title: Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells.
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.
authors.forename: Deivendran
authors.initials: D
authors.lastname: Rengaraj
authors.forename: Sang In
authors.initials: SI
authors.lastname: Lee
authors.forename: Tae Sub
authors.initials: TS
authors.lastname: Park
authors.forename: Hong Jo
authors.initials: HJ
authors.lastname: Lee
authors.forename: Young Min
authors.initials: YM
authors.lastname: Kim
authors.forename: Yoon Ah
authors.initials: YA
authors.lastname: Sohn
authors.forename: Myunghee
authors.initials: M
authors.lastname: Jung
authors.forename: Seung-Jae
authors.initials: SJ
authors.lastname: Noh
authors.forename: Hojin
authors.initials: H
authors.lastname: Jung
authors.affiliation: 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. jaehan@snu.ac.kr.
authors.forename: Jae Yong
authors.initials: JY
authors.lastname: Han
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000235:genetics* / Q000378:metabolism; D030161:Avian Proteins / Q000235:genetics* / Q000378:metabolism; D001756:Blastoderm / Q000378:metabolism*; D002642:Chick Embryo; D002645:Chickens; D053903:DNA Breaks, Double-Stranded; D018507:Gene Expression Regulation, Developmental; D055785:Gene Knockdown Techniques; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D034741:RNA, Small Interfering / Q000235:genetics*; D017422:Sequence Analysis, DNA; D015398:Signal Transduction
chemical_list: D060565:Argonaute Proteins; D030161:Avian Proteins; D034741:RNA, Small Interfering