Nineteen additional unpredicted transcripts from human chromosome 21.
The identification of all human chromosome 21 (HC21) genes is a necessary step in understanding the molecular pathogenesis of trisomy 21 (Down syndrome). The first analysis of the sequence of 21q included 127 previously characterized genes and predicted an additional 98 novel anonymous genes. Recently we evaluated the quality of this annotation by characterizing a set of HC21 open reading frames (C21orfs) identified by mapping spliced expressed sequence tags (ESTs) and predicted genes (PREDs), identified only in silico. This study underscored the limitations of in silico-only gene prediction, as many PREDs were incorrectly predicted. To refine the HC21 annotation, we have developed a reliable algorithm to extract and stringently map sequences that contain bona fide 3' transcript ends to the genome. We then created a specific 21q graphical display allowing an integrated view of the data that incorporates new ESTs as well as features such as CpG islands, repeats, and gene predictions. Using these tools we identified 27 new putative genes. To validate these, we sequenced previously cloned cDNAs and carried out RT-PCR, 5'- and 3'-RACE procedures, and comparative mapping. These approaches substantiated 19 new transcripts, thus increasing the HC21 gene count by 9.5%. These transcripts were likely not previously identified because they are small and encode small proteins. We also identified four transcriptional units that are spliced but contain no obvious open reading frame. The HC21 data presented here further emphasize that current gene prediction algorithms miss a substantial number of transcripts that nevertheless can be identified using a combination of experimental approaches and multiple refined algorithms.
Reymond
Alexandre
A
Division of Medical Genetics, University of Geneva Medical School, 1211 Geneva, Switzerland.
Camargo
Anamaria A
AA
Deutsch
Samuel
S
Stevenson
Brian J
BJ
Parmigiani
Raphael B
RB
Ucla
Catherine
C
Bettoni
Fabiana
F
Rossier
Colette
C
Lyle
Robert
R
Guipponi
Michel
M
de Souza
Sandro
S
Iseli
Christian
C
Jongeneel
C Victor
CV
Bucher
Philipp
P
Simpson
Andrew J G
AJ
Antonarakis
Stylianos E
SE
D002891:Chromosomes, Human, Pair 21; D020224:Expressed Sequence Tags; D015894:Genome, Human; D006801:Humans; D008969:Molecular Sequence Data; D009928:Organ Specificity; D014158:Transcription, Genetic