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Transcriptome stability profiling using 5'-bromouridine IP chase (BRIC-seq) identifies novel and functional microRNA targets in human melanoma cells.

ABSTRACT: RNA half-life is closely related to its cellular physiological function, so stability determinants may have regulatory functions. Micro(mi)RNAs have primarily been studied with respect to post-transcriptional mRNA regulation and target degradation. Here we study the impact of the tumour suppressive melanoma miRNA miR-211 on transcriptome stability and phenotype in the non-pigmented melanoma cell line, A375. Using 5ʹ-bromouridine IP chase (BRIC)-seq, transcriptome-wide RNA stability profiles revealed highly regulated genes and pathways important in this melanoma cell line. By combining BRIC-seq, RNA-seq and in silico predictions, we identified both existing and novel direct miR-211 targets. We validated DUSP3 as one such novel miR-211 target, which itself sustains colony formation and invasion in A375 cells via MAPK/PI3K signalling. miRNAs have the capacity to control RNA turnover as a gene expression mechanism, and RNA stability profiling is an excellent tool for interrogating functionally relevant gene regulatory pathways and miRNA targets when combined with other high-throughput and in silico approaches.

ORGANISM(S): Homo sapiens

PROVIDER: GSE126784 | GEO | 2019/02/20

REPOSITORIES: GEO

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Gene-level expression data in melanocytes and in melanoma cell lines WM1552C and A375 over-expressing miR211

Project description:MicroRNAs (miRNAs) influence cancer development through post-transcriptional negative regulation of both tumor suppressors and oncogenes. We subjected melanoma cell lines, normal melanocytes, and keratinocytes to array based miRNA profiling, and identified several distinct miRNAs with differential expression. Specifically, miR-211 levels were depleted in all eight melanoma cell lines examined, and also in 23 of 30 distinct patient melanoma samples (graded as primary in situ, regional metastatic, distant metastatic and nodal metastatic). Putative target genes of miR-211 were identified, and their anticipated increased expression levels were confirmed in melanoma cell lines, which were reduced in two melanoma cell lines that artificially over-expressed miR-211. Four such target genes (TCF12, RAB22A, KCNMA1 and SLC37A3) were confirmed by a target cleavage assay. Stable over-expression of miR-211 in two melanoma cell lines caused significant growth inhibition and reduced invasiveness. The differential expression of miR-211 in a variety of melanoma cell lines and clinical samples, consistent inverse correlation between miR-211 and its target mRNA levels, and growth retardation and reduced invasiveness of melanoma cell lines by miR-211 are all consistent with the idea that the depletion of miR-211 is a key step in melanoma development and/or progression The 15 Samples in this submission represent gene-level expression profiling of isolated total RNA from WM1552C, WM1552+miRNA211, A375, A375+miRNA211 and melanocytes hybridized to Affymetrix exon ararys.

2010-05-20 | E-GEOD-15281 | biostudies-arrayexpress

Transcriptome stability profiling using 5'-bromouridine IP chase (BRIC-seq) identifies novel and functional microRNA targets in human melanoma cells.

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miR-204-5p and miR-211-5p contribute to BRAF inhibitor resistance in melanoma

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Gene-level expression data in melanocytes and in melanoma cell lines WM1552C and A375 over-expressing miR211

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2016-08-09 | E-GEOD-72619 | biostudies-arrayexpress

Expression profiling of fibroblasts treated with miR-211 and miR-320c

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