PMC:5118421 / 12042-15834 JSONTXT

{"project":"TEST0","denotations":[{"id":"27920779-108-113-3100221","span":{"begin":215,"end":216},"obj":"[\"8011289\"]"},{"id":"27920779-77-82-3100222","span":{"begin":296,"end":297},"obj":"[\"20805563\"]"},{"id":"27920779-80-86-3100223","span":{"begin":299,"end":301},"obj":"[\"23181829\", \"18677426\", \"18621685\", \"15968001\"]"},{"id":"27920779-193-198-3100224","span":{"begin":412,"end":413},"obj":"[\"20805563\"]"},{"id":"27920779-159-164-3100225","span":{"begin":575,"end":576},"obj":"[\"20805563\", \"25634361\", \"8011289\"]"},{"id":"27920779-164-170-3100226","span":{"begin":580,"end":582},"obj":"[\"7651532\"]"},{"id":"27920779-75-81-3100227","span":{"begin":3302,"end":3304},"obj":"[\"7651532\"]"}],"text":"AGY Ser Codons, but Not TCN Ser Codons, Are Enriched in Germline-Encoded CDR Sequences of IgV-Region Genes\nIt is well established that CDR Arg residues play a major role in specifying the nuclear reactivity of ANA (3). Moreover, in spontaneous SLE, many ANA arise by SHM of non-autoreactive Abs (1, 28–31), and this is often associated with the conversion of CDR germline-encoded AGY Ser codons into Arg codons (1). At the same time, germline IgVH, Vκ, and Vλ genes have unusually high frequencies of AGY Ser codons in CDRs, and this tendency holds for both mice and humans (1–3, 17).\nIf AGY Ser codon abundance in Ab CDRs were merely due to a selection pressure to preserve Ser residues among germline-encoded V-region genes, we would expect equally high frequencies of four other serine codons (TCN). However, CDR TCN codon abundance, as defined by observed/expected ratios, was inconsistent across mouse and human VH, Vκ, and Vλ genes, reaching only 2.3-fold more than expected in the most extreme case (mouse Vκ) and less than expected in mouse and human VH genes and mouse Vλ genes (Figure 1A). Moreover, in most cases, TCN abundance was higher in FRs than in CDRs. In contrast, AGY codons were far more abundant in CDRs than expected and consistently much more so than in FRs (Figure 1A). To avoid a bias in our analyses, we took expected frequencies from codon usage tables for mouse and human genes rather than the random expected frequency of 0.016 (1/61) for a given codon. This is because the TCG codon includes the rare CpG dinucleotide, so using 0.016 would inflate the expected cumulative frequency of TCN codons, thereby reducing observed/expected ratios for TCN.\nFigure 1 High frequencies of AGY, but not TCN Ser codons among germline-encoded CDR sequences of IgV-region genes. (A) Ratio observed/expected for AGY and TCN Ser codons in human and mouse IgV-region genes. Germline CDRs and FRs were defined using the Kabat numbering system. Expected ratio was defined by frequencies of 52,926 mouse codons and 40,662,582 human codons at http://www.kazusa.or.jp/codon/. (B). Total numbers of AGY or TCN Ser codons per germline-encoded CDR sequences. Box plots were generated as indicated in Section “Materials and Methods.” Briefly, the center line indicates the median; box limits indicate the 25th and 75th percentiles; whiskers extend to minimum and maximum values, and crosses represent sample means. Notches represent the 95% confidence interval for each median. (C) Donut graphs represent the number of CDR1\u00262 AGY Ser codons minus the number of TCN Ser codons for a given gene. The gray, white, and black areas denote the number of IgV genes in which AGY Ser codon numbers are greater than, equal to, or less than TCN codon numbers respectively. Number of sequences indicated in center. p values were determined using a two-tailed paired t-test. ***p \u003c 0.0001. In addition to comparing observed/expected ratios for AGY and TCN codons, we also compared absolute numbers of these codons in mouse and human germline VH, Vκ, and Vλ genes. Despite a greater number of possible TCN codons, the bias favoring AGY Ser codons was still evident in all three major families of V genes for both species (Figures 1B,C). These abundance data are in agreement with data reported by Wagner et al. (17), showing that CDR AGY codons outnumber TCN codons at most CDR positions. Finally, the serine codon bias was not restricted to the idiosyncrasies of the Kabat CDR/FR definitions used in our analyses because it also applied to CDRs defined by the IMGT system (Figure S1 in Supplementary Material). Collectively, these results show that high frequencies of germline AGY serine codons in CDRs cannot be explained solely by a selection pressure favoring germline-encoded CDR serine residues."}

