Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios

Abstract Genomic imprinting is an important epigenetic process that silences one of the parentally-inherited alleles of a gene and thereby exhibits allelic-specific expression (ASE). Detection of human imprinting events is hampered by the infeasibility of the reciprocal mating system in humans and t...

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Autores principales:	Trees-Juen Chuang, Yu-Hsiang Tseng, Chia-Ying Chen, Yi-Da Wang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/60da6d5be5c544158fbf70dff5372a33
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spelling	oai:doaj.org-article:60da6d5be5c544158fbf70dff5372a332021-12-02T11:51:02ZAssessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios10.1038/s41598-017-07514-z2045-2322https://doaj.org/article/60da6d5be5c544158fbf70dff5372a332017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-07514-zhttps://doaj.org/toc/2045-2322Abstract Genomic imprinting is an important epigenetic process that silences one of the parentally-inherited alleles of a gene and thereby exhibits allelic-specific expression (ASE). Detection of human imprinting events is hampered by the infeasibility of the reciprocal mating system in humans and the removal of ASE events arising from non-imprinting factors. Here, we describe a pipeline with the pattern of reciprocal allele descendants (RADs) through genotyping and transcriptome sequencing data across independent parent-offspring trios to discriminate between varied types of ASE (e.g., imprinting, genetic variation-dependent ASE, and random monoallelic expression (RME)). We show that the vast majority of ASE events are due to sequence-dependent genetic variant, which are evolutionarily conserved and may themselves play a cis-regulatory role. Particularly, 74% of non-RAD ASE events, even though they exhibit ASE biases toward the same parentally-inherited allele across different individuals, are derived from genetic variation but not imprinting. We further show that the RME effect may affect the effectiveness of the population-based method for detecting imprinting events and our pipeline can help to distinguish between these two ASE types. Taken together, this study provides a good indicator for categorization of different types of ASE, opening up this widespread and complex mechanism for comprehensive characterization.Trees-Juen ChuangYu-Hsiang TsengChia-Ying ChenYi-Da WangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Trees-Juen Chuang Yu-Hsiang Tseng Chia-Ying Chen Yi-Da Wang Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
description	Abstract Genomic imprinting is an important epigenetic process that silences one of the parentally-inherited alleles of a gene and thereby exhibits allelic-specific expression (ASE). Detection of human imprinting events is hampered by the infeasibility of the reciprocal mating system in humans and the removal of ASE events arising from non-imprinting factors. Here, we describe a pipeline with the pattern of reciprocal allele descendants (RADs) through genotyping and transcriptome sequencing data across independent parent-offspring trios to discriminate between varied types of ASE (e.g., imprinting, genetic variation-dependent ASE, and random monoallelic expression (RME)). We show that the vast majority of ASE events are due to sequence-dependent genetic variant, which are evolutionarily conserved and may themselves play a cis-regulatory role. Particularly, 74% of non-RAD ASE events, even though they exhibit ASE biases toward the same parentally-inherited allele across different individuals, are derived from genetic variation but not imprinting. We further show that the RME effect may affect the effectiveness of the population-based method for detecting imprinting events and our pipeline can help to distinguish between these two ASE types. Taken together, this study provides a good indicator for categorization of different types of ASE, opening up this widespread and complex mechanism for comprehensive characterization.
format	article
author	Trees-Juen Chuang Yu-Hsiang Tseng Chia-Ying Chen Yi-Da Wang
author_facet	Trees-Juen Chuang Yu-Hsiang Tseng Chia-Ying Chen Yi-Da Wang
author_sort	Trees-Juen Chuang
title	Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
title_short	Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
title_full	Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
title_fullStr	Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
title_full_unstemmed	Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
title_sort	assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/60da6d5be5c544158fbf70dff5372a33
work_keys_str_mv	AT treesjuenchuang assessmentofimprintingandgeneticvariationdependentmonoallelicexpressionusingreciprocalalleledescendantsbetweenhumanfamilytrios AT yuhsiangtseng assessmentofimprintingandgeneticvariationdependentmonoallelicexpressionusingreciprocalalleledescendantsbetweenhumanfamilytrios AT chiayingchen assessmentofimprintingandgeneticvariationdependentmonoallelicexpressionusingreciprocalalleledescendantsbetweenhumanfamilytrios AT yidawang assessmentofimprintingandgeneticvariationdependentmonoallelicexpressionusingreciprocalalleledescendantsbetweenhumanfamilytrios
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Assessment of imprinting- and genetic variation-dependent monoallelic expression using reciprocal allele descendants between human family trios

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