The 3D Architecture and Dynamics of the Immunoglobin Heavy-Chain and other Loci and its Functional Implications for Genome Organization

The general 3D architecture of the immunoglobin heavy-chain (Igh) and other loci was determined by a novel interdisciplinary combination of high-resolution FISH and high-resolution epifluorescence spectral distance microscopy with analytical analysis, computer simulations, as well as trilateration (Cell 133, 265-279, 2008). The Igh locus is organized into distinct regions that contain multiple variable (VH), diversity (DH), joining (JH) and constant (CH) coding elements. Determination of distance distributions between genomic markers across the entire locus showed that the Igh locus is organized into compartments consisting of small loops separated by linkers with in detail dynamic functional relevance: VH, DH, JH, and CH elements showed striking conformational changes involving VH and DH-JH elements during early B cell development, culminating in a merger and juxtaposition of the entire repertoire of VH regions to the DH elements in pro-B cells allowing long-range genomic interactions with relatively high frequency. This is in agreement with our recent study of the Prader-Willi/Angelmann region using a similar approach (Differentiation 76, 66-82, 2008) and in agreement with the Multi-Loop-Subcompartment (MLS) model of chromosome organization predicting 60-150 kbp loop aggregates separated by a similar linker (Knoch, ISBN 3-00-009959-X, 2002). With a new technology we are also able to proof, that this holds for other loci as well. Synopsis with previous spatial distance measurement studies and combination with sequence correlation analysis of the DNA sequence, fine-structure multi-scaling analysis of the chromatin fiber topology or in vivo morphology of entire cell nuclei, electron microscopy of chromosome spreading studies and even the diffusion behaviour within the cell nucleus, are all suggesting such an MLS architecture. This framework reveals a consistent picture of genome organization joining structural and dynamical aspects ranging from the DNA sequence to the entire nuclear morphology level with functional aspects of gene location and regulation. Many previously contradictory viewpoints are resolved by this framework as well. Consequently, the determination of the general 3D architecture of the Igh and other loci has beyond its major functional relevance, huge implications for the understanding of the entire genome understanding in a holistic system-biological manner.