Treatment- and population-dependent activity patterns of behavioral and expression QTLs.
Genetic control of gene expression and higher-order phenotypes is almost invariably dependent on environment and experimental conditions. We use two families of recombinant inbred strains of mice (LXS and BXD) to study treatment- and genotype-dependent control of hippocampal gene expression and beha...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22359631/?tool=EBI |
| _version_ | 1818845916659974144 |
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| author | Jesse D Ziebarth Melloni N Cook Xusheng Wang Robert W Williams Lu Lu Yan Cui |
| author_facet | Jesse D Ziebarth Melloni N Cook Xusheng Wang Robert W Williams Lu Lu Yan Cui |
| author_sort | Jesse D Ziebarth |
| collection | DOAJ |
| description | Genetic control of gene expression and higher-order phenotypes is almost invariably dependent on environment and experimental conditions. We use two families of recombinant inbred strains of mice (LXS and BXD) to study treatment- and genotype-dependent control of hippocampal gene expression and behavioral phenotypes. We analyzed responses to all combinations of two experimental perturbations, ethanol and restraint stress, in both families, allowing for comparisons across 8 combinations of treatment and population. We introduce the concept of QTL activity patterns to characterize how associations between genomic loci and traits vary across treatments. We identified several significant behavioral QTLs and many expression QTLs (eQTLs). The behavioral QTLs are highly dependent on treatment and population. We classified eQTLs into three groups: cis-eQTLs (expression variation that maps to within 5 Mb of the cognate gene), syntenic trans-eQTLs (the gene and the QTL are on the same chromosome but not within 5 Mb), and non-syntenic trans-eQTLs (the gene and the QTL are on different chromosomes). We found that most non-syntenic trans-eQTLs were treatment-specific whereas both classes of syntenic eQTLs were more conserved across treatments. We also found there was a correlation between regions along the genome enriched for eQTLs and SNPs that were conserved across the LXS and BXD families. Genes with eQTLs that co-localized with the behavioral QTLs and displayed similar QTL activity patterns were identified as potential candidate genes associated with the phenotypes, yielding identification of novel genes as well as genes that have been previously associated with responses to ethanol. |
| first_indexed | 2024-12-19T05:37:16Z |
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| id | doaj.art-80ea68498bb64f48af3131e52e8e04b5 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T05:37:16Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS ONE |
| spelling | doaj.art-80ea68498bb64f48af3131e52e8e04b52022-12-21T20:34:06ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0172e3180510.1371/journal.pone.0031805Treatment- and population-dependent activity patterns of behavioral and expression QTLs.Jesse D ZiebarthMelloni N CookXusheng WangRobert W WilliamsLu LuYan CuiGenetic control of gene expression and higher-order phenotypes is almost invariably dependent on environment and experimental conditions. We use two families of recombinant inbred strains of mice (LXS and BXD) to study treatment- and genotype-dependent control of hippocampal gene expression and behavioral phenotypes. We analyzed responses to all combinations of two experimental perturbations, ethanol and restraint stress, in both families, allowing for comparisons across 8 combinations of treatment and population. We introduce the concept of QTL activity patterns to characterize how associations between genomic loci and traits vary across treatments. We identified several significant behavioral QTLs and many expression QTLs (eQTLs). The behavioral QTLs are highly dependent on treatment and population. We classified eQTLs into three groups: cis-eQTLs (expression variation that maps to within 5 Mb of the cognate gene), syntenic trans-eQTLs (the gene and the QTL are on the same chromosome but not within 5 Mb), and non-syntenic trans-eQTLs (the gene and the QTL are on different chromosomes). We found that most non-syntenic trans-eQTLs were treatment-specific whereas both classes of syntenic eQTLs were more conserved across treatments. We also found there was a correlation between regions along the genome enriched for eQTLs and SNPs that were conserved across the LXS and BXD families. Genes with eQTLs that co-localized with the behavioral QTLs and displayed similar QTL activity patterns were identified as potential candidate genes associated with the phenotypes, yielding identification of novel genes as well as genes that have been previously associated with responses to ethanol.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22359631/?tool=EBI |
| spellingShingle | Jesse D Ziebarth Melloni N Cook Xusheng Wang Robert W Williams Lu Lu Yan Cui Treatment- and population-dependent activity patterns of behavioral and expression QTLs. PLoS ONE |
| title | Treatment- and population-dependent activity patterns of behavioral and expression QTLs. |
| title_full | Treatment- and population-dependent activity patterns of behavioral and expression QTLs. |
| title_fullStr | Treatment- and population-dependent activity patterns of behavioral and expression QTLs. |
| title_full_unstemmed | Treatment- and population-dependent activity patterns of behavioral and expression QTLs. |
| title_short | Treatment- and population-dependent activity patterns of behavioral and expression QTLs. |
| title_sort | treatment and population dependent activity patterns of behavioral and expression qtls |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22359631/?tool=EBI |
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