{"project":"2_test","denotations":[{"id":"27920779-8011289-34707944","span":{"begin":215,"end":216},"obj":"8011289"},{"id":"27920779-20805563-34707945","span":{"begin":296,"end":297},"obj":"20805563"},{"id":"27920779-23181829-34707946","span":{"begin":299,"end":301},"obj":"23181829"},{"id":"27920779-18677426-34707946","span":{"begin":299,"end":301},"obj":"18677426"},{"id":"27920779-18621685-34707946","span":{"begin":299,"end":301},"obj":"18621685"},{"id":"27920779-15968001-34707946","span":{"begin":299,"end":301},"obj":"15968001"},{"id":"27920779-20805563-34707947","span":{"begin":412,"end":413},"obj":"20805563"},{"id":"27920779-20805563-34707948","span":{"begin":575,"end":576},"obj":"20805563"},{"id":"27920779-25634361-34707948","span":{"begin":575,"end":576},"obj":"25634361"},{"id":"27920779-8011289-34707948","span":{"begin":575,"end":576},"obj":"8011289"},{"id":"27920779-7651532-34707949","span":{"begin":580,"end":582},"obj":"7651532"},{"id":"27920779-7651532-34707950","span":{"begin":3302,"end":3304},"obj":"7651532"}],"text":"AGY Ser Codons, but Not TCN Ser Codons, Are Enriched in Germline-Encoded CDR Sequences of IgV-Region Genes\nIt is well established that CDR Arg residues play a major role in specifying the nuclear reactivity of ANA (3). Moreover, in spontaneous SLE, many ANA arise by SHM of non-autoreactive Abs (1, 28–31), and this is often associated with the conversion of CDR germline-encoded AGY Ser codons into Arg codons (1). At the same time, germline IgVH, Vκ, and Vλ genes have unusually high frequencies of AGY Ser codons in CDRs, and this tendency holds for both mice and humans (1–3, 17).\nIf AGY Ser codon abundance in Ab CDRs were merely due to a selection pressure to preserve Ser residues among germline-encoded V-region genes, we would expect equally high frequencies of four other serine codons (TCN). However, CDR TCN codon abundance, as defined by observed/expected ratios, was inconsistent across mouse and human VH, Vκ, and Vλ genes, reaching only 2.3-fold more than expected in the most extreme case (mouse Vκ) and less than expected in mouse and human VH genes and mouse Vλ genes (Figure 1A). Moreover, in most cases, TCN abundance was higher in FRs than in CDRs. In contrast, AGY codons were far more abundant in CDRs than expected and consistently much more so than in FRs (Figure 1A). To avoid a bias in our analyses, we took expected frequencies from codon usage tables for mouse and human genes rather than the random expected frequency of 0.016 (1/61) for a given codon. This is because the TCG codon includes the rare CpG dinucleotide, so using 0.016 would inflate the expected cumulative frequency of TCN codons, thereby reducing observed/expected ratios for TCN.\nFigure 1 High frequencies of AGY, but not TCN Ser codons among germline-encoded CDR sequences of IgV-region genes. (A) Ratio observed/expected for AGY and TCN Ser codons in human and mouse IgV-region genes. Germline CDRs and FRs were defined using the Kabat numbering system. Expected ratio was defined by frequencies of 52,926 mouse codons and 40,662,582 human codons at http://www.kazusa.or.jp/codon/. (B). Total numbers of AGY or TCN Ser codons per germline-encoded CDR sequences. Box plots were generated as indicated in Section “Materials and Methods.” Briefly, the center line indicates the median; box limits indicate the 25th and 75th percentiles; whiskers extend to minimum and maximum values, and crosses represent sample means. Notches represent the 95% confidence interval for each median. (C) Donut graphs represent the number of CDR1\u00262 AGY Ser codons minus the number of TCN Ser codons for a given gene. The gray, white, and black areas denote the number of IgV genes in which AGY Ser codon numbers are greater than, equal to, or less than TCN codon numbers respectively. Number of sequences indicated in center. p values were determined using a two-tailed paired t-test. ***p \u003c 0.0001. In addition to comparing observed/expected ratios for AGY and TCN codons, we also compared absolute numbers of these codons in mouse and human germline VH, Vκ, and Vλ genes. Despite a greater number of possible TCN codons, the bias favoring AGY Ser codons was still evident in all three major families of V genes for both species (Figures 1B,C). These abundance data are in agreement with data reported by Wagner et al. (17), showing that CDR AGY codons outnumber TCN codons at most CDR positions. Finally, the serine codon bias was not restricted to the idiosyncrasies of the Kabat CDR/FR definitions used in our analyses because it also applied to CDRs defined by the IMGT system (Figure S1 in Supplementary Material). Collectively, these results show that high frequencies of germline AGY serine codons in CDRs cannot be explained solely by a selection pressure favoring germline-encoded CDR serine residues."}

