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DNA polymerase η is an A-T mutator in somatic hypermutation of immunoglobulin variable genes
Abstract
To determine whether DNA polymerase eta plays a role in the hypermutation of immunoglobulin variable genes, we examined the frequency and pattern of substitutions in variable VH6 genes from the peripheral blood lymphocytes of three patients with xeroderma pigmentosum variant disease, whose polymerase eta had genetic defects. The frequency of mutation was normal but the types of base changes were different: there was a decrease in mutations at A and T and a concomitant rise in mutations at G and C. We propose that more than one polymerase contributes to hypermutation and that if one is absent, others compensate. The data indicate that polymerase eta is involved in generating errors that occur predominantly at A and T and that another polymerase(s) may preferentially generate errors opposite G and C.
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“is characterized by a pattern of mutations that has been attributed to pol h (see the Discussion section for details) recruited for the repair of DNA damaged by AID during somatic hypermutation in immunoglobulin genes [28][29][30] .”
From DNA polymerase η mutational signatures are found in a variety of different types of cancer (2018) · cites this paper as [30]
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“In addition, expression of TLS polymerases critical to SHM, such as DNA polymerase (pol) θ, pol η and pol ζ, is significantly upregulated in B cells by the same stimuli that induce AID expression and SHM (Poltoratsky et al., 2001; Zan et al., 2001; Zeng et al., 2001; Zan et al., 2005), suggesting that SHM is a tightly…”
BackgroundInfluentialReflections on the state of play in somatic hypermutation
Steele, E. J. (2008) · Molecular Immunology · doi:10.1016/j.molimm.2008.02.002 · Cited by 7
Somatic mutation patterns at Ig and Non-Ig Loci
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“Polymerase g is the major polymerase incorporating mutations opposite A:T templates (5,6,10,56,57), and polymerases j (11), i (26), f (40), and Rev1 (18) are involved less frequently.”
BackgroundSelf-citation129-Derived Mouse Strains Express an Unstable but Catalytically Active DNA Polymerase Iota Variant
Aoufouchi, S., Smet, A. D., Delbos, F., Gelot, C., Guerrera, I. C., Weill, J., & Reynaud, C. (2015) · Molecular and Cellular Biology · doi:10.1128/mcb.00371-15 · Cited by 7
“The Ig gene mutation patterns of memory B cells from XP11BR and XP31BE patients (as well as from XP7BR patients, whose genomic POLH mutations are identical to those of the XP6DU patients studied here) have been reported previously (24, 25).”
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Franklin, A., & Blanden, R. V. (2008) · Trends in Immunology · doi:10.1016/j.it.2008.01.008 · Cited by 7
Hypermutation Rate Normalized by Chronological Time
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“The strand containing the uracil or even the strand opposite (21) the uracil might be excised, and error-prone polymerases (25, 26) repairing the section may introduce incorrectly paired bases, not only at the site of the original deaminated C but also other nearby bases.”
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Azhar, A., Begum, N. A., & Husain, A. (2021) · Vaccines · doi:10.3390/vaccines9101050 · Cited by 7
Lindley, R. A. (2020) · Medical Research Archives · doi:10.18103/mra.v8i8.2177 · Cited by 6
“A critical evaluation of the literature illuminates key issues not shown in the Burns et al rendition of the model, particularly the A/T targeted phase involving the supposed mutagenic gap filling of AID/APOBEC mediated lesions by the Y family translesion DNA repair enzyme DNA polymerase-eta (pol-eta) which is the onl…”
BackgroundInfluentialImpact of Chk1 dosage on somatic hypermutation in vivo
Bello, A., & Jungnickel, B. (2021) · Immunology and Cell Biology · doi:10.1111/imcb.12480 · Cited by 5
“In this case, following mismatch recognition and nucleotide excision on one DNA strand, the ssDNA patch refill is carried out by Polg recruited via monoubiquitination of the proliferating cell nuclear antigen.(15,16) Furthermore, the processing of AID-induced lesions may generate DSBs whose unfaithful repair by nonhom…”
BackgroundGearhart, P. J. (2003) · Oncogene · doi:10.1038/sj.onc.1206874 · Cited by 6
“Polymerases Z (Zeng et al., 2001) and i (Faili et al., 2002) could then either fill in the gap with one nucleotide, or displace it and synthesize several bases.”
