TABLE 1 | Evidence for widespread transcription

From the following article:

Genome-wide transcription and the implications for genomic organization

Philipp Kapranov, Aarron T. Willingham & Thomas R. Gingeras

Nature Reviews Genetics 8, 413-423 (June 2007)

doi:10.1038/nrg2083

MethodOrganismRefs
Abundance of polysome-associated polyA RNAHomo sapiens82
Nucleic acid hybridization reassociation kinetics (Cot curves)Strongylocentrotus purpuratus (sea urchin)83
 H. sapiens84
Transcription of satellite DNA on chromosomes in oogenesisTriturus cristatus carnifex (crested newt)85
Abundance of 5'-capped RNAs versus those with 3' polyACricetulus griseus (hamster)86
Tiling arrays
Whole genomeEscherichia coli87
 Arabidopsis thaliana88
 Drosophila melanogaster15,89
 H. sapiens90
 Oryza sativa (rice)91
 S. purpuratus92
Whole genome, high resolutionSaccharomyces cerevisiae93
 H. sapiens9
Ten chromosomes, high resolutionH. sapiens3
Chromosome 21–22H. sapiens94
Chromosome 22H. sapiens95
Sequencing
CAGE tagsH. sapiens and Mus musculus7
CAGE tags to identify promotersH. sapiens and M. musculus13,96
PET tagsM. musculus97
SAGE tagsH. sapiens98
LongSAGE tagsH. sapiens11,99
Short RNAsCaenorhabditis elegans100–102
 A. thaliana103
Testes-specific short RNAsH. sapiens, M. musculus and Rattus norvegicus104–108
MPSSH. sapiens109
Human Invitational, 41,118 full-length cDNAsH. sapiens6
FANTOM2, 60,770 full-length cDNAsM. musculus110
FANTOM3, 102,281 full-length cDNAsM. musculus7
Chromatin IP
ChIP–chip: p53, Sp1, cMycH. sapiens23
ChIP–chip:: NFkappaBH. sapiens24
ChIP–chip:: RNA Pol IIH. sapiens111
PET-sequencing-based: p53H. sapiens112
CAGE, cap analysis of gene expression; ChIP–chip, chromatin immunoprecipitation and hybridization to DNA microarray; FANTOM, Functional Annotation of Mouse; MPSS, massively parallel signature sequencing; PET, paired-end ditag; polyA, polyadenylated; SAGE, serial analysis of gene expression.

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