Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.

Imprinted genes display differential allelic expression in a manner that depends on the sex of the transmitting parent. The degree of imprinting is often tissue-specific and/or developmental stage-specific, and may be altered in some diseases including cancer. Here we applied Illumina/Solexa sequenc...

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Autores principales:	Xu Wang, Qi Sun, Sean D McGrath, Elaine R Mardis, Paul D Soloway, Andrew G Clark
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5876a12a29d64617ad0d654fd41afc4e
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spelling	oai:doaj.org-article:5876a12a29d64617ad0d654fd41afc4e2021-11-25T06:18:19ZTranscriptome-wide identification of novel imprinted genes in neonatal mouse brain.1932-620310.1371/journal.pone.0003839https://doaj.org/article/5876a12a29d64617ad0d654fd41afc4e2008-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19052635/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Imprinted genes display differential allelic expression in a manner that depends on the sex of the transmitting parent. The degree of imprinting is often tissue-specific and/or developmental stage-specific, and may be altered in some diseases including cancer. Here we applied Illumina/Solexa sequencing of the transcriptomes of reciprocal F1 mouse neonatal brains and identified 26 genes with parent-of-origin dependent differential allelic expression. Allele-specific Pyrosequencing verified 17 of them, including three novel imprinted genes. The known and novel imprinted genes all are found in proximity to previously reported differentially methylated regions (DMRs). Ten genes known to be imprinted in placenta had sufficient expression levels to attain a read depth that provided statistical power to detect imprinting, and yet all were consistent with non-imprinting in our transcript count data for neonatal brain. Three closely linked and reciprocally imprinted gene pairs were also discovered, and their pattern of expression suggests transcriptional interference. Despite the coverage of more than 5000 genes, this scan only identified three novel imprinted refseq genes in neonatal brain, suggesting that this tissue is nearly exhaustively characterized. This approach has the potential to yield an complete catalog of imprinted genes after application to multiple tissues and developmental stages, shedding light on the mechanism, bioinformatic prediction, and evolution of imprinted genes and diseases associated with genomic imprinting.Xu WangQi SunSean D McGrathElaine R MardisPaul D SolowayAndrew G ClarkPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 12, p e3839 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Xu Wang Qi Sun Sean D McGrath Elaine R Mardis Paul D Soloway Andrew G Clark Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.
description	Imprinted genes display differential allelic expression in a manner that depends on the sex of the transmitting parent. The degree of imprinting is often tissue-specific and/or developmental stage-specific, and may be altered in some diseases including cancer. Here we applied Illumina/Solexa sequencing of the transcriptomes of reciprocal F1 mouse neonatal brains and identified 26 genes with parent-of-origin dependent differential allelic expression. Allele-specific Pyrosequencing verified 17 of them, including three novel imprinted genes. The known and novel imprinted genes all are found in proximity to previously reported differentially methylated regions (DMRs). Ten genes known to be imprinted in placenta had sufficient expression levels to attain a read depth that provided statistical power to detect imprinting, and yet all were consistent with non-imprinting in our transcript count data for neonatal brain. Three closely linked and reciprocally imprinted gene pairs were also discovered, and their pattern of expression suggests transcriptional interference. Despite the coverage of more than 5000 genes, this scan only identified three novel imprinted refseq genes in neonatal brain, suggesting that this tissue is nearly exhaustively characterized. This approach has the potential to yield an complete catalog of imprinted genes after application to multiple tissues and developmental stages, shedding light on the mechanism, bioinformatic prediction, and evolution of imprinted genes and diseases associated with genomic imprinting.
format	article
author	Xu Wang Qi Sun Sean D McGrath Elaine R Mardis Paul D Soloway Andrew G Clark
author_facet	Xu Wang Qi Sun Sean D McGrath Elaine R Mardis Paul D Soloway Andrew G Clark
author_sort	Xu Wang
title	Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.
title_short	Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.
title_full	Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.
title_fullStr	Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.
title_full_unstemmed	Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.
title_sort	transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/5876a12a29d64617ad0d654fd41afc4e
work_keys_str_mv	AT xuwang transcriptomewideidentificationofnovelimprintedgenesinneonatalmousebrain AT qisun transcriptomewideidentificationofnovelimprintedgenesinneonatalmousebrain AT seandmcgrath transcriptomewideidentificationofnovelimprintedgenesinneonatalmousebrain AT elainermardis transcriptomewideidentificationofnovelimprintedgenesinneonatalmousebrain AT pauldsoloway transcriptomewideidentificationofnovelimprintedgenesinneonatalmousebrain AT andrewgclark transcriptomewideidentificationofnovelimprintedgenesinneonatalmousebrain
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Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.

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