Abstract
MicroRNA (miRNA) biogenesis is finely controlled by complex layers of post-transcriptional regulators, including RNA-binding proteins (RBPs). Here, we show that an RBP, QKI5, activates the processing of primary miR-124-1 (pri-124-1) during erythropoiesis. QKI5 recognizes a distal QKI response element and recruits Microprocessor through interaction with DGCR8. Furthermore, the recruited Microprocessor is brought to pri-124-1 stem loops by a spatial RNA-RNA interaction between two complementary sequences. Thus, mutations disrupting their base-pairing affect the strength of QKI5 activation. When erythropoiesis proceeds, the concomitant decrease of QKI5 releases Microprocessor from pri-124-1 and reduces mature miR-124 levels to facilitate erythrocyte maturation. Mechanistically, miR-124 targets TAL1 and c-MYB, two transcription factors involved in normal erythropoiesis. Importantly, this QKI5-mediated regulation also gives rise to a unique miRNA signature, which is required for erythroid differentiation. Taken together, these results demonstrate the pivotal role of QKI5 in primary miRNA processing during erythropoiesis and provide new insights into how a distal element on primary transcripts affects miRNA biogenesis.
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Acknowledgements
We are thankful to Lingling Chen (Institute of Biochemistry and Cell Biology, CAS, China) for the MS2-MBP plasmid, and Bin Zhu (Peking Union Hospital, China) for assistance in umbilical cord blood preparation, and Bo Wen (Fudan University, China) for helpful discussions. J Yu lab is supported by the National Key Research and Development Program of China (2016YFA0100601), the National Key Basic Research Program of China (2015CB94300), the National Natural Science Foundation of China (81530007, 9144011, 31371322 and 31471227) and CAMS Initiative for Innovative Medicine (2016-12M-3-002).
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( Supplementary information is linked to the online version of the paper on the Cell Research website.)
Supplementary information
Supplementary information, Table S1
List of miRNA candidates involved in the initial screening, related to Figure 1B. (PDF 117 kb)
Supplementary information, Table S2
The real-time PCR results of different transcripts of miRNAs, related to Figure 1B. (XLS 32 kb)
Supplementary information, Table S3
RNA binding protein (RBP) that are predicted to bind primary miR-124-1 (from RBPDB database), related to Figure 2. (XLS 93 kb)
Supplementary information, Table S4
Oligo sequences used in this study. (XLS 60 kb)
Supplementary information, Table S5
Microarry results from GSE30380. (XLS 22 kb)
Supplementary information, Table S6
The real-time PCR results of different transcripts of miRNAs, related to Figure 8C. (XLS 23 kb)
Supplementary information, Table S7
The Gene Ontology analysis of individual and overlapping miRNA targets. (XLS 231 kb)
Supplementary information, Figure S1
The post-transcriptional regulation of miR-124-1 during erythroipoiesis. (PDF 693 kb)
Supplementary information, Figure S2
QKI5 regulates pri-124-1 processing in erythroid cells. (PDF 480 kb)
Supplementary information, Figure S3
QKI5 binds to pri-124-1 transcript. (PDF 218 kb)
Supplementary information, Figure S4
The regulation of QKI5 on pri-124-1 processing is dependent on the QRE. (PDF 107 kb)
Supplementary information, Figure S5
QKI5 acts on the processing of QRE-introduced pri-23a∼27a∼24-2 transcripts. (PDF 228 kb)
Supplementary information, Figure S6
QKI5 and miR-124 are negative regulators for HPCs erythroid differentiation. (PDF 448 kb)
Supplementary information, Figure S7
Functional “rescue assay” in HPCs. (PDF 842 kb)
Supplementary information, Figure S8
QKI5 and miR-124 are negative regulators for in vivo erythroid differentiation. (PDF 215 kb)
Supplementary information, Figure S9
The regulation of multiple miRNAs by QKI5 in erythroid cells. (PDF 1136 kb)
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Wang, F., Song, W., Zhao, H. et al. The RNA-binding protein QKI5 regulates primary miR-124-1 processing via a distal RNA motif during erythropoiesis. Cell Res 27, 416–439 (2017). https://doi.org/10.1038/cr.2017.26
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DOI: https://doi.org/10.1038/cr.2017.26
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