Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination

Abstract

We show that the physical distribution of nucleosomes at antigen receptor loci is subject to regulated cell type-specific and lineagespecific positioning and correlates with the accessibility of these gene segments to recombination. At the Ig heavy chain locus (IgH), a nucleosome in pro-B cells is generally positioned over each IgH variable (VH) coding segment, directly adjacent to the recombination signal sequence (RSS), placing the RSS in a position accessible to the recombination activating gene (RAG) recombinase. These changes result in establishment of a specific chromatin organization at the RSS that facilitates accessibility of the genomic DNA for the RAG recombinase. In contrast, in mouse embryonic fibroblasts the coding segment is depleted of nucleosomes, which instead cover the RSS, thereby rendering it inaccessible. Pro-T cells exhibit a pattern intermediate between pro-B cells and mouse embryonic fibroblasts. We also find large-scale variations of nucleosome density over hundreds of kilobases, delineating chromosomal domains within IgH, in a cell typedependent manner. These findings suggest that developmentally regulated changes in nucleosome location and occupancy, in addition to the known chromatin modifications, play a fundamental role in regulating V(D)J recombination. Nucleosome positioning-which has previously been observed to vary locally at individual enhancers and promoters-may be a more general mechanism by which cells can regulate the accessibility of the genome during development, at scales ranging from several hundred base pairs to many kilobases.T he diverse repertoire of antigen receptors in vertebrates is generated by an ordered series of somatic site-specific DNA rearrangement events, collectively termed V(D)J recombination. Antigen receptor genes are assembled from V, D, and J gene segments organized into seven different loci [T-cell receptor (TCR) α, β, γ, and δ, and Ig H, κ, and λ], each of which undergoes a series of recombination reactions to generate a functional TCR or B-cell receptor (BCR) (1, 2) Rearrangement is lineage-specific, such that BCR genes are fully rearranged only in B cells and TCR genes are assembled only in T cells. Rearrangement also occurs in a preferred temporal order. For example, at the human and murine IgH loci, joining of D to J segments precedes V to DJ joining, and IgH joining precedes joining at Igκ (or Igλ) (3). In addition, recombination at several loci shows "allelic exclusion": Functional VDJH or VJκ/Jλ joining occurs only on one allele (4).Recombination is initiated by the lymphocyte-specific recombination activating gene (RAG)1/RAG2 endonuclease. RAG1/2 cleaves at the recombination signal sequences (RSSs) flanking all antigen receptor gene segments. The consensus RSS consists of a heptamer sequence directly adjacent to the coding element and an A/T-rich nonamer separated from the heptamer by a spacer region of conserved length (12 or 23 bp) but relatively nonconserved sequence. The broken ends are then joined with the aid of DNA repair proteins,...

Nucleosome repositioning during differentiation of a human myeloid leukemia cell line

“…Our observation that, during HL-60/S4 differentiation, nucleosome loss and nucleosome gain affect gene expression asymmetrically (i.e., a clear association with nucleosome loss and a more complicated response to nucleosome gain) agrees with the concept that there are several different mechanisms by which nucleosome positioning can affect gene expression. Interestingly, these changes in nucleosome occupancy involve extended regions of one to several kb, which is different from previously considered single-nucleosome repositioning scenarios and parallels a similar effect recently found at the V(D)J recombination domains 48 The molecular mechanisms of the change of chromatin density in extended regions that we report here may be linked to chromatin compartmentalization in domains such as TADs (topologically associated domains), 49,50 which have been recently shown to be correlated with regions of differential chromatin accessibility 51 . An exploration of this idea may provide a direction for new studies.…”

Compound Heterozygous Mutations of IL2-Inducible T cell Kinase in a Swedish Patient: the Importance of Early Genetic Diagnosis

“…It is well known that both during immune cell differentiation and B or T cell activation, DNA methylation combined with the transcription factors play a vital role in the regulation of gene expression (78), which through DNA methylation of cytosines in the context of cytosineguanine dinucleotides (CpG), often located in clusters (CpG islands) within regulatory regions such as promoters and enhancers. Epigenetics is also thought to be essential for V(D)J rearrangement, and immunological memory (79,80) and recent studies have identified DNA methylation alterations in common variable immunodeficiency (CVID) (78), the Immunodeficiency, Centromere instability and Facial anomalies (ICF) (81,82) and ATM deficiency (83).…”

LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks

“…The DNA segment connecting two adjacent nucleosomes is referred to as a linker. Nucleosome positioning is critical to various biological processes, primarily because this precise positioning modulates the accessibility of underlying genomic sequence to DNA-binding proteins to regulate transcription (Liu M. et al , 2015; Schones et al , 2008; Tilgner et al , 2009; Whitehouse et al , 2007), genetic replication (Eaton et al , 2010; Liu et al , 2017; Vasseur et al , 2016), and recombination (Pulivarthy, 2016; Smagulova et al , 2011). Therefore, the identification of nucleosome positioning along genomic sequences may allow an in-depth understanding of various biological outcomes.…”