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Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective
In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic effects at more than 1,300 loci in the developing brain and two adult brain regions, including hundreds present in only males or females. Ou...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315459/ https://www.ncbi.nlm.nih.gov/pubmed/22479196 http://dx.doi.org/10.1371/journal.pgen.1002600 |
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author | DeVeale, Brian van der Kooy, Derek Babak, Tomas |
author_facet | DeVeale, Brian van der Kooy, Derek Babak, Tomas |
author_sort | DeVeale, Brian |
collection | PubMed |
description | In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic effects at more than 1,300 loci in the developing brain and two adult brain regions, including hundreds present in only males or females. Our independent replication of the embryonic brain stage, where the majority of novel imprinted genes were discovered and the majority of previously known imprinted genes confirmed, resulted in only 12.9% concordance among the novel imprinted loci. Further analysis and pyrosequencing-based validation revealed that the vast majority of the novel reported imprinted loci are false-positives explained by technical and biological variation of the experimental approach. We show that allele-specific expression (ASE) measured with RNA–Seq is not accurately modeled with statistical methods that assume random independent sampling and that systematic error must be accounted for to enable accurate identification of imprinted expression. Application of a robust approach that accounts for these effects revealed 50 candidate genes where allelic bias was predicted to be parent-of-origin–dependent. However, 11 independent validation attempts through a range of allelic expression biases confirmed only 6 of these novel cases. The results emphasize the importance of independent validation and suggest that the number of imprinted genes is much closer to the initial estimates. |
format | Online Article Text |
id | pubmed-3315459 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-33154592012-04-04 Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective DeVeale, Brian van der Kooy, Derek Babak, Tomas PLoS Genet Research Article In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic effects at more than 1,300 loci in the developing brain and two adult brain regions, including hundreds present in only males or females. Our independent replication of the embryonic brain stage, where the majority of novel imprinted genes were discovered and the majority of previously known imprinted genes confirmed, resulted in only 12.9% concordance among the novel imprinted loci. Further analysis and pyrosequencing-based validation revealed that the vast majority of the novel reported imprinted loci are false-positives explained by technical and biological variation of the experimental approach. We show that allele-specific expression (ASE) measured with RNA–Seq is not accurately modeled with statistical methods that assume random independent sampling and that systematic error must be accounted for to enable accurate identification of imprinted expression. Application of a robust approach that accounts for these effects revealed 50 candidate genes where allelic bias was predicted to be parent-of-origin–dependent. However, 11 independent validation attempts through a range of allelic expression biases confirmed only 6 of these novel cases. The results emphasize the importance of independent validation and suggest that the number of imprinted genes is much closer to the initial estimates. Public Library of Science 2012-03-29 /pmc/articles/PMC3315459/ /pubmed/22479196 http://dx.doi.org/10.1371/journal.pgen.1002600 Text en DeVeale et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article DeVeale, Brian van der Kooy, Derek Babak, Tomas Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective |
title | Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective |
title_full | Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective |
title_fullStr | Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective |
title_full_unstemmed | Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective |
title_short | Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective |
title_sort | critical evaluation of imprinted gene expression by rna–seq: a new perspective |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315459/ https://www.ncbi.nlm.nih.gov/pubmed/22479196 http://dx.doi.org/10.1371/journal.pgen.1002600 |
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