Non-coding RNA Task Force

Most eukaryote organisms possess a remarkably conserved RNA silencing mechanism in which double-stranded RNA (dsRNA) precursors are processed into 20~24 nucleotide small RNAs (sRNAs) that regulate the activity of genes, genetic elements, and invading viruses in a sequence-specific manner. Nevertheless the sRNAs landscape is quite diverse among different phyla, some of the RNA silencing machinery between most eukaryotes is conserved. These small non-coding RNAs include several classes molecules: microRNAs (miRNAs) endogenously expressed, small non-coding RNA molecules which play a key role in regulation of gene expression at the post-transcriptional level; small interfering RNAs (siRNAs) acting both at transcriptional and post transcriptional level; Piwi-interacting RNAs (piRNAs) encoded by repetitive elements of the genome; viroid-derived small RNAs (vd-sRNAs) produced from the host defensive response, via RNA silencing and etc.

The currently established next-generation sequencing (NGS) technologies have significantly improved our capacity of small RNA (sRNA) exploration and repertoire discovery. Thanks to the high-throughput feature of massive parallel sequencing, huge amounts of sRNA sequencing data have been accumulated. However, much more research efforts are needed to further exploit these valuable data. Proper analysis of such datasets containing millions of small RNA molecules can reveal not only their class and features but also can identify state changes in expression of particular sRNA playing key role in biological processes, stress responses or antiviral defence.

Primary objective of the task force “Non-coding RNAs data analysis” as part of COST action SeqAhead is to coordinate and establishes research community of scientists related to small RNA analysis from NGS datasets. The force task will facilitate and disseminate “best practices” of sRNA analysis by providing and developing bioinformatics solutions such as software packages and tools for analysis of small RNA-seq NGS data. A key outcome of this task force will be exchanging the analysis solutions and among “small RNA analysis” community and building schemes/protocols/pipelines optimized for small RNA-seq analysis.

The outcomes and deliverables of this task force will be achieved by focusing on the following research issues:

  • Hardware and IT infrastructure for data storage and analysis of small RNAs
  • QC and filtering of small RNA-seq datasets
  • Mapping softwares for short sRNA sequences
  • Analysis of small RNAs without reference genome
  • Classification and annotation of sRNAs
  • Statistics and differential expression of small RNAs from NGS data
  • Repository of existing external and internal tools for sRNAs NGS analysis
  • Protocols and recopies for specific problems in small RNA data analysis


  • “small RNAs data analysis” meetings
  1. Task force meeting on ”NGS and non-coding RNA data analysis” Bari, Italy; 17 - 18 April 2013


  • Lists of protocols, recipes, best practice related to small RNA-seq analysis
  • Lists of Labs and researchers in small RNA data analysis field
  • Software repository linked to the specific analysis protocols
  • Blog page, mail distribution lists


  • Vesselin Baev, University of Plovdiv, Dept. Plant Phys. and Molecular Biology, Plovdiv, Bulgaria
  • Andreas GIsel, CNR, Institute for Biomedical Technologies, Bari, Italy
Last modified: 2013/05/13 10:29 by Andreas Gisel
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