Recruitment of RAG1 and RAG2 to Chromatinized DNA during V(D)J Recombination

EBF1, PAX5, and MYC: regulation on B cell development and association with hematologic neoplasms

During lymphocyte development, a diverse repertoire of lymphocyte antigen receptors is produced to battle against pathogens, which is the basis of adaptive immunity. The diversity of the lymphocyte antigen receptors arises primarily from recombination-activated gene (RAG) protein-mediated V(D)J rearrangement in early lymphocytes. Furthermore, transcription factors (TFs), such as early B cell factor 1 (EBF1), paired box gene 5 (PAX5), and proto-oncogene myelocytomatosis oncogene (MYC), play critical roles in regulating recombination and maintaining normal B cell development. Therefore, the aberrant expression of these TFs may lead to hematologic neoplasms.

Genetic and epigenetic determinants of B-cell lymphoma evolution

PURPOSE OF REVIEW

The success of targeted therapies fostered the development of increasingly specific and effective therapeutics for B-cell malignancies. However, cancer plasticity facilitates disease relapse, whereby intratumoral heterogeneity fuels tumor evolution into a more aggressive and resistant form. Understanding cancer heterogeneity and the evolutionary processes underlying disease relapse is key for overcoming this limitation of current treatment strategies. In the present review, we delineate the current understanding of cancer evolution and the advances in both genetic and epigenetic fields, with a focus on non-Hodgkin B-cell lymphomas.

RECENT FINDINGS

The use of massively parallel sequencing has provided insights into tumor heterogeneity, allowing determination of intratumoral genetic and epigenetic variability and identification of cancer driver mutations and (epi-)mutations. Increased heterogeneity prior to treatment results in faster disease relapse, and in many cases studying pretreatment clonal admixtures predicts the future evolutionary trajectory of relapsed disease.

SUMMARY

Understanding the mechanisms underlying tumor heterogeneity and evolution provides valuable tools for the design of therapy within an evolutionary framework. This framework will ultimately aid in accurately predicting the evolutionary paths of B-cell malignancies, thereby guiding therapeutic strategies geared at directly anticipating and addressing cancer evolution.

RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2

The RAG1/RAG2 endonuclease initiates V(D)J recombination at antigen receptor loci but also binds to thousands of places outside of these loci. RAG2 localizes directly to lysine 4 trimethylated histone 3 (H3K4me3) through a plant homeodomain (PHD) finger. The relative contribution of RAG2-dependent and RAG1-intrinsic mechanisms in determining RAG1 binding patterns is not known. Through analysis of deep RAG1 ChIP-seq data, we provide a quantitative description of the forces underlying genome-wide targeting of RAG1. Surprisingly, sequence-specific DNA binding contributes minimally to RAG1 targeting outside of antigen receptor loci. Instead, RAG1 binding is driven by two distinct modes of interaction with chromatin: the first is driven by H3K4me3, promoter-focused and dependent on the RAG2 PHD, and the second is defined by H3K27Ac, enhancer-focused and dependent on ‘non-core’ portions of RAG1. Based on this and additional chromatin and genomic features, we formulated a predictive model of RAG1 targeting to the genome. RAG1 binding sites predicted by our model correlate well with observed patterns of RAG1-mediated breaks in human pro-B acute lymphoblastic leukemia. Overall, this study provides an integrative model for RAG1 genome-wide binding and off-target activity and reveals a novel role for the RAG1 non-core region in RAG1 targeting.

Human RAG mutations: biochemistry and clinical implications

The recombination-activating gene 1 (RAG1) and RAG2 proteins initiate the V(D)J recombination process, which ultimately enables the generation of T cells and B cells with a diversified repertoire of antigen-specific receptors. Mutations of the RAG genes in humans are associated with a broad spectrum of clinical phenotypes, ranging from severe combined immunodeficiency to autoimmunity. Recently, novel insights into the phenotypic diversity of this disease have been provided by resolving the crystal structure of the RAG complex, by developing novel assays to test recombination activity of the mutant RAG proteins and by characterizing the molecular and cellular basis of immune dysregulation in patients with RAG deficiency.