The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

摘要

Chromatin organization plays an important role in genome function. Chro-matin has been shown to contain loops and rosette-like structures, and thesestructures influence gene expression over large genomic distances, forexample by bringing into proximity enhancer and promoter regions. Theimmunoglobulin heavy- and light-chain genes are known to undergo rear-rangement in an orderly manner during development, starting from the earli-est distinctive B-cell lineage cells (pre-pro-B cells), to the pro-B cells andthe mature B cells. However, it has been unclear how the chromatin fiberreorganizes prior to DNA recombination. This study analyzes the topogra-phy of the murine immunoglobulin heavy-chain locus (Igh), which consistsof the variable (VH), diversity (DH), joining (JH), and constant (CH) regions,using spectral high-precision epifluorescence microscopy. An anchormarker that binds to a region downstream of the Igh locus and 1 1 Igh-spe-cific markers were used to determine spatial distance distributions during B-cell development (Fig. 1).Data showed that during the differentiation of pre-pro-B cells to pro-B cells,the Igh locus rearranges itself such that the VH regions all have similar dis-tances to the DHJH elements, which is important because the large numberof VH regions spanning over 2 Mbp of genomic distance need to encounterDH elements with similar probabilities. This involves folding of the Ighfiber, allowing the 2-Mbp genomic VH region to be packed as bundles ofloops which gives it valuable access to the DHJH elements. This process wasproposed to happen during early B-cell development to permit VH regions torearrange with frequencies independent of genomic distance. In general, Ighof pre-pro B cells is extensively compacted compared with that of nonlym-phoid cells and becomes even more compacted in pro-B cells.Igh locus topology did not fit into the self-avoiding random walk or worm-like chain models. Igh topology of pre-pro-B cells appears to be consistentwith the MLS model, which assumes the presence of 1- to 2-Mbp rosettesconnected by variable-sized linkers, and exhibits relatively fixed positions.In contrast, pro-B cells show more flexibility. The authors conclude thatlong-range genomic interactions in pro-B cells are dependent on Igh topol-ogy.