{"project":"MyTest","denotations":[{"id":"27920779-8011289-34707944","span":{"begin":215,"end":216},"obj":"8011289"},{"id":"27920779-20805563-34707945","span":{"begin":296,"end":297},"obj":"20805563"},{"id":"27920779-23181829-34707946","span":{"begin":299,"end":301},"obj":"23181829"},{"id":"27920779-18677426-34707946","span":{"begin":299,"end":301},"obj":"18677426"},{"id":"27920779-18621685-34707946","span":{"begin":299,"end":301},"obj":"18621685"},{"id":"27920779-15968001-34707946","span":{"begin":299,"end":301},"obj":"15968001"},{"id":"27920779-20805563-34707947","span":{"begin":412,"end":413},"obj":"20805563"},{"id":"27920779-20805563-34707948","span":{"begin":575,"end":576},"obj":"20805563"},{"id":"27920779-25634361-34707948","span":{"begin":575,"end":576},"obj":"25634361"},{"id":"27920779-8011289-34707948","span":{"begin":575,"end":576},"obj":"8011289"},{"id":"27920779-7651532-34707949","span":{"begin":580,"end":582},"obj":"7651532"},{"id":"27920779-7651532-34707950","span":{"begin":3302,"end":3304},"obj":"7651532"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"AGY Ser Codons, but Not TCN Ser Codons, Are Enriched in Germline-Encoded CDR Sequences of IgV-Region Genes\nIt is well established that CDR Arg residues play a major role in specifying the nuclear reactivity of ANA (3). Moreover, in spontaneous SLE, many ANA arise by SHM of non-autoreactive Abs (1, 28–31), and this is often associated with the conversion of CDR germline-encoded AGY Ser codons into Arg codons (1). At the same time, germline IgVH, Vκ, and Vλ genes have unusually high frequencies of AGY Ser codons in CDRs, and this tendency holds for both mice and humans (1–3, 17).\nIf AGY Ser codon abundance in Ab CDRs were merely due to a selection pressure to preserve Ser residues among germline-encoded V-region genes, we would expect equally high frequencies of four other serine codons (TCN). However, CDR TCN codon abundance, as defined by observed/expected ratios, was inconsistent across mouse and human VH, Vκ, and Vλ genes, reaching only 2.3-fold more than expected in the most extreme case (mouse Vκ) and less than expected in mouse and human VH genes and mouse Vλ genes (Figure 1A). Moreover, in most cases, TCN abundance was higher in FRs than in CDRs. In contrast, AGY codons were far more abundant in CDRs than expected and consistently much more so than in FRs (Figure 1A). To avoid a bias in our analyses, we took expected frequencies from codon usage tables for mouse and human genes rather than the random expected frequency of 0.016 (1/61) for a given codon. This is because the TCG codon includes the rare CpG dinucleotide, so using 0.016 would inflate the expected cumulative frequency of TCN codons, thereby reducing observed/expected ratios for TCN.\nFigure 1 High frequencies of AGY, but not TCN Ser codons among germline-encoded CDR sequences of IgV-region genes. (A) Ratio observed/expected for AGY and TCN Ser codons in human and mouse IgV-region genes. Germline CDRs and FRs were defined using the Kabat numbering system. Expected ratio was defined by frequencies of 52,926 mouse codons and 40,662,582 human codons at http://www.kazusa.or.jp/codon/. (B). Total numbers of AGY or TCN Ser codons per germline-encoded CDR sequences. Box plots were generated as indicated in Section “Materials and Methods.” Briefly, the center line indicates the median; box limits indicate the 25th and 75th percentiles; whiskers extend to minimum and maximum values, and crosses represent sample means. Notches represent the 95% confidence interval for each median. (C) Donut graphs represent the number of CDR1\u00262 AGY Ser codons minus the number of TCN Ser codons for a given gene. The gray, white, and black areas denote the number of IgV genes in which AGY Ser codon numbers are greater than, equal to, or less than TCN codon numbers respectively. Number of sequences indicated in center. p values were determined using a two-tailed paired t-test. ***p \u003c 0.0001. In addition to comparing observed/expected ratios for AGY and TCN codons, we also compared absolute numbers of these codons in mouse and human germline VH, Vκ, and Vλ genes. Despite a greater number of possible TCN codons, the bias favoring AGY Ser codons was still evident in all three major families of V genes for both species (Figures 1B,C). These abundance data are in agreement with data reported by Wagner et al. (17), showing that CDR AGY codons outnumber TCN codons at most CDR positions. Finally, the serine codon bias was not restricted to the idiosyncrasies of the Kabat CDR/FR definitions used in our analyses because it also applied to CDRs defined by the IMGT system (Figure S1 in Supplementary Material). Collectively, these results show that high frequencies of germline AGY serine codons in CDRs cannot be explained solely by a selection pressure favoring germline-encoded CDR serine residues."}