High-resolution mapping of expression-QTLs yields insight into human gene regulation.
Recent studies of the HapMap lymphoblastoid cell lines have identified large numbers of quantitative trait loci for gene expression (eQTLs). Reanalyzing these data using a novel Bayesian hierarchical model, we were able to create a surprisingly high-resolution map of the typical locations of sites t...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2008-10-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC2556086?pdf=render |
| _version_ | 1811207126227353600 |
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| author | Jean-Baptiste Veyrieras Sridhar Kudaravalli Su Yeon Kim Emmanouil T Dermitzakis Yoav Gilad Matthew Stephens Jonathan K Pritchard |
| author_facet | Jean-Baptiste Veyrieras Sridhar Kudaravalli Su Yeon Kim Emmanouil T Dermitzakis Yoav Gilad Matthew Stephens Jonathan K Pritchard |
| author_sort | Jean-Baptiste Veyrieras |
| collection | DOAJ |
| description | Recent studies of the HapMap lymphoblastoid cell lines have identified large numbers of quantitative trait loci for gene expression (eQTLs). Reanalyzing these data using a novel Bayesian hierarchical model, we were able to create a surprisingly high-resolution map of the typical locations of sites that affect mRNA levels in cis. Strikingly, we found a strong enrichment of eQTLs in the 250 bp just upstream of the transcription end site (TES), in addition to an enrichment around the transcription start site (TSS). Most eQTLs lie either within genes or close to genes; for example, we estimate that only 5% of eQTLs lie more than 20 kb upstream of the TSS. After controlling for position effects, SNPs in exons are approximately 2-fold more likely than SNPs in introns to be eQTLs. Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation. |
| first_indexed | 2024-04-12T03:59:46Z |
| format | Article |
| id | doaj.art-bbec05394a01491cb9aadc1830350d25 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-12T03:59:46Z |
| publishDate | 2008-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-bbec05394a01491cb9aadc1830350d252022-12-22T03:48:45ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042008-10-01410e100021410.1371/journal.pgen.1000214High-resolution mapping of expression-QTLs yields insight into human gene regulation.Jean-Baptiste VeyrierasSridhar KudaravalliSu Yeon KimEmmanouil T DermitzakisYoav GiladMatthew StephensJonathan K PritchardRecent studies of the HapMap lymphoblastoid cell lines have identified large numbers of quantitative trait loci for gene expression (eQTLs). Reanalyzing these data using a novel Bayesian hierarchical model, we were able to create a surprisingly high-resolution map of the typical locations of sites that affect mRNA levels in cis. Strikingly, we found a strong enrichment of eQTLs in the 250 bp just upstream of the transcription end site (TES), in addition to an enrichment around the transcription start site (TSS). Most eQTLs lie either within genes or close to genes; for example, we estimate that only 5% of eQTLs lie more than 20 kb upstream of the TSS. After controlling for position effects, SNPs in exons are approximately 2-fold more likely than SNPs in introns to be eQTLs. Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation.http://europepmc.org/articles/PMC2556086?pdf=render |
| spellingShingle | Jean-Baptiste Veyrieras Sridhar Kudaravalli Su Yeon Kim Emmanouil T Dermitzakis Yoav Gilad Matthew Stephens Jonathan K Pritchard High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genetics |
| title | High-resolution mapping of expression-QTLs yields insight into human gene regulation. |
| title_full | High-resolution mapping of expression-QTLs yields insight into human gene regulation. |
| title_fullStr | High-resolution mapping of expression-QTLs yields insight into human gene regulation. |
| title_full_unstemmed | High-resolution mapping of expression-QTLs yields insight into human gene regulation. |
| title_short | High-resolution mapping of expression-QTLs yields insight into human gene regulation. |
| title_sort | high resolution mapping of expression qtls yields insight into human gene regulation |
| url | http://europepmc.org/articles/PMC2556086?pdf=render |
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