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

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

Publication date: Jun 10, 2019

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 tumor suppressive melanoma miRNA miR-211 on transcriptome stability and phenotype in the non-pigmented melanoma cell line, A375. Using 5′-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 signaling. 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.

Joshi, P., Seki, T., Kitamura, S., Bergano, A., Lee, B., and Perera, R.J. Transcriptome stability profiling using 5′-bromouridine IP chase (BRIC-seq) identifies novel and functional microRNA targets in human melanoma cells. 22928. 2019 RNA Biol.

Concepts Keywords
BRIC MicroRNA sequencing
Colony RNA-Seq
MAPK MicroRNA
Melanoma Biochemistry
MicroRNA Gene expression
MiRNA Branches of biology
MRNA RNA
Phenotype Suppressive melanoma
PI3K Non pigmented melanoma
RNA Seq Pathways important melanoma
Throughput
Transcriptome
Tumor Suppressive

Semantics

Type Source Name
pathway BSID Gene Expression
gene UNIPROT DUSP3
gene UNIPROT MLXIP
gene UNIPROT MYLIP
gene UNIPROT MARCH8
disease MESH tumor
gene UNIPROT IMPACT
gene UNIPROT SLC35G1
disease DOID melanoma
pathway BSID Melanoma
disease MESH melanoma
gene UNIPROT ATP8B1

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