Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments.
Microarrays provide the opportunity to measure transcription from regions of the genome without bias towards the location of known genes. This technology thus offers an important source of genomic sequence annotation that is complementary to cDNA sequencing and computational gene-finding methods. Recent "tiling" microarray experiments that assay transcription at regular intervals throughout the genome have shown evidence of large amounts of transcription outside the boundaries of known genes. This transcription is observed in polyadenylated RNA samples and appears to be derived from intergenic regions, from introns of known genes and from sequences antisense to known transcripts. In this article, we discuss different explanations for this phenomenon.
Johnson
Jason M
JM
Rosetta Inpharmatics LLC, 401 Terry Avenue North, Seattle, WA 98109, USA. jason_johnson@merck.com
Edwards
Stephen
S
Shoemaker
Daniel
D
Schadt
Eric E
EE
D000818:Animals; D002892:Chromosomes, Human, Pair 22; D019295:Computational Biology; D018076:DNA, Complementary / Q000378:metabolism; D005091:Exons; D016678:Genome; D006801:Humans; D007438:Introns; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016376:Oligonucleotides, Antisense / Q000737:chemistry; D020033:Protein Isoforms; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D012984:Software; D013223:Statistics as Topic; D014158:Transcription, Genetic
D018076:DNA, Complementary; D016376:Oligonucleotides, Antisense; D020033:Protein Isoforms; D012333:RNA, Messenger