Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage

Autor: Manu Kandpal, Rita Sharma, Namrata Dhaka
Rok vydání: 2021
Předmět:
Zdroj: Physiol Mol Biol Plants
ISSN: 0974-0430
0971-5894
DOI: 10.1007/s12298-021-01059-2
Popis: Long intergenic non-coding RNAs (lincRNAs) belong to the category of long non-coding RNAs (lncRNAs), originated from intergenic regions, which do not code for proteins. LincRNAs perform prominent role in regulation of gene expression during plant development and stress response by directly interacting with DNA, RNA, or proteins, or triggering production of small RNA regulatory molecules. Here, we identified 2973 lincRNAs and investigated their expression dynamics during peduncle elongation in two Indian rice cultivars, Pokkali and Swarna, at the time of heading. Differential expression analysis revealed common and cultivar-specific expression patterns, which we utilized to infer the lincRNA candidates with potential involvement in peduncle elongation and panicle exsertion. Their putative targets were identified using in silico prediction methods followed by pathway mapping and literature-survey based functional analysis. Further, to infer the mechanism of action, we identified the lincRNAs which potentially act as miRNA precursors or target mimics. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01059-2.
Databáze: OpenAIRE
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