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General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq

BACKGROUND: Species with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic XX/XY systems suggest that dosage compensation mechanisms are in place to mitigate the detrimental effects of gene dose...

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Autores principales: Wolf, Jochen BW, Bryk, Jarosław
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040151/
https://www.ncbi.nlm.nih.gov/pubmed/21284834
http://dx.doi.org/10.1186/1471-2164-12-91
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author Wolf, Jochen BW
Bryk, Jarosław
author_facet Wolf, Jochen BW
Bryk, Jarosław
author_sort Wolf, Jochen BW
collection PubMed
description BACKGROUND: Species with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic XX/XY systems suggest that dosage compensation mechanisms are in place to mitigate the detrimental effects of gene dose differences. However, recent genomic research on female heterogametic ZZ/ZW systems has generated surprising results. In two bird species and one lepidopteran no evidence for a global dosage compensating mechanism has been found. The recent advent of massively parallel RNA sequencing now opens up the possibility to gauge the generality of this observation with a broader phylogenetic sampling. It further allows assessing the validity of microarray-based inference on dosage compensation with a novel technology. RESULTS: We here expemplify this approach using massively parallel sequencing on barcoded individuals of a bird species, the European crow (Corvus corone), where previously no genetic resources were available. Testing for Z-linkage with quantitative PCR (qPCR,) we first establish that orthology with distantly related species (chicken, zebra finch) can be used as a good predictor for chromosomal affiliation of a gene. We then use a digital measure of gene expression (RNA-seq) on brain transcriptome and confirm a global lack of dosage compensation on the Z chromosome. RNA-seq estimates of male-to-female (m:f) expression difference on the Z compare well to previous microarray-based estimates in birds and lepidopterans. The data further lends support that an up-regulation of female Z-linked genes conveys partial compensation and suggest a relationship between sex-bias and absolute expression level of a gene. Correlation of sex-biased gene expression on the Z chromosome across all three bird species further suggests that the degree of compensation has been partly conserved across 100 million years of avian evolution. CONCLUSIONS: This work demonstrates that the study of dosage compensation has become amenable to species where previously no genetic resources were available. Massively parallele transcriptome sequencing allows re-assessing the degree of dosage compensation with a novel tool in well-studies species and, in addition, gain valuable insights into the generality of mechanisms across independent taxonomic group for both the XX/XY and ZZ/ZW system.
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spelling pubmed-30401512011-02-17 General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq Wolf, Jochen BW Bryk, Jarosław BMC Genomics Research Article BACKGROUND: Species with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic XX/XY systems suggest that dosage compensation mechanisms are in place to mitigate the detrimental effects of gene dose differences. However, recent genomic research on female heterogametic ZZ/ZW systems has generated surprising results. In two bird species and one lepidopteran no evidence for a global dosage compensating mechanism has been found. The recent advent of massively parallel RNA sequencing now opens up the possibility to gauge the generality of this observation with a broader phylogenetic sampling. It further allows assessing the validity of microarray-based inference on dosage compensation with a novel technology. RESULTS: We here expemplify this approach using massively parallel sequencing on barcoded individuals of a bird species, the European crow (Corvus corone), where previously no genetic resources were available. Testing for Z-linkage with quantitative PCR (qPCR,) we first establish that orthology with distantly related species (chicken, zebra finch) can be used as a good predictor for chromosomal affiliation of a gene. We then use a digital measure of gene expression (RNA-seq) on brain transcriptome and confirm a global lack of dosage compensation on the Z chromosome. RNA-seq estimates of male-to-female (m:f) expression difference on the Z compare well to previous microarray-based estimates in birds and lepidopterans. The data further lends support that an up-regulation of female Z-linked genes conveys partial compensation and suggest a relationship between sex-bias and absolute expression level of a gene. Correlation of sex-biased gene expression on the Z chromosome across all three bird species further suggests that the degree of compensation has been partly conserved across 100 million years of avian evolution. CONCLUSIONS: This work demonstrates that the study of dosage compensation has become amenable to species where previously no genetic resources were available. Massively parallele transcriptome sequencing allows re-assessing the degree of dosage compensation with a novel tool in well-studies species and, in addition, gain valuable insights into the generality of mechanisms across independent taxonomic group for both the XX/XY and ZZ/ZW system. BioMed Central 2011-02-01 /pmc/articles/PMC3040151/ /pubmed/21284834 http://dx.doi.org/10.1186/1471-2164-12-91 Text en Copyright ©2011 Wolf and Bryk; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Wolf, Jochen BW
Bryk, Jarosław
General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq
title General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq
title_full General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq
title_fullStr General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq
title_full_unstemmed General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq
title_short General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq
title_sort general lack of global dosage compensation in zz/zw systems? broadening the perspective with rna-seq
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040151/
https://www.ncbi.nlm.nih.gov/pubmed/21284834
http://dx.doi.org/10.1186/1471-2164-12-91
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