Article (Scientific journals)
Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells
Kozar, Ines; Philippidou, Demetra; Margue, Christiane et al.
2021In Cancers
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Keywords :
melanoma; microRNA; qCLASH; cancer; BRAF; resistance
Abstract :
[en] MicroRNAs are key post-transcriptional gene regulators often displaying aberrant expression patterns in cancer. As microRNAs are promising disease-associated biomarkers and modulators of responsiveness to anti-cancer therapies, a solid understanding of their targetome is crucial. Despite enormous research efforts, the success rates of available tools to reliably predict microRNAs (miRNA)-target interactions remains limited. To investigate the disease-associated miRNA targetome, we have applied modified cross-linking ligation and sequencing of hybrids (qCLASH) to BRAF-mutant melanoma cells. The resulting RNA-RNA hybrid molecules provide a comprehensive and unbiased snapshot of direct miRNA-target interactions. The regulatory effects on selected miRNA target genes in predicted vs. non-predicted binding regions was validated by miRNA mimic experiments. Most miRNA–target interactions deviate from the central dogma of miRNA targeting up to 60% interactions occur via non-canonical seed pairing with a strong contribution of the 3′ miRNA sequence, and over 50% display a clear bias towards the coding sequence of mRNAs. miRNAs targeting the coding sequence can directly reduce gene expression (miR-34a/CD68), while the majority of non-canonical miRNA interactions appear to have roles beyond target gene suppression (miR-100/AXL). Additionally, non-mRNA targets of miRNAs (lncRNAs) whose interactions mainly occur via non-canonical binding were identified in melanoma. This first application of CLASH sequencing to cancer cells identified over 8 K distinct miRNA–target interactions in melanoma cells. Our data highlight the importance non-canonical interactions, revealing further layers of complexity of post-transcriptional gene regulation in melanoma, thus expanding the pool of miRNA–target interactions, which have so far been omitted in the cancer field.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Kozar, Ines ;  University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)
Philippidou, Demetra ;  University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)
Margue, Christiane  ;  University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)
Gay, Lauren;  University of Florida > Department of Molecular Genetics and Microbiology
Renne, Rolf;  University of Florida > Department of Molecular Genetics and Microbiology
Kreis, Stephanie ;  University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)
External co-authors :
yes
Language :
English
Title :
Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells
Publication date :
04 March 2021
Journal title :
Cancers
ISSN :
2072-6694
Publisher :
MDPI AG, Switzerland
Special issue title :
Non-coding RNA in Cancer: A Focus on Mechanisms of Action, Biomarker Properties, and Treatment Options
Peer reviewed :
Peer Reviewed verified by ORBi
Name of the research project :
PRIDE15/10675146/CANBIO
Funders :
FNR - Fonds National de la Recherche [LU]
Available on ORBilu :
since 10 March 2021

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