The Usage of Human IGHJ Genes Follows a Particular Non-random Selection: The Recombination Signal Sequence May Affect the Usage of Human IGHJ Genes.

Bin Shi,Danhua Su,Juan Pan,Xinsheng Yao,Xiaoyan He,Suhong Sun,Long Ma,Qingqing Ma,Xiaoheng Dong,Xiaomei Wang,Jiang Yu

doi:10.3389/fgene.2020.524413

Abstract

The formation of the B cell receptor (BCR) heavy chain variable region is derived from the germline V(D)J gene rearrangement according to the “12/23” rule and the “beyond 12/23” rule. The usage frequency of each V(D)J gene in the peripheral BCR repertoires is related to the initial recombination, self-tolerance selection, and the clonal proliferative response. However, their specific differences and possible mechanisms are still unknown. We analyzed in-frame and out-of-frame BCR-H repertoires from human samples with normal physiological and various pathological conditions by high-throughput sequencing. Our results showed that IGHJ gene frequency follows a similar pattern which is previously known, where IGHJ4 is used at high frequency (>40%), IGHJ6/IGHJ3/IGHJ5 is used at medium frequencies (10∼20%), and IGH2/IGHJ1 is used at low frequency (<4%) under whether normal physiological or various pathological conditions. However, our analysis of the recombination signal sequences suggested that the conserved non-amer and heptamer and certain 23 bp spacer length may affect the initial IGHD-IGHJ recombination, which results in different frequencies of IGHJ genes among the initial BCR-H repertoire. Based on this “initial repertoire,” we recommend that re-evaluation and further investigation are needed when analyzing the significance and mechanism of IGHJ gene frequency in self-tolerance selection and the clonal proliferative response.

Highlights

The diversity of the initial vertebrate B cell receptor (BCR) originates from the recombination of multiple germline genes (V(D)J) and insertion and deletion during the recombination process
The order of frequency of IGHJ genes was IGHJ4 > IGHJ6 > IGHJ3 > IGHJ5 > IGHJ2 > IGHJ1, while out-of-frame sequences followed an order of IGHJ4 > IGHJ6 > IGHJ5 > IGHJ3 > IGHJ1 > IGHJ2 (Figure 1A and Supplementary Table 1)
We analyzed the ratio of unique to total sequences of each IGHJ gene and found no differences in 6 IGHJ gene families (Supplementary Tables 1, 2, and Figure 2), which suggests that the multiplex PCR library and the experimental system of high-throughput sequencing (HTS) did not show obvious bias. These results indicate that IGHJ gene frequency follows a similar pattern where IGHJ4 is used at high frequency (>40%), IGHJ6/IGHJ3/IGHJ5 is used at medium frequencies (10∼20%), and IGH2/IGHJ1 is used at low frequencies (

Summary

Introduction

The diversity of the initial vertebrate B cell receptor (BCR) originates from the recombination of multiple germline genes (V(D)J) and insertion and deletion during the recombination process. Compared with RSSs with one or more base mutations, the corresponding gene subfamily of RSSs with a consensus heptamer/non-amer (conserved) has preferred usage (Hesse et al, 1987; Akamatsu et al, 1994; Ramsden et al, 1996; Steen et al, 1997; Larijani et al, 1999). The usage frequency of the corresponding gene segment will be affected when the lengths of the 12 bp spacer/23 bp spacer in RSSs increase or decrease (Akamatsu et al, 1994; Ramsden et al, 1996; Steen et al, 1997) and when the base sequences of the 12 bp spacer/23 bp spacer in RSS change (Fanning et al, 1996; Nadel et al, 1998; Montalbano et al, 2003). Expression level of transcription factors and changes in chromatin structure may influence individual V gene rearrangement frequency (Feeney et al, 2004)

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Conclusion