Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation.
We have developed a DNA tag sequencing and mapping strategy called gene identification signature (GIS) analysis, in which 5' and 3' signatures of full-length cDNAs are accurately extracted into paired-end ditags (PETs) that are concatenated for efficient sequencing and mapped to genome sequences to demarcate the transcription boundaries of every gene. GIS analysis is potentially 30-fold more efficient than standard cDNA sequencing approaches for transcriptome characterization. We demonstrated this approach with 116,252 PET sequences derived from mouse embryonic stem cells. Initial analysis of this dataset identified hundreds of previously uncharacterized transcripts, including alternative transcripts of known genes. We also uncovered several intergenically spliced and unusual fusion transcripts, one of which was confirmed as a trans-splicing event and was differentially expressed. The concept of paired-end ditagging described here for transcriptome analysis can also be applied to whole-genome analysis of cis-regulatory and other DNA elements and represents an important technological advance for genome annotation.
Ng
Patrick
P
Genome Institute of Singapore, 60 Biopolis Street, Genome 02-01, Singapore 138672.
Wei
Chia-Lin
CL
Sung
Wing-Kin
WK
Chiu
Kuo Ping
KP
Lipovich
Leonard
L
Ang
Chin Chin
CC
Gupta
Sanjay
S
Shahab
Atif
A
Ridwan
Azmi
A
Wong
Chee Hong
CH
Liu
Edison T
ET
Ruan
Yijun
Y
D024506:5' Flanking Region / Q000235:genetics; D000818:Animals; D002460:Cell Line; D002874:Chromosome Mapping / Q000379:methods*; D015342:DNA Probes / Q000235:genetics*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D051379:Mice; D020543:Proteome / Q000235:genetics* / Q000378:metabolism*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods; D013234:Stem Cells / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism*
D015342:DNA Probes; D020543:Proteome; D014157:Transcription Factors