Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation
Creators
-
Zhuang, Qinwei
(Researcher)1, 2
- Bauermeister, Klara (Researcher)1
- Gálvez, José Héctor (Researcher)3
-
Alogayil, Najla
(Researcher)1
- Batdorj, Enkhjin (Researcher)1
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Pardo Manuel de Villena, Fernando
(Researcher)4, 5
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Taketo, Teruko
(Researcher)6, 7, 8
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Bourque, Guillaume
(Supervisor)1, 2, 3
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Naumova, Anna K.
(Supervisor)1, 6, 8
- 1. Department of Human Genetics, McGill University, Montreal, QC H3A 1C7, Canada
- 2. Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, 606-8303, Japan
- 3. Canadian Centre for Computational Genomics, Montreal, QC H3A 0G1, Canada
- 4. Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- 5. Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- 6. The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- 7. Department of Surgery, McGill University, Montreal, QC H4A 3J1, Canada
- 8. Department of Obstetrics and Gynecology, McGill University, Montreal, QC H4A 3J1, Canada
Description
This collection contains processed files from the manuscript Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation. Briefly, each of the four zipped files contains bigwig track files (.bw files, separate for forward and reverse strands) in respective organs. In addition, bed files are provided for sex-biased signals (e.g. sDETE, sDEG, and slncRNA et. al.).
ABSTRACT
Background
Sex-biased gene regulation is the basis of sexual dimorphism in phenotypes and has been studied across different cell types and different developmental stages. However, sex-biased expression of transposable elements (TEs), which represent nearly half of the mammalian genome and have the potential of influencing genome integrity and regulation, remains underexplored.
Results
We report a survey of gene, lncRNA and TE expression in four organs from mice with different combinations of gonadal and genetic sex. The data show remarkable variability among organs with respect to the impact of gonadal sex on transcription with the strongest effects observed in liver. In contrast, the X-chromosome dosage alone had modest influence on sex-biased transcription across organs, albeit interaction between X-dosage and gonadal sex cannot be ruled out. The presence of the Y-chromosome influences TE, but not gene or lncRNA, expression in liver. Notably, 90% of sex-biased TEs (sDETEs) reside in clusters. Moreover, 54% of these clusters overlap or reside less than 100 kb from sex-biased genes or lncRNAs, share the same sex bias, and also have higher expression levels than sDETE clusters that do not co-localize with other types of sex-biased transcripts. We test the heterochromatic sink hypothesis that predicts higher expression of TEs in XX individuals finding no evidence to support it.
Conclusions
Our data show that sex-biased expression of TEs varies among organs with highest numbers of sDETEs found in liver following trends observed for genes and lncRNAs. It is enhanced by proximity to other types of sex-biased transcripts.
Files
brain_bigWig.zip
Files
(36.7 GB)
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Additional details
Funding
- Natural Sciences and Engineering Research Council
- Discovery Grant program and Discovery Accelerator Supplement to Dr. Anna K. Naumova
- Canadian Institutes of Health Research
- Canada Institute of Health Research (CIHR) program grant (CEE-151618) for the McGill Epigenomics Mapping Center, which is part of the Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) Network (to Dr. Guillaume Bourque) CEE-151618
- Fonds de Recherche du Québec - Santé
- FRQ-S Distinguished Research Scholar award to Dr. Guillaume Bourque
- Canada Research Chairs
- Canada Research Chair Tier 1 award to Dr. Guillaume Bourque
- Fonds de Recherche du Québec - Santé
- Doctoral Training Scholarship to Qinwei Zhuang
- Japan Science and Technology Agency
- Support for Pioneering Research Initiated by the Next Generation (JST SPRING) Doctoral Training Scholarship to Qinwei Zhuang
- McGill University Health Centre
- RI MUHC graduate scholarship to Najla Alogayil
Software
- Repository URL
- https://github.com/qzhuang8/sex-biased-TEs-paper-script