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Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a
- Source :
- PLoS Genetics, PLoS Genetics, Vol 17, Iss 12, p e1009934 (2021)
- Publication Year :
- 2021
- Publisher :
- Public Library of Science, 2021.
-
Abstract
- MicroRNAs (miRNA) are short non-coding RNAs widely implicated in gene regulation. Most metazoan miRNAs utilize the RNase III enzymes Drosha and Dicer for biogenesis. One notable exception is the RNA polymerase II transcription start sites (TSS) miRNAs whose biogenesis does not require Drosha. The functional importance of the TSS-miRNA biogenesis is uncertain. To better understand the function of TSS-miRNAs, we applied a modified Crosslinking, Ligation, and Sequencing of Hybrids on Argonaute (AGO-qCLASH) to identify the targets for TSS-miRNAs in HCT116 colorectal cancer cells with or without DROSHA knockout. We observed that miR-320a hybrids dominate in TSS-miRNA hybrids identified by AGO-qCLASH. Targets for miR-320a are enriched for the eIF2 signaling pathway, a downstream component of the unfolded protein response. Consistently, in miR-320a mimic- and antagomir- transfected cells, differentially expressed gene products are associated with eIF2 signaling. Within the AGO-qCLASH data, we identified the endoplasmic reticulum (ER) chaperone calnexin as a direct miR-320a down-regulated target, thus connecting miR-320a to the unfolded protein response. During ER stress, but not amino acid deprivation, miR-320a up-regulates ATF4, a critical transcription factor for resolving ER stress. In summary, our study investigates the targetome of the TSS-miRNAs in colorectal cancer cells and establishes miR-320a as a regulator of unfolded protein response.<br />Author summary MicroRNA biogenesis factors, such as Drosha and Dicer, are frequently dysregulated in cancer, resulting in the disruption of miRNA-mediated gene regulation. Independent of Drosha-processing, transcription start site microRNA levels are elevated compared to most microRNAs in cancer cells with low DROSHA expression. By sequencing Argonaute-bound miRNA/mRNA pairs in colorectal cancer cells in the absence of Drosha, we identify the targetome for transcription start site microRNAs. We discovered a transcription start site miRNA, miR-320a, that down-regulates expression of the endoplasmic reticulum chaperone calnexin, activates expression of ATF4, and thus activates the unfolded protein response.
- Subjects :
- Ribonuclease III
Cancer Research
Calnexin
Eukaryotic Initiation Factor-2
QH426-470
Endoplasmic Reticulum
Biochemistry
DEAD-box RNA Helicases
Gene Knockout Techniques
Untranslated Regions
Cell Movement
Medicine and Health Sciences
Genetics (clinical)
Secretory Pathway
Messenger RNA
Endoplasmic Reticulum Stress
Precipitation Techniques
Nucleic acids
Oncology
Cell Processes
Argonaute Proteins
293T cells
Cell lines
Cellular Structures and Organelles
Transcription Initiation Site
Biological cultures
Colorectal Neoplasms
Research Article
Signal Transduction
3' Utr
Transfection
Research and Analysis Methods
Genetics
Immunoprecipitation
Humans
Non-coding RNA
Molecular Biology Techniques
Molecular Biology
Ecology, Evolution, Behavior and Systematics
Cell Proliferation
Colorectal Cancer
Natural antisense transcripts
Biology and life sciences
Cancers and Neoplasms
Antagomirs
Cell Biology
HCT116 Cells
Activating Transcription Factor 4
Gene regulation
MicroRNAs
RNA
Gene expression
Subjects
Details
- Language :
- English
- ISSN :
- 15537404 and 15537390
- Volume :
- 17
- Issue :
- 12
- Database :
- OpenAIRE
- Journal :
- PLoS Genetics
- Accession number :
- edsair.doi.dedup.....2751f59bdc12b02f26048aa7f841188d