Transcriptome sequencing of Chinese and Caucasian population identifies ethnic-associated differential transcript abundance of heterogeneous nuclear ribonucleoprotein K (hnRNPK)

Genomics - Tập 103 - Trang 56-64 - 2014
Jing-Woei Li1,2,3, Keng-Po Lai3, Arthur K.K. Ching3, Ting-Fung Chan1,2
1School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
2Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Shatin, Hong Kong
3Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong

Tài liệu tham khảo

Genomes Project C., 2010, A map of human genome variation from population-scale sequencing, Nature, 467, 1061, 10.1038/nature09534 Genomes Project C., 2012, An integrated map of genetic variation from 1,092 human genomes, Nature, 491, 56, 10.1038/nature11632 Tennessen, 2012, Evolution and functional impact of rare coding variation from deep sequencing of human exomes, Science, 337, 64, 10.1126/science.1219240 Morley, 2004, Genetic analysis of genome-wide variation in human gene expression, Nature, 430, 743, 10.1038/nature02797 Goring, 2007, Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes, Nat. Genet., 39, 1208, 10.1038/ng2119 Emilsson, 2008, Genetics of gene expression and its effect on disease, Nature, 452, 423, 10.1038/nature06758 Cheung, 2010, Polymorphic cis- and trans-regulation of human gene expression, PLoS Biol., 8, 10.1371/journal.pbio.1000480 Lappalainen, 2013, Transcriptome and genome sequencing uncovers functional variation in humans, Nature, 501, 506, 10.1038/nature12531 Rosenberg, 2002, Genetic structure of human populations, Science, 298, 2381, 10.1126/science.1078311 Li, 2008, Worldwide human relationships inferred from genome-wide patterns of variation, Science, 319, 1100, 10.1126/science.1153717 Rotimi, 2010, Ancestry and disease in the age of genomic medicine, N. Engl. J. Med., 363, 1551, 10.1056/NEJMra0911564 Adeyemo, 2010, Genetic variants associated with complex human diseases show wide variation across multiple populations, Public Health Genomics, 13, 72, 10.1159/000218711 Li, 2010, Gene expression variability within and between human populations and implications toward disease susceptibility, PLoS Comput. Biol., 6, e1000910, 10.1371/journal.pcbi.1000910 Spielman, 2007, Common genetic variants account for differences in gene expression among ethnic groups, Nat. Genet., 39, 226, 10.1038/ng1955 Hull, 2007, Identification of common genetic variation that modulates alternative splicing, PLoS Genet., 3, e99, 10.1371/journal.pgen.0030099 Zhang, 2009, Identification of common genetic variants that account for transcript isoform variation between human populations, Hum. Genet., 125, 81, 10.1007/s00439-008-0601-x Stover, 2011, Comparative vertebrate evolutionary analyses of type I collagen: potential of COL1a1 gene structure and intron variation for common bone-related diseases, Mol. Biol. Evol., 28, 533, 10.1093/molbev/msq221 Chan, 2008, Natural variation in four human collagen genes across an ethnically diverse population, Genomics, 91, 307, 10.1016/j.ygeno.2007.12.008 Li, 2009, Fast and accurate short read alignment with Burrows–Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 Trapnell, 2009, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120 Au, 2010, Detection of splice junctions from paired-end RNA-seq data by SpliceMap, Nucleic Acids Res., 38, 4570, 10.1093/nar/gkq211 Wang, 2010, MapSplice: accurate mapping of RNA-seq reads for splice junction discovery, Nucleic Acids Res., 38, e178, 10.1093/nar/gkq622 Tabas-Madrid, 2012, GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics, Nucleic Acids Res., 40, W478, 10.1093/nar/gks402 Anders, 2010, Differential expression analysis for sequence count data, Genome Biol., 11, R106, 10.1186/gb-2010-11-10-r106 Fan, 2009, Interindividual and interethnic variation in genomewide gene expression: insights into the biological variation of gene expression and clinical implications, Clin. Chem., 55, 774, 10.1373/clinchem.2008.119107 Grant, 2011, Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM), Bioinformatics, 27, 2518, 10.1093/bioinformatics/btr427 Kasowski, 2010, Variation in transcription factor binding among humans, Science, 328, 232, 10.1126/science.1183621 Montgomery, 2010, Transcriptome genetics using second generation sequencing in a Caucasian population, Nature, 464, 773, 10.1038/nature08903 Lalonde, 2011, RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression, Genome Res., 21, 545, 10.1101/gr.111211.110 Toung, 2011, RNA-sequence analysis of human B-cells, Genome Res., 21, 991, 10.1101/gr.116335.110 Wetterbom, 2010, Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing, Genome Biol., 11, R78, 10.1186/gb-2010-11-7-r78 Pickrell, 2010, Understanding mechanisms underlying human gene expression variation with RNA sequencing, Nature, 464, 768, 10.1038/nature08872 Kapranov, 2010, The majority of total nuclear-encoded non-ribosomal RNA in a human cell is ‘dark matter’ un-annotated RNA, BMC Biol., 8, 149, 10.1186/1741-7007-8-149 van Bakel, 2010, Most “dark matter” transcripts are associated with known genes, PLoS Biol., 8, e1000371, 10.1371/journal.pbio.1000371 van Bakel, 2009, Establishing legitimacy and function in the new transcriptome, Brief Funct. Genomics Proteomics, 8, 424, 10.1093/bfgp/elp037 Li, 2012, SEQanswers: an open access community for collaboratively decoding genomes, Bioinformatics, 28, 1272, 10.1093/bioinformatics/bts128 Roberts, 2011, Improving RNA-Seq expression estimates by correcting for fragment bias, Genome Biol., 12, R22, 10.1186/gb-2011-12-3-r22 Kramer, 2011, Constant splice-isoform ratios in human lymphoblastoid cells support the concept of a splico-stat, Genetics, 187, 761, 10.1534/genetics.110.125096 Wang, 2011, Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens, BMC Bioinforma., 12, S5 Pan, 2008, Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing, Nat. Genet., 40, 1413, 10.1038/ng.259 Halvardson, 2013, Exome RNA sequencing reveals rare and novel alternative transcripts, Nucleic Acids Res., 41, e6, 10.1093/nar/gks816 Zamft, 2012, Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases, Proc. Natl. Acad. Sci. U. S. A., 109, 8948, 10.1073/pnas.1205063109 Rajala, 2010, Effects of transcriptional pausing on gene expression dynamics, PLoS Comput. Biol., 6, e1000704, 10.1371/journal.pcbi.1000704 Moumen, 2005, hnRNP K: an HDM2 target and transcriptional coactivator of p53 in response to DNA damage, Cell, 123, 1065, 10.1016/j.cell.2005.09.032 Pelisch, 2012, DNA damage-induced heterogeneous nuclear ribonucleoprotein K sumoylation regulates p53 transcriptional activation, J. Biol. Chem., 287, 30789, 10.1074/jbc.M112.390120 Witherspoon, 2007, Genetic similarities within and between human populations, Genetics, 176, 351, 10.1534/genetics.106.067355 Pickrell, 2010, Noisy splicing drives mRNA isoform diversity in human cells, PLoS Genet., 6, e1001236, 10.1371/journal.pgen.1001236 Kwan, 2007, Heritability of alternative splicing in the human genome, Genome Res., 17, 1210, 10.1101/gr.6281007 Wu, 2013, Variation and genetic control of protein abundance in humans, Nature, 499, 79, 10.1038/nature12223