Clonally stable V\u03ba allelic choice instructs Ig\u03ba repertoire

Rena Levin-Klein,Anne E Corcoran,Michal Lichtenstein,Louise S Matheson,Shira Fraenkel,Osnat Bartok,Sebastian Kadener,Yuval Nevo,Yehudit Bergman,Howard Cedar

doi:10.1038/ncomms15575

Rena Levin-Klein, Anne E Corcoran + Show 8 more

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https://doi.org/10.1038/ncomms15575

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Abstract

Although much has been done to understand how rearrangement of the Igκ locus is regulated during B-cell development, little is known about the way the variable (V) segments themselves are selected. Here we show, using B6/Cast hybrid pre-B-cell clones, that a limited number of V segments on each allele is stochastically activated as characterized by the appearance of non-coding RNA and histone modifications. The activation states are clonally distinct, stable across cell division and developmentally important in directing the Ig repertoire upon differentiation. Using a new approach of allelic ATAC-seq, we demonstrate that the Igκ V alleles have differential chromatin accessibility, which may serve as the underlying basis of clonal maintenance at this locus, as well as other instances of monoallelic expression throughout the genome. These findings highlight a new level of immune system regulation that optimizes gene diversity.

Highlights

Much has been done to understand how rearrangement of the Igk locus is regulated during B-cell development, little is known about the way the variable (V) segments themselves are selected
We first chose a single clone (E9-3) and carried out anti-histone H3Ac ChIP, which was assayed by PCR analysis of various V segments within the k locus, using polymorphisms at restriction-enzyme binding sites to distinguish between the alleles (Fig. 1a)
The data we have presented suggest that while the choice of Vs on each allele is mainly stochastic, some sites appear to have a fixed bias for either B6 or Cast, suggesting that genetic factors may play a role in this choosing process. To address this question in a general manner, we carried out principal component analysis (PCA) on the ncRNA spectrum measured in several different pre-B-cell populations (Fig. 3), Strikingly, we found that all the individual clones have ncRNA patterns far removed from the profile observed in a pool of pre-B cells derived from bone marrow

Summary

Introduction

Much has been done to understand how rearrangement of the Igk locus is regulated during B-cell development, little is known about the way the variable (V) segments themselves are selected. Using a new approach of allelic ATAC-seq, we demonstrate that the Igk V alleles have differential chromatin accessibility, which may serve as the underlying basis of clonal maintenance at this locus, as well as other instances of monoallelic expression throughout the genome These findings highlight a new level of immune system regulation that optimizes gene diversity. The results indicate that each parental chromosome independently activates a select number of V segments Once chosen, these activity states are maintained in clonal populations probably through their highly stable accessible chromatin structure. In the case of the Igk locus, this ‘choice’ of V segments seems to generate alternate recombination patterns on each allele, providing a mechanism for enhancing the chances of each B cell to produce functional antibodies This same chromatin-based model may serve as the basis for the maintenance of differential expression at a large number of monoallelic loci present in the genome

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