Advances in next generation sequencing technologies, particularly RNA-seq, have revealed an unexpectedly large extent of human genome transcription, estimated between 60-90%, and propelled the rapidly growing field of transcriptomics. Since protein-coding genes account for less than 3% of the human genome (numbering about 20,000, or half that of Oryza sativa (rice), and about the same as the roundworm Caenorhabditis elegans), there is an unsurprising and burgeoning interest in understanding the possible functions of the vast numbers of noncoding transcripts (ncRNAs).
ncRNAs may be involved in functional networks that contribute layers of molecular regulation and control, helping to account for the complexity of organisms with relatively small protein-coding genome fractions. Indeed, in addition to the long established and abundant housekeeping ncRNAs such as ribosomal and transfer RNA, in the last decades novel small ncRNAs such as microRNA (miRNA) and small interfering RNA (siRNA), among others, were discovered to be the responsible agents for various regulatory and inhibitory functions.
These studies provided evidence that those huge amounts of non-protein-coding, so-called ‘junk DNA’ present in our genomes were worth another look. Recent findings include a growing number of disease-associated ncRNAs and the largely tissue-specific long ncRNAs, but approaches for detecting, comparing and analyzing these sequences versus protein-coding sequences have different requirements; ncRNA sequences may be conserved only at the level of functional structure versus the linear amino acid-coding sequence of mRNAs, and necessitate different analytical methodologies.
In ‘Detecting and Comparing Non-Coding RNAs in the High-Throughput Era‘, in the current IJMS Special Issue Regulation by non-coding RNAs, Giovanni Bussotti, Cedric Notredame and Anton J. Enright from the European Bioinformatics Institute, Cambridge (GB, AJE) and the Centre for Genomic Regulation, Barcelona, (CN), provide an overview of the conceptual and practical issues in studies of ncRNA sequence, including current analytical methods and clarifications of technical challenges yet to be resolved.