formation in fibroblasts of these patients, which could be complemented by the wild-type Artemis gene. The cells containing the missense mutations in the SNM1 homology domain had the same recombination phenotype as the cells with the large deletion, indicating that these amino acid residues are indispensable for Artemis function. Immunogenotyping and immunophenotyping of bone marrow samples of 2 RS-SCID patients showed the absence of complete V(H)-J(H) gene rearrangements and consequently a complete B-cell differentiation arrest at the pre-B-cell receptor checkpoint-that is, at the transition from CyIgmu(-) pre-B-I cells to CyIgmu(+) pre-B-II cells. The completeness of this arrest illustrates the importance of Artemis at this stage of lymphoid differentiation.     

Genetic evidence that the RAG1 protein directly participates in V(D)J recombination through substrate recognition.

RAG1 protein is essential for the activation of V(D)J recombination in developing lymphocytes (V, variable; D, diversity; J, joining). However, it has not been determined whether its role involves substrate recognition and catalysis. A single amino acid substitution mutation in the RAG1 gene has now been identified that renders its activity sensitive to the sequence of the coding region abutting the heptamer site in the recombination signal sequence. These results strongly imply that RAG1 interacts directly with DNA.