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Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues

BACKGROUND: Human endogenous retroviruses (HERV) constitute approximately 8% of the human genome and have long been considered "junk". The sheer number and repetitive nature of these elements make studies of their expression methodologically challenging. Hence, little is known of transcrip...

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Detalles Bibliográficos
Autores principales: Nellåker, Christoffer, Li, Fang, Uhrzander, Fredrik, Tyrcha, Joanna, Karlsson, Håkan
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779825/
https://www.ncbi.nlm.nih.gov/pubmed/19919688
http://dx.doi.org/10.1186/1471-2164-10-532
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author Nellåker, Christoffer
Li, Fang
Uhrzander, Fredrik
Tyrcha, Joanna
Karlsson, Håkan
author_facet Nellåker, Christoffer
Li, Fang
Uhrzander, Fredrik
Tyrcha, Joanna
Karlsson, Håkan
author_sort Nellåker, Christoffer
collection PubMed
description BACKGROUND: Human endogenous retroviruses (HERV) constitute approximately 8% of the human genome and have long been considered "junk". The sheer number and repetitive nature of these elements make studies of their expression methodologically challenging. Hence, little is known of transcription of genomic regions harboring such elements. RESULTS: Applying a recently developed technique for obtaining high resolution melting temperature data, we examined the frequency distributions of HERV-W gag element into 13 Tm categories in human tissues. Transcripts containing HERV-W gag sequences were expressed in non-random patterns with extensive variations in the expression between both tissues, including different brain regions, and individuals. Furthermore, the patterns of such transcripts varied more between individuals in brain regions than other tissues. CONCLUSION: Thus, regulated expression of non-coding regions of the human genome appears to include the HERV-W family of repetitive elements. Although it remains to be established whether such expression patterns represent leakage from transcription of functional regions or specific transcription, the current approach proves itself useful for studying detailed expression patterns of repetitive regions.
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spelling pubmed-27798252009-11-20 Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues Nellåker, Christoffer Li, Fang Uhrzander, Fredrik Tyrcha, Joanna Karlsson, Håkan BMC Genomics Research article BACKGROUND: Human endogenous retroviruses (HERV) constitute approximately 8% of the human genome and have long been considered "junk". The sheer number and repetitive nature of these elements make studies of their expression methodologically challenging. Hence, little is known of transcription of genomic regions harboring such elements. RESULTS: Applying a recently developed technique for obtaining high resolution melting temperature data, we examined the frequency distributions of HERV-W gag element into 13 Tm categories in human tissues. Transcripts containing HERV-W gag sequences were expressed in non-random patterns with extensive variations in the expression between both tissues, including different brain regions, and individuals. Furthermore, the patterns of such transcripts varied more between individuals in brain regions than other tissues. CONCLUSION: Thus, regulated expression of non-coding regions of the human genome appears to include the HERV-W family of repetitive elements. Although it remains to be established whether such expression patterns represent leakage from transcription of functional regions or specific transcription, the current approach proves itself useful for studying detailed expression patterns of repetitive regions. BioMed Central 2009-11-17 /pmc/articles/PMC2779825/ /pubmed/19919688 http://dx.doi.org/10.1186/1471-2164-10-532 Text en Copyright ©2009 Nellåker et al; 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
Nellåker, Christoffer
Li, Fang
Uhrzander, Fredrik
Tyrcha, Joanna
Karlsson, Håkan
Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues
title Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues
title_full Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues
title_fullStr Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues
title_full_unstemmed Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues
title_short Expression profiling of repetitive elements by melting temperature analysis: variation in HERV-W gag expression across human individuals and tissues
title_sort expression profiling of repetitive elements by melting temperature analysis: variation in herv-w gag expression across human individuals and tissues
topic Research article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779825/
https://www.ncbi.nlm.nih.gov/pubmed/19919688
http://dx.doi.org/10.1186/1471-2164-10-532
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