Open Access Research article

Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells

Deivendran Rengaraj12, Sang In Lee1, Tae Sub Park3, Hong Jo Lee1, Young Min Kim1, Yoon Ah Sohn1, Myunghee Jung4, Seung-Jae Noh4, Hojin Jung4 and Jae Yong Han1*

Author Affiliations

1 Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea

2 Department of Animal Science and Technology, Chung-Ang University, Anseong 456-756, Korea

3 Graduate School of International Agricultural Technology and Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang-gun, Gangwon-do 232-916, Korea

4 Codes Division, Insilicogen, Inc, Suwon 441-813, Korea

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BMC Genomics 2014, 15:757  doi:10.1186/1471-2164-15-757

Published: 4 September 2014

Abstract

Background

Genes, RNAs, and proteins play important roles during germline development. However, the functions of non-coding RNAs (ncRNAs) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncRNAs, including micro RNAs (miRNAs), small-interfering RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs). These ncRNAs are functionally important in the genome, however, the identification and annotation of ncRNAs in a genome is challenging. The aim of this study was to identify different types of small ncRNAs particularly piRNAs, and the role of piRNA pathway genes in the protection of chicken primordial germ cells (PGCs).

Results

At first, we performed next-generation sequencing to identify ncRNAs in chicken PGCs, and we performed ab initio predictive analysis to identify putative piRNAs in PGCs. Then, we examined the expression of three repetitive sequence-linked piRNAs and 14 genic-transcript-linked piRNAs along with their linked genes using real-time PCR. All piRNAs and their linked genes were highly expressed in PGCs. Subsequently, we knocked down two known piRNA pathway genes of chicken, PIWI-like protein 1 (CIWI) and 2 (CILI), in PGCs using siRNAs. After knockdown of CIWI and CILI, we examined their effects on the expression of six putative piRNA-linked genes and DNA double-strand breakage in PGCs. The knockdown of CIWI and CILI upregulated chicken repetitive 1 (CR1) element and RAP2B, a member of RAS oncogene family, and increased DNA double-strand breakage in PGCs.

Conclusions

Our results increase the understanding of PGC-expressed piRNAs and the role of piRNA pathway genes in the protection of germ cells.

Keywords:
Aves; Non-coding RNA; piRNA; Primordial Germ Cells