Cargando…

Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines

Gene expression is a complex and quantitative trait that is influenced by both genetic and non-genetic regulators including environmental factors. Evaluating the contribution of environment to gene expression regulation and identifying which genes are more likely to be influenced by environmental fa...

Descripción completa

Detalles Bibliográficos
Autores principales: Tang, Ke, Zhang, Wei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911945/
https://www.ncbi.nlm.nih.gov/pubmed/27326381
http://dx.doi.org/10.7717/peerj.2123
_version_ 1782438199906271232
author Tang, Ke
Zhang, Wei
author_facet Tang, Ke
Zhang, Wei
author_sort Tang, Ke
collection PubMed
description Gene expression is a complex and quantitative trait that is influenced by both genetic and non-genetic regulators including environmental factors. Evaluating the contribution of environment to gene expression regulation and identifying which genes are more likely to be influenced by environmental factors are important for understanding human complex traits. We hypothesize that by living together as couples, there can be commonly co-regulated genes that may reflect the shared living environment (e.g., diet, indoor air pollutants, behavioral lifestyle). The lymphoblastoid cell lines (LCLs) derived from unrelated couples of African ancestry (YRI, Yoruba people from Ibadan, Nigeria) from the International HapMap Project provided a unique model for us to characterize gene expression pattern in couples by comparing gene expression levels between husbands and wives. Strikingly, 778 genes were found to show much smaller variances in couples than random pairs of individuals at a false discovery rate (FDR) of 5%. Since genetic variation between unrelated family members in a general population is expected to be the same assuming a random-mating society, non-genetic factors (e.g., epigenetic systems) are more likely to be the mediators for the observed transcriptional similarity in couples. We thus evaluated the contribution of modified cytosines to those genes showing transcriptional similarity in couples as well as the relationships these CpG sites with other gene regulatory elements, such as transcription factor binding sites (TFBS). Our findings suggested that transcriptional similarity in couples likely reflected shared common environment partially mediated through cytosine modifications.
format Online
Article
Text
id pubmed-4911945
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher PeerJ Inc.
record_format MEDLINE/PubMed
spelling pubmed-49119452016-06-20 Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines Tang, Ke Zhang, Wei PeerJ Bioinformatics Gene expression is a complex and quantitative trait that is influenced by both genetic and non-genetic regulators including environmental factors. Evaluating the contribution of environment to gene expression regulation and identifying which genes are more likely to be influenced by environmental factors are important for understanding human complex traits. We hypothesize that by living together as couples, there can be commonly co-regulated genes that may reflect the shared living environment (e.g., diet, indoor air pollutants, behavioral lifestyle). The lymphoblastoid cell lines (LCLs) derived from unrelated couples of African ancestry (YRI, Yoruba people from Ibadan, Nigeria) from the International HapMap Project provided a unique model for us to characterize gene expression pattern in couples by comparing gene expression levels between husbands and wives. Strikingly, 778 genes were found to show much smaller variances in couples than random pairs of individuals at a false discovery rate (FDR) of 5%. Since genetic variation between unrelated family members in a general population is expected to be the same assuming a random-mating society, non-genetic factors (e.g., epigenetic systems) are more likely to be the mediators for the observed transcriptional similarity in couples. We thus evaluated the contribution of modified cytosines to those genes showing transcriptional similarity in couples as well as the relationships these CpG sites with other gene regulatory elements, such as transcription factor binding sites (TFBS). Our findings suggested that transcriptional similarity in couples likely reflected shared common environment partially mediated through cytosine modifications. PeerJ Inc. 2016-06-14 /pmc/articles/PMC4911945/ /pubmed/27326381 http://dx.doi.org/10.7717/peerj.2123 Text en ©2016 Tang and Zhang http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Tang, Ke
Zhang, Wei
Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines
title Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines
title_full Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines
title_fullStr Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines
title_full_unstemmed Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines
title_short Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines
title_sort transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911945/
https://www.ncbi.nlm.nih.gov/pubmed/27326381
http://dx.doi.org/10.7717/peerj.2123
work_keys_str_mv AT tangke transcriptionalsimilarityincouplesrevealstheimpactofsharedenvironmentandlifestyleongeneregulationthroughmodifiedcytosines
AT zhangwei transcriptionalsimilarityincouplesrevealstheimpactofsharedenvironmentandlifestyleongeneregulationthroughmodifiedcytosines