Large-Scale trans-eQTLs Affect Hundreds of Transcripts and Mediate Patterns of Transcriptional Co-regulation

Boel Brynedal, Jin Myung Choi, Towfique Raj, Robert Bjornson, Barbara Elaine Stranger, Benjamin M. Neale, Benjamin F. Voight, Chris Cotsapas*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

52 Scopus citations

Abstract

Efforts to decipher the causal relationships between differences in gene regulation and corresponding differences in phenotype have been stymied by several basic technical challenges. Although detecting local, cis-eQTLs is now routine, trans-eQTLs, which are distant from the genes of origin, are far more difficult to find because millions of SNPs must currently be compared to thousands of transcripts. Here, we demonstrate an alternative approach: we looked for SNPs associated with the expression of many genes simultaneously and found that hundreds of trans-eQTLs each affect hundreds of transcripts in lymphoblastoid cell lines across three African populations. These trans-eQTLs target the same genes across the three populations and show the same direction of effect. We discovered that target transcripts of a high-confidence set of trans-eQTLs encode proteins that interact more frequently than expected by chance, are bound by the same transcription factors, and are enriched for pathway annotations indicative of roles in basic cell homeostasis. We thus demonstrate that our approach can uncover trans-acting transcriptional control circuits that affect co-regulated groups of genes: a key to understanding how cellular pathways and processes are orchestrated.

Original languageEnglish (US)
Pages (from-to)581-591
Number of pages11
JournalAmerican journal of human genetics
Volume100
Issue number4
DOIs
StatePublished - Apr 6 2017

Funding

Computing resources at Yale were funded partly by NIH grants RR19895 and RR029676-01. B.B. was supported by a post-doctoral fellowship from the Swedish Research Council (grant 524-2012-6881).

Keywords

  • cross phenotype meta analysis
  • master regulator
  • regulatory network
  • trans-eQTL
  • transcription

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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