Cell Reports
Volume 39, Issue 4, 26 April 2022, 110745
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Article
Critical contribution of 3′ non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA

https://doi.org/10.1016/j.celrep.2022.110745Get rights and content
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Highlights

  • Single nucleotide at g11–g16 are critical for in vivo function of microRNA let-7a

  • let-7a 3′ pairing mediates both perfect and imperfect seed interactions

  • A multiplicity of let-7a target genes is regulated through 3′ non-seed pairing

  • The let-7a 3′ sequence cannot be replaced by that of a close family paralog

Summary

Base pairing of the seed region (g2–g8) is essential for microRNA targeting; however, the in vivo function of the 3′ non-seed region (g9–g22) is less well understood. Here, we report a systematic investigation of the in vivo roles of 3′ non-seed nucleotides in microRNA let-7a, whose entire g9–g22 region is conserved among bilaterians. We find that the 3′ non-seed sequence functionally distinguishes let-7a from its family paralogs. The complete pairing of g11–g16 is essential for let-7a to fully repress multiple key targets, including evolutionarily conserved lin-41, daf-12, and hbl-1. Nucleotides at g17–g22 are less critical but may compensate for mismatches in the g11–g16 region. Interestingly, a certain minimal complementarity to let-7a 3′ non-seed sequence can be required even for sites with perfect seed pairing. These results provide evidence that the specific configurations of both seed and 3′ non-seed base pairing can critically influence microRNA-mediated gene regulation in vivo.

Research topic(s)

CP: Molecular biology

Keywords

microRNA
let-7
lin-41
3′ non-seed pairing
post-transcriptional regulation
daf-12

Data and code availability

  • The raw and processed data of ribosome profiling, RNA-seq, and small RNA seq in this study have been deposited at NCBI Gene Expression Omnibus (GEO) with accession number GSE171748 (Edgar et al., 2002) and are publicly available.

  • All original code has been deposited at GitHub (https://github.com/IsanaVekslerLublinsky/Let7_Proj_code.git.) with Zenodo DOI 6465945, and is publicly available.

  • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

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