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

Hulf T, Sibbritt T, Wiklund ED, Bert S, Strbenac D, Statham AL, Robinson MD, Clark SJ - BMC Genomics (2011)

Bottom Line: Cancer is commonly associated with widespread disruption of DNA methylation, chromatin modification and miRNA expression.We find miR-205, miR-21, and miR-196b to be epigenetically repressed, and miR-615 epigenetically activated in prostate cancer cells.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia.

ABSTRACT

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.

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Related in: MedlinePlus

Schematic displaying experimental discovery pipeline used for identification of miRNAs epigenetically deregulated in cancer. To identify epigenetically regulated miRNAs, we employed an integrative approach assessing changes in epigenetic marks, primary miRNA transcript, and mature miRNA. (A, B) Custom tiling arrays probing all miRNA loci (miRBase12.0, 668 miRNA loci) were used to assay primary miRNA transcription and epigenetic marks (H3K9Ac and DNA methylation) from PrEC and LNCaP cells. Example tiling array intensity plots are shown of the 2000 bp region spanning the miR-205 gene for both expression (A), and DNA methylation (B), showing the chromosomal coordinate (x-axis) and the hybridization intensity (y-axis), with regions displaying significant differences highlighted. (C) Global mature miRNA expression levels in PrEC and LNCaP cells +/- 5-Aza-CdR treatment (3 μM LNCaP, 1 μM PrEC; 72 hours) as determined by TLDA qRT-PCR (368 miRNAs).
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Figure 1: Schematic displaying experimental discovery pipeline used for identification of miRNAs epigenetically deregulated in cancer. To identify epigenetically regulated miRNAs, we employed an integrative approach assessing changes in epigenetic marks, primary miRNA transcript, and mature miRNA. (A, B) Custom tiling arrays probing all miRNA loci (miRBase12.0, 668 miRNA loci) were used to assay primary miRNA transcription and epigenetic marks (H3K9Ac and DNA methylation) from PrEC and LNCaP cells. Example tiling array intensity plots are shown of the 2000 bp region spanning the miR-205 gene for both expression (A), and DNA methylation (B), showing the chromosomal coordinate (x-axis) and the hybridization intensity (y-axis), with regions displaying significant differences highlighted. (C) Global mature miRNA expression levels in PrEC and LNCaP cells +/- 5-Aza-CdR treatment (3 μM LNCaP, 1 μM PrEC; 72 hours) as determined by TLDA qRT-PCR (368 miRNAs).

Mentions: We proposed that epigenetically de-regulated miRNAs in cancer would show three characteristics: first, differential expression at the primary transcript level, second, differential mature miRNA expression, and finally an associated change in one or more epigenetic marks. To eliminate post-transcriptionally regulated miRNAs that showed accumulation of epigenetic marks independent of their transcription, an integrative pipeline that assessed all three criteria was developed (Figure 1).


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

Hulf T, Sibbritt T, Wiklund ED, Bert S, Strbenac D, Statham AL, Robinson MD, Clark SJ - BMC Genomics (2011)

Schematic displaying experimental discovery pipeline used for identification of miRNAs epigenetically deregulated in cancer. To identify epigenetically regulated miRNAs, we employed an integrative approach assessing changes in epigenetic marks, primary miRNA transcript, and mature miRNA. (A, B) Custom tiling arrays probing all miRNA loci (miRBase12.0, 668 miRNA loci) were used to assay primary miRNA transcription and epigenetic marks (H3K9Ac and DNA methylation) from PrEC and LNCaP cells. Example tiling array intensity plots are shown of the 2000 bp region spanning the miR-205 gene for both expression (A), and DNA methylation (B), showing the chromosomal coordinate (x-axis) and the hybridization intensity (y-axis), with regions displaying significant differences highlighted. (C) Global mature miRNA expression levels in PrEC and LNCaP cells +/- 5-Aza-CdR treatment (3 μM LNCaP, 1 μM PrEC; 72 hours) as determined by TLDA qRT-PCR (368 miRNAs).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3037319&req=5

Figure 1: Schematic displaying experimental discovery pipeline used for identification of miRNAs epigenetically deregulated in cancer. To identify epigenetically regulated miRNAs, we employed an integrative approach assessing changes in epigenetic marks, primary miRNA transcript, and mature miRNA. (A, B) Custom tiling arrays probing all miRNA loci (miRBase12.0, 668 miRNA loci) were used to assay primary miRNA transcription and epigenetic marks (H3K9Ac and DNA methylation) from PrEC and LNCaP cells. Example tiling array intensity plots are shown of the 2000 bp region spanning the miR-205 gene for both expression (A), and DNA methylation (B), showing the chromosomal coordinate (x-axis) and the hybridization intensity (y-axis), with regions displaying significant differences highlighted. (C) Global mature miRNA expression levels in PrEC and LNCaP cells +/- 5-Aza-CdR treatment (3 μM LNCaP, 1 μM PrEC; 72 hours) as determined by TLDA qRT-PCR (368 miRNAs).
Mentions: We proposed that epigenetically de-regulated miRNAs in cancer would show three characteristics: first, differential expression at the primary transcript level, second, differential mature miRNA expression, and finally an associated change in one or more epigenetic marks. To eliminate post-transcriptionally regulated miRNAs that showed accumulation of epigenetic marks independent of their transcription, an integrative pipeline that assessed all three criteria was developed (Figure 1).

Bottom Line: Cancer is commonly associated with widespread disruption of DNA methylation, chromatin modification and miRNA expression.We find miR-205, miR-21, and miR-196b to be epigenetically repressed, and miR-615 epigenetically activated in prostate cancer cells.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus