Sequence and Characterization of the Ig Heavy Chain Constant and Partial Variable Region of the Mouse Strain 129S1

Abstract

Although the entire mouse genome has been sequenced, there remain challenges concerning the elucidation of particular complex and polymorphic genomic loci. In the murine Igh locus, different haplotypes exist in different inbred mouse strains. For example, the Ighb haplotype sequence of the Mouse Genome Project strain C57BL/6 differs considerably from the Igha haplotype of BALB/c, which has been widely used in the analyses of Ab responses. We have sequenced and annotated the 3′ half of the Igha locus of 129S1/SvImJ, covering the CH region and approximately half of the VH region. This sequence comprises 128 VH genes, of which 49 are judged to be functional. The comparison of the Igha sequence with the homologous Ighb region from C57BL/6 revealed two major expansions in the germline repertoire of Igha. In addition, we found smaller haplotype-specific differences like the duplication of five VH genes in the Igha locus. We generated a VH allele table by comparing the individual VH genes of both haplotypes. Surprisingly, the number and position of DH genes in the 129S1 strain differs not only from the sequence of C57BL/6 but also from the map published for BALB/c. Taken together, the contiguous genomic sequence of the 3′ part of the Igha locus allows a detailed view of the recent evolution of this highly dynamic locus in the mouse.

The mouse antibody heavy chain repertoire is germline-focused and highly variable between inbred strains

“…php). Subsequently, half of the heavy chain IGHV gene locus of the 129/Sv mouse strain was sequenced, providing additional allelic variants [22]. Studies to further clarify the immunoglobulin genes of different mouse strains then appear to have stopped.…”

Chapter 1 Cis‐Regulatory Elements and Epigenetic Changes Control Genomic Rearrangements of the IgH Locus

“…These V H gene families are partially interspersed with one another but, depending on position, can be divided into proximal (3′ part of the V H cluster, close to IgH-D region, for example, V H 7183), intermediate (e.g., V H S107), and distal (5′ part of the V H cluster, distant from IgH-D region, for example, V H J558) families. 3′ of the V H elements, separated by ~90 kb, lie 10-15 D segments (Retter et al, 2007;Ye, 2004) followed by 4 J H elements. Because to the uniform transcriptional orientation of V, D, and J segments, V(D)J recombination events at the IgH locus result in deletion of the intervening sequence.…”

Highly sensitive and unbiased approach for elucidating antibody repertoires

“…There are 100s of V H s in the several megabase distal portion of the IgH, with the number varying substantially in certain mouse strains (4). The V H s lie ∼100 kb upstream from a 50-kb region containing 13 D H s, which is followed several kilobases downstream by a 2-kb region containing four J H s. The IgH constant region (C H ) exons lie downstream of the J H s. After assembly of a V H DJ H exon, transcription initiates upstream of the V H and terminates downstream of the C H exons, with V(D)J and C H portions being fused into the ultimate IgH messenger RNA (mRNA) via splicing of the primary transcript.…”