BackgroundSelf-citationDoes activation-induced deaminase initiate antibody diversification by DNA deamination?
Stavnezer, J., & Bradley, S. P. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02799-3 · Cited by 6
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“The non-canonical role of Pol η in the generation of immunoglobulin diversity during somatic hypermutation (SHM) of immunoglobulin (Ig) genes is well-established [39–41 , 163– 166].”
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“By these biologic and genetic criteria, the breaks are likely to be intermediates in the SHM pathway.”
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DNA polymerase ι of mammals as a participant in translesion synthesis of DNA
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Rapid cell division contributes to efficient induction of A/T mutations during Ig gene hypermutation
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AID preferentially targets the top strand in nucleosome sequences
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“. In contrast, the mutation spectra of polymerase η -deficient B cells from human and mice lack a significant fraction of A/T mutations”
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BackgroundEffect of pH on the Misincorporation Rate of DNA Polymerase η
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“SBS16 is, thus, an A:T bp-focused signature at ATA, ATG, ATT motifs, which are core WA motifs for both ADAR1 mediated A-to-I pre-mRNA modifications [60] and indeed DNA Polymerase eta [83,84] during Ig SHM in vivo [27].”
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“normal individuals[25], and the comparison of the in vitro mutation specificity of Pol η with the mutational spectra of different Ig genes of healthy individuals suggested that this polymerase could play an important role in SH[26].”
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“Humans deficient for polymerase (pol) (2) or mice deficient in MSH2–MSH6 (3–6) show a significant reduction in hypermutation at A:T sites.”
DNA polymerase β prevents AID-instigated mutagenic non-canonical mismatch DNA repairPreprint
Bahjat, M., Stratigopoulou, M., Pilzecker, B., van Dam, T. P., Mobach, S., Bende, R. J., van Noesel, C. J. M., Jacobs, H., & Guikema, J. E. J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.30.926964 · Cited by 4
“Subsequent gap-filling by the error-prone TLS DNA polymerase η (Polη) contributes to A:T mutagenesis, focused on the WA motif (Bardwell et al., 2004; Delbos et al., 2007; Martin et al., 2003; Martomo et al., 2004; Rogozin et al., 2001; Wilson et al., 2005; Zeng et al., 2001).”
BackgroundMechanism and regulation of secondary immunoglobulin diversification
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“In this context, RGYW is an AID-preferred DNA motif [65–67] and mutation at the TAA motif is due to activities of error-prone DNA polymerase η [68].”
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“In the absence of functional Pol η , as seen in xeroderma pigmentosum variant (XP-V) patients and Pol η -deficient mice, the mutation spectrum shifts away from mutations at A:T towards mutations at G:C (Delbos et al., 2005; Martomo et al., 2005; Zeng et al., 2001).”
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“Furthermore, translesion DNA polymerase η fi lls in the gaps in immunoglobulin genes, generated by the concerted action of the enzymes AID, UDG, and APE1, in an error-prone manner 5 .”
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“…and REV1 have been shown to be important for SHM (Delbos et al., 2007; Delbos et al., 2005; Diaz et al., 2001; Faili et al., 2002; Jansen et al., 2006; Masuda et al., 2005; Mayorov et al., 2005; McDonald et al., 2003; Ross and Sale, 2006; Schenten et al., 2009; Zan et al., 2001; Zeng et al., 2001).”
BackgroundA tribute to Michael S. Neuberger
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Molecular Mechanism of Hepatitis C Virus Carcinogenesis
Machida, K., Ou, J. J., & Lai, M. M. C. (2009) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789812833471_0003 · Cited by 1
“Pol ι, Pol η, and Pol ζ are involved in these pathways (Faili et al., 2002; Zan et al., 2001; Zeng et al., 2001).”
Dieckman, L. M. (2013) · doi:10.17077/etd.5pihvjjx · Cited by 1
“Likewise, humans who are deficient in pol η have normal frequencies of hypermutations at these loci but fewer A:T mutations, implicating pol η in this process as well [147-149].”
