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Identification of common genetic variants that account for transcript isoform variation between human populations

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Abstract

In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribution to transcript isoform variation has been reported in individuals of recent European descent. We report here results of an investigation of the differences in AS patterns between human populations. AS patterns in 176 HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry were evaluated using the Affymetrix GeneChip® Human Exon 1.0 ST Array. A variety of biological processes such as response to stimulus and transcription were found to be enriched among the differentially spliced genes. The differentially spliced genes also include some involved in human diseases that have different prevalence or susceptibility between populations. The genetic contribution to the population differences in transcript isoform variation was then evaluated by a genome-wide association using the HapMap genotypic data on single nucleotide polymorphisms (SNPs). The results suggest that local and distant genetic variants account for a substantial fraction of the observed transcript isoform variation between human populations. Our findings provide new insights into the complexity of the human genome as well as the health disparities between the two populations.

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Acknowledgments

This Pharmacogenetics of Anticancer Agents Research (PAAR) Group (http://www.pharmacogenetics.org) study was supported by NIH/NIGMS grants U01 GM61393 and U01 GM61374. We are grateful to Dr. Jeong-Ah Kang for maintaining cell lines, Cheryl A. Roe for reviewing the manuscript and Drs. James Fackenthal and Emily Kistner for helpful discussion. T.A.C., T.X.C., A.C.S., and J.E.B. are employees of Affymetrix, Inc.

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Authors and Affiliations

  1. Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Box MC6091, 5841 S. Maryland Ave., Chicago, IL, 60637, USA

    Wei Zhang, Shiwei Duan, Wasim K. Bleibel, Steven A. Wisel, R. Stephanie Huang, Xiaolin Wu, Lijun He, M. Eileen Dolan & Nancy J. Cox

  2. Expression Research Laboratory, Affymetrix Inc., Santa Clara, CA, 95051, USA

    Tyson A. Clark, Tina X. Chen, Anthony C. Schweitzer & John E. Blume

  3. Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA

    Nancy J. Cox

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  1. Wei Zhang
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Correspondence to Nancy J. Cox.

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W. Zhang and S. Duan contributed equally to this work.

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439_2008_601_MOESM1_ESM.xls

Supplemental Table S1. Differentially spliced probesets between the CEU and YRI samples, Supplemental Table S2. Associated SNP’s with the differentially spliced probesets, Supplemental Table S3. Primers used in the validation of differentially spliced probesets (XLS 746 kb)

439_2008_601_MOESM2_ESM.tif

Supplemental Fig. 1 The workflow chart. Exon-level expression of the CEU and YRI trios was measured using theAffymetrix Human Exon 1.0ST array. Splicing index values were compared between the twopopulations to identify differential probesets. Genetic variants associated with the differentialprobesets and enriched pathways and/or Gene Ontology terms were then identified.254x190mm (72 x 72 DPI) (TIFF 110 kb)

439_2008_601_MOESM3_ESM.tif

Supplemental Fig. 2 PS3527423 (PARP2) is differentially spliced among 54 unrelated CEU samples. Blue indicates thepresence of both spliced and unspliced isoforms (300bp and 400bp); Red indicates unsplicedisoforms (400bp); Black indicates spliced isoforms (300bp).254x190mm (72 x 72 DPI) (TIFF 116 kb)

439_2008_601_MOESM4_ESM.tif

Supplemental Fig. 3 Validation of transcript isoform variation between populations using quantitative Real-Time PCR. Therelative expression between the exon of interest (EOI) and the neighboring, housekeeping exon(HKE) was shown. (A) MPRL43 (probeset: 3303658) has a lower ratio (one-tail t test p = 0.02) inCEU, consistent with the trend of SI (CEU SI mean = -0.02; YRI SI mean = 0.06). (B) MTMR4(probeset: 3764493) has a lower ratio (one-tail t test p = 0.05) in CEU consistent with the trend ofSI (CEU SI mean = 0.004; YRI SI mean = 0.024).254x190mm (72 x 72 DPI) (TIFF 64 kb)

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Zhang, W., Duan, S., Bleibel, W.K. et al. Identification of common genetic variants that account for transcript isoform variation between human populations. Hum Genet 125, 81–93 (2009). https://doi.org/10.1007/s00439-008-0601-x

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