Novel exons and splice variants in the human antibody heavy chain identified by single cell and single molecule sequencing

PLoS ONE

Volumn 10, Issue 1, 2015, Pages

  Vollmers, Christopher ^a   Penland, Lolita ^a   Kanbar, Jad N ^c   Quake, Stephen R ^a,b,c  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN ANTIBODY; IMMUNOGLOBULIN CLASS; IMMUNOGLOBULIN HEAVY CHAIN; ISOPROTEIN; PROTEIN IGHA1; PROTEIN IGHA2; PROTEIN IGHM; RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

3' UNTRANSLATED REGION; ARTICLE; EXON; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; IMMUNOGLOBULIN VARIABLE REGION; RNA SEQUENCE; RNA SPLICING; SEQUENCE ANALYSIS; SINGLE CELL RNA SEQUENCING; SINGLE MOLECULE RNA SEQUENCING; B LYMPHOCYTE; GENETICS;

B-LYMPHOCYTES; EXONS; HUMANS; IMMUNOGLOBULIN HEAVY CHAINS; RNA SPLICING; SEQUENCE ANALYSIS, RNA;

EID: 84921933739     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0117050     Document Type: Article

References (25)

1. Cox DW, Markovic VD, Teshima IE (1982) Genes for immunoglobulin heavy chains and for alpha 1-antitrypsin are localized to specific regions of chromosome 14q. Nature 297: 428-430. PMID: 6804874
2. Croce CM, Shander M, Martinis J, Cicurel L, D'Ancona GG, et al. (1979) Chromosomal location of the genes for human immunoglobulin heavy chains. Proc Natl Acad Sci U S A 76: 3416-3419. PMID: 114999
3. Flanagan JG, Rabbitts TH (1982) Arrangement of human immunoglobulin heavy chain constant region genes implies evolutionary duplication of a segment containing gamma, epsilon and alpha genes. Nature 300: 709-713. PMID: 6817141
4. Ellison J, Hood L (1982) Linkage and sequence homology of two human immunoglobulin gamma heavy chain constant region genes. Proc Natl Acad Sci U S A 79: 1984-1988. PMID: 6804948
5. Ellison JW, Berson BJ, Hood LE (1982) The nucleotide sequence of a human immunoglobulin C gamma1 gene. Nucleic Acids Res 10: 4071-4079. PMID: 6287432
6. Rabbitts TH, Forster A, Milstein CP (1981) Human immunoglobulin heavy chain genes: evolutionary comparisons of C mu, C delta and C gamma genes and associated switch sequences. Nucleic Acids Res 9: 4509-4524. PMID: 6795593
7. Bensmana M, Lefranc MP (1990) Gene segments encoding membrane domains of the human immunoglobulin gamma 3 and alpha chains. Immunogenetics 32: 321-330. PMID: 1979064
8. Alt FW, Bothwell AL, Knapp M, Siden E, Mather E, et al. (1980) Synthesis of secreted and membrane-bound immunoglobulin mu heavy chains is directed by mRNAs that differ at their 30′ ends. Cell 20: 293-301. PMID: 6771018
9. Cushley W, Coupar BE, Mickelson CA, Williamson AR (1982) A common mechanism for the synthesis of membrane and secreted immunoglobulin alpha, gamma and mu chains. Nature 298: 77-79. PMID: 6806665
10. Cook GP, Tomlinson IM, Walter G, Riethman H, Carter NP, et al. (1994) A map of the human immunoglobulin VH locus completed by analysis of the telomeric region of chromosome 14q. Nat Genet 7: 162-168. PMID: 7920635
11. Watson CT, Steinberg KM, Huddleston J, Warren RL, Malig M, et al. (2013) Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation. Am J Hum Genet 92: 530-546. doi: 10.1016/j.ajhg.2013.03.004 PMID: 23541343
12. Weinstein JA, Jiang N, White RA 3rd, Fisher DS, Quake SR (2009) High-throughput sequencing of the zebrafish antibody repertoire. Science 324: 807-810. PMID: 19423829
13. Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, et al. (2009) Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med 1: 12ra23. PMID: 20161664
14. Vollmers C, Sit RV, Weinstein JA, Dekker CL, Quake SR (2013) Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc Natl Acad Sci U S A 110: 13463-13468. doi: 10.1073/pnas.1312146110 PMID: 23898164
15. Bruls T, Gyapay G, Petit JL, Artiguenave F, Vico V, et al. (2001) A physical map of human chromosome 14. Nature 409: 947-948.
16. Heilig R, Eckenberg R, Petit JL, Fonknechten N, Da Silva C, et al. (2003) The DNA sequence and analysis of human chromosome 14. Nature 421: 601-607. PMID: 12508121
17. Sharon D, Tilgner H, Grubert F, Snyder M (2013) A single-molecule long-read survey of the human transcriptome. Nat Biotechnol 31: 1009-1014. doi: 10.1038/nbt.2705 PMID: 24108091
18. Treutlein B, Gokce O, Quake SR, Sudhof TC (2014) Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. Proc Natl Acad Sci U S A 111: E1291-1299. doi: 10.1073/pnas.1403244111 PMID: 24639501
19. Kehry M, Ewald S, Douglas R, Sibley C, Raschke W, et al. (1980) The immunoglobulin mu chains of membrane-bound and secreted IgM molecules differ in their C-terminal segments. Cell 21: 393-406. PMID: 6773668
20. Lefranc M-P, Lefranc G (2001) The immunoglobulin factsbook. San Diego: Academic Press. xiv, 457 p. p. PMID: 24127508
21. Dogan RI, Getoor L, Wilbur WJ, Mount SM (2007) SplicePort - an interactive splice-site analysis tool. Nucleic Acids Res 35: W285-291. PMID: 17576680
22. Ye J, Ma N, Madden TL, Ostell JM (2013) IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res 41: W34-40. doi: 10.1093/nar/gkt382 PMID: 23671333
23. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664.
24. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, et al. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36. doi: 10.1186/gb-2013-14-4-r36 PMID: 23618408
25. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455-477. PMID: 22506599