title: Does every transcript originate from a gene?
abstract: Outdated gene definitions favored regions corresponding to mature messenger RNAs, in particular, the open reading frame. In eukaryotes, the intergenic space was widely regarded nonfunctional and devoid of RNA transcription. Original concepts were based on the assumption that RNA expression was restricted to known protein-coding genes and a few so-called structural RNA genes, such as ribosomal RNAs or transfer RNAs. With the discovery of introns and, more recently, sensitive techniques for monitoring genome-wide transcription, this view had to be substantially modified. Tiling microarrays and RNA deep sequencing revealed myriads of transcripts, which cover almost entire genomes. The tremendous complexity of non-protein-coding RNA transcription has to be integrated into novel gene definitions. Despite an ever-growing list of functional RNAs, questions concerning the mass of identified transcripts are under dispute. Here, we examined genome-wide transcription from various angles, including evolutionary considerations, and suggest, in analogy to novel alternative splice variants that do not persist, that the vast majority of transcripts represent raw material for potential, albeit rare, exaptation events.
authors.affiliation: Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany.
authors.forename: Carsten A
authors.initials: CA
authors.lastname: Raabe
authors.forename: Jürgen
authors.initials: J
authors.lastname: Brosius
mesh_terms: D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods; D016678:Genome / Q000235:genetics; D007438:Introns / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012333:RNA, Messenger / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger; D012335:RNA, Ribosomal; D022661:RNA, Untranslated; D012343:RNA, Transfer
keywords: coding definition; evolutionary raw material; exaptation; genomic plasticity; stochastic transcription