BackgroundDevoret, R. (2006) · Wiley-VCH eBooks · doi:10.1002/3527600906.mcb.200500026
Mierau, M. (2005) · Electronic Theses of LMU Munich (Ludwig-Maximilians-Universität München) · doi:10.5282/edoc.4837
AID to overcome the limitations of genomic information by introducing somatic DNA alterations
Honjo, T., Muramatsu, M., Nagaoka, H., Kinoshita, K., & Shinkura, R. (2006) · Proceedings of the Japan Academy Series B · doi:10.2183/pjab.82.104
Error-prone polymerases make efficient immunity
Toma, T. (2001) · Genome biology · doi:10.1186/gb-spotlight-20010601-01
Human DNA Polymerase η and Its Regulatory Mechanisms
Masutani, C. (2012) · Genes and Environment · doi:10.3123/jemsge.34.63
DNA Damage Tolerance and Translesion Synthesis
Lehmann, A. R. (2009) · Springer eBooks · doi:10.1007/978-90-481-2561-6_10
“decrease in SHM at A:T bases and an increase at G:C sites [158].”
Self-citationSomatic Hypermutation of Antigen Receptor Genes: Evolution
Diaz, M., & Verkoczy, L. K. (2008) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0006121.pub2
Tobollik, S. (2007) · Electronic Theses of LMU Munich (Ludwig-Maximilians-Universität München) · doi:10.5282/edoc.8980
The Molecular Basis of Lymphoid Architecture in the Mouse
Vinuesa, C. G., & Cook, M. (2007) · Elsevier eBooks · doi:10.1016/b978-012369454-6/50079-0
A Novel Targeted Deletion of Mbd4 Reveals an Unappreciated Role in Class Switch Recombination
Grigera, F. (2013) · Figshare
immunoglobulin class switch recombination and somatic hypermutation
Pan‐Hammarström, Q., Lähdesmäki, A., Zhao, Y., Du, L., Zhao, Z., Wen, S., Ruiz‐Pérez, V. L., Dunn‐Walters, D. K., Goodship, J. A., & Hammarström, L. L. G. (2006)
The DNA Deamination Model of Somatic Antibody Diversification
Rajewsky, K. (2015) · The Journal of Immunology · doi:10.4049/jimmunol.1403252
“Evidence from other laboratories suggested that in mice and humans, following detection of AID-generated lesions in DNA (17220), nucleotide misincorporation by DNA polymerase h is the major contributor to SHM at A:T pairs in vivo (21, 22).”
BackgroundCoping with DNA Damage and Replication Stress
Ulrich, H. D. (2009) · Royal Society of Chemistry eBooks · doi:10.1039/9781847559852-00178
Error-Prone Mismatch and Base Excision DNA Repair in Somatic Hypermutation
Wang, S., Chahwan, R., Wei, L., et al. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-374279-7.05015-3
Metadata
- Authors
- Zeng, X., Winter, D. B., Kasmer, C., Kraemer, K. H., Lehmann, A. R., & Gearhart, P. J.
- Affiliations
- National Institutes of Health (US)
- Walter Reed Army Institute of Research (US)
- University of Sussex (GB)
- Corresponding author
- Gearhart, Patricia J.
- Venue
- Nature Immunology
- Published
- 2001-06
- Volume
- 2
- Issue
- 6
- Pages
- 537-541
- ISSN
- 1529-2908 (ISSN-L)
- 1529-2916
- OpenAlex
- W1560486125
- Semantic Scholar
- 8a9d17ca74ddcb4e43d0ff02f4b768b9cb457829
- Cited by
- 420
- References
- 49
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 6 · 2023: 6 · 2022: 7 · 2021: 11 · 2020: 12 · 2019: 12 · 2018: 10 · 2017: 10 · 2016: 11 · 2015: 8 · 2014: 12 · 2013: 15 · 2012: 15
- FWCI
- 13.73
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Immunology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (Z01BC004517)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- DNA polymerase eta, somatic hypermutation, immunoglobulin variable region genes, xeroderma pigmentosum variant, peripheral blood lymphocytes, error-prone mutagenesis
- MeSH terms
- Y-Family DNA Polymerases, Animals, B-Lymphocytes, Base Sequence, DNA, DNA-Directed DNA Polymerase, Genes, Immunoglobulin, Humans, Immunoglobulin Variable Region, Molecular Sequence Data, Mutation, Xeroderma Pigmentosum, Base Pairing, Mice
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