Identification and characterization of L1-specific endo-siRNAs essential for early embryonic development in pig.

Heng Zhang,Jiawei Lv,Xiaolei Zhang,Jilong Liu,Shichao Liu,Jiaming Zhang,Yurong Tai,Zhonghua Liu,Qingran Kong

doi:10.18632/oncotarget.15517

Heng Zhang, Jiawei Lv + Show 7 more

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https://doi.org/10.18632/oncotarget.15517

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Abstract

Small noncoding RNAs (sncRNAs) play important roles in RNA interference (RNAi). In addition to microRNA (miRNA) and Piwi-interacting RNA (piRNA), one key member of sncRNAs group is endogenous small interfering RNA (endo-siRNA). Some studies do show the role of endo-siRNAs in Dicer and/or Ago mutants, however, the biological functions of specific endo-siRNAs remains mostly unanswered. In the study, we have performed a comparative analysis of endo-siRNAs present in porcine sperms, oocytes and zygotes, identified by deep sequencing and bioinformatics analysis. Further, we observe a large amount of endo-siRNAs specific binding on ORF2 and 3′ UTR of porcine L1 (L1-siRNAs). And, 9 L1-siRNAs generated from a dsRNA formed between L1 transcript and a newly identified an antisense noncoding RNA was characterized. We show the L1-siRNAs regulate early embryonic development by inhibiting the activity of L1 retrotransposition. This work can contribute to understanding the functional role of abundant endo-siRNAs in embryonic development.

Highlights

RNA interference (RNAi) is a sequence-dependent mechanism in gene regulation [1]
Due to small noncoding RNAs (sncRNAs) populations have been less studied in pig, so the first challenge of the study was to classify the sncRNAs into miRNAs, Piwi-interacting RNA (piRNA) and endo-siRNAs
To identify long hairpin RNA-associated siRNAs, we searched the genome region compassing more than 15 unique sncRNA sequences less than 10kb, and we extracted the regions of every clusters to predict RNA secondary structure using RNAfold, and we characterized the endo-siRNAs mapped in the predicted long hairpin RNA as Lhp-siRNAs (Supplementary Table 3)

Summary

Introduction

RNA interference (RNAi) is a sequence-dependent mechanism in gene regulation [1]. The mechanism is determined by a family of small noncoding RNAs (sncRNAs), including microRNA (miRNA), Piwiinteracting RNA (piRNA) and endogenous small interfering RNA (endo-siRNA) [2, 3]. Endo-siRNAs are processed from long doublestranded RNA (dsRNA) precursors by digestion with an RNase III enzyme, DICER, and one of the two strands guides AGO2,the endonucleolytic component of RNA-induced silencing complex (RISC), to cleave the targets [4, 5]. Endo-siRNAs are perfectly complementary to their targets and trigger pre-mRNA/mRNA cleavage. The structures of the dsRNA precursors of endo-siRNAs are derived from transposable elements, complementary annealed transcripts, and long “fold-back” transcripts called hairpin RNAs (hpRNAs) [5,6,7]. According to the dsRNA structures, endo-siRNAs can be characterized

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