Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription

BACKGROUND: Cancer is commonly associated with widespread disruption of DNA methylation, chromatin modification and miRNA expression. In this study, we established a robust discovery pipeline to identify epigenetically deregulated miRNAs in cancer. RESULTS: Using an integrative approach that combine...

Descripción completa

Detalles Bibliográficos
Autores principales: Hulf, Toby, Sibbritt, Tennille, Wiklund, Erik D, Bert, Saul, Strbenac, Dario, Statham, Aaron L, Robinson, Mark D, Clark, Susan J
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Methodology Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037319/
https://www.ncbi.nlm.nih.gov/pubmed/21255435
http://dx.doi.org/10.1186/1471-2164-12-54
_version_ 1782197971941588992
author Hulf, Toby
Sibbritt, Tennille
Wiklund, Erik D
Bert, Saul
Strbenac, Dario
Statham, Aaron L
Robinson, Mark D
Clark, Susan J
author_facet Hulf, Toby
Sibbritt, Tennille
Wiklund, Erik D
Bert, Saul
Strbenac, Dario
Statham, Aaron L
Robinson, Mark D
Clark, Susan J
author_sort Hulf, Toby
collection PubMed
description BACKGROUND: Cancer is commonly associated with widespread disruption of DNA methylation, chromatin modification and miRNA expression. In this study, we established a robust discovery pipeline to identify epigenetically deregulated miRNAs in cancer. RESULTS: Using an integrative approach that combines primary transcription, genome-wide DNA methylation and H3K9Ac marks with microRNA (miRNA) expression, we identified miRNA genes that were epigenetically modified in cancer. We find miR-205, miR-21, and miR-196b to be epigenetically repressed, and miR-615 epigenetically activated in prostate cancer cells. CONCLUSIONS: We show that detecting changes in primary miRNA transcription levels is a valuable method for detection of local epigenetic modifications that are associated with changes in mature miRNA expression.
format Text
id pubmed-3037319
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-30373192011-02-11 Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription Hulf, Toby Sibbritt, Tennille Wiklund, Erik D Bert, Saul Strbenac, Dario Statham, Aaron L Robinson, Mark D Clark, Susan J BMC Genomics Methodology Article BACKGROUND: Cancer is commonly associated with widespread disruption of DNA methylation, chromatin modification and miRNA expression. In this study, we established a robust discovery pipeline to identify epigenetically deregulated miRNAs in cancer. RESULTS: Using an integrative approach that combines primary transcription, genome-wide DNA methylation and H3K9Ac marks with microRNA (miRNA) expression, we identified miRNA genes that were epigenetically modified in cancer. We find miR-205, miR-21, and miR-196b to be epigenetically repressed, and miR-615 epigenetically activated in prostate cancer cells. CONCLUSIONS: We show that detecting changes in primary miRNA transcription levels is a valuable method for detection of local epigenetic modifications that are associated with changes in mature miRNA expression. BioMed Central 2011-01-21 /pmc/articles/PMC3037319/ /pubmed/21255435 http://dx.doi.org/10.1186/1471-2164-12-54 Text en Copyright ©2011 Hulf 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 Methodology Article
Hulf, Toby
Sibbritt, Tennille
Wiklund, Erik D
Bert, Saul
Strbenac, Dario
Statham, Aaron L
Robinson, Mark D
Clark, Susan J
Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription
title Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription
title_full Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription
title_fullStr Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription
title_full_unstemmed Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription
title_short Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription
title_sort discovery pipeline for epigenetically deregulated mirnas in cancer: integration of primary mirna transcription
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037319/
https://www.ncbi.nlm.nih.gov/pubmed/21255435
http://dx.doi.org/10.1186/1471-2164-12-54
work_keys_str_mv AT hulftoby discoverypipelineforepigeneticallyderegulatedmirnasincancerintegrationofprimarymirnatranscription
AT sibbritttennille discoverypipelineforepigeneticallyderegulatedmirnasincancerintegrationofprimarymirnatranscription
AT wiklunderikd discoverypipelineforepigeneticallyderegulatedmirnasincancerintegrationofprimarymirnatranscription
AT bertsaul discoverypipelineforepigeneticallyderegulatedmirnasincancerintegrationofprimarymirnatranscription
AT strbenacdario discoverypipelineforepigeneticallyderegulatedmirnasincancerintegrationofprimarymirnatranscription
AT stathamaaronl discoverypipelineforepigeneticallyderegulatedmirnasincancerintegrationofprimarymirnatranscription
AT robinsonmarkd discoverypipelineforepigeneticallyderegulatedmirnasincancerintegrationofprimarymirnatranscription
AT clarksusanj discoverypipelineforepigeneticallyderegulatedmirnasincancerintegrationofprimarymirnatranscription

Ejemplares similares