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Detection of large intergenic non-coding RNA

ABSTRACT: Members of the ARGONAUTE gene family are known to have roles in RNA-mediated silencing during development. One of these, MEL1, was shown to be germ-cell specific and essential for progression through sporogenesis at both premeiotic mitosis and meiosis. To understand how the MEL1 gene product is responsible for these effects requires analysis of the changes of the transcriptome. The mel1 gene was identified by TOS 17 insertion mutagenesis of Oryza sativa Japonica, cultivar Nipponbare. The TOS 17 insertion line of mel1 and the wild-type parent were the sources of RNA. RNA was extracted from rice panicle (3 cM) of rice grown under natural conditions in rice fields. Small RNAs associated with MEL1 and small RNAs in total RNA were sequenced by Illumina GAII.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Reina Komiya

PROVIDER: E-MTAB-4365 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs.

Komiya Reina R Ohyanagi Hajime H Niihama Mitsuru M Watanabe Toshiaki T Nakano Mutsuko M Kurata Nori N Nonomura Ken-Ichi K

The Plant journal : for cell and molecular biology 20140415 3

Small RNAs that interact with Argonaute (AGO) proteins play central roles in RNA-mediated silencing. MEIOSIS ARRESTED AT LEPTOTENE1 (MEL1), a rice AGO, has specific functions in the development of pre-meiotic germ cells and the progression of meiosis. Here, we show that MEL1, which is located mostly in the cytoplasm of germ cells, associates preferentially with 21-nucleotide phased small interfering RNAs (phasiRNAs) that bear a 5'-terminal cytosine. Most phasiRNAs are derived from 1171 intergeni ...[more]

PMID: 24635777

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