Nineteen Additional Unpredicted Transcripts from Human Chromosome 21

Reymond, Alexandre; Camargo, Anamaria A.; Deutsch, Samuel; Stevenson, Brian J.; Parmigiani, Raphael B.; Ucla, Catherine; Bettoni, Fabiana; Rossier, Colette; Lyle, Robert; Guipponi, Michel; Souza, Sandro de; Iseli, Christian; Jongeneel, C. Victor; Bücher, Philipp; Simpson, Andrew J.G.; Antonarakis, Stylianos E.

doi:10.1006/geno.2002.6781

Cited by 46 publications

(37 citation statements)

References 47 publications

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“…Recently, these findings have been challenged in two articles that used combinations of gene prediction and mRNA expression analysis to show, in one case, that the number of putative genes on this chromosome may be up to 10-fold higher (43,44). Our data support this assumption, for in the chromosome 21 sequencing paper, only two exons were found by gene prediction analysis on the domain described here.…”

Section: Discussionsupporting

confidence: 67%

Characterization of a First Domain of Human High Glycine-Tyrosine and High Sulfur Keratin-associated Protein (KAP) Genes on Chromosome 21q22.1

Rogers¹,

Langbein²,

Winter³

et al. 2002

Journal of Biological Chemistry

103

106

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Analysis of the EBI/GeneBankTM data base using nonhuman hair keratin-associated protein (KAP) cDNA sequences as a query resulted in the identification of a first domain of high glycine-tyrosine and high sulfur KAP genes located on human chromosome 21q22.1. This domain, present on the DNA accession numbers AP001078 and AP001709, was ϳ535 kb in size and contained 17 high glycine-tyrosine and 7 high sulfur KAP genes, as well as 9 KAP pseudogenes. Based on amino acid sequence comparisons of the encoded proteins, the KAP genes could be divided into seven high glycinetyrosine gene families (KAP6 -KAP8, and KAP19 -KAP22) and four high sulfur gene families (KAP11, KAP13, KAP15, and KAP23). The high glycine-tyrosine genes described here appear to represent the complete set of this type of KAP genes present in the human genome. Both systematic cDNA isolation studies from an arrayed scalp cDNA library and in situ hybridization expression studies of all of the KAP genes identified in the 21q22.1 region revealed varying degrees and regions of expression of 11 members of the high tyrosine-glycine genes and 6 members of the high sulfur KAP genes in the hair forming compartment.

show abstract

Section: Discussionsupporting

confidence: 67%

Characterization of a First Domain of Human High Glycine-Tyrosine and High Sulfur Keratin-associated Protein (KAP) Genes on Chromosome 21q22.1

Rogers¹,

Langbein²,

Winter³

et al. 2002

Journal of Biological Chemistry

103

106

View full text Add to dashboard Cite

show abstract

“…Sequence conservation around mammalian splice sites can be predicted by divergence at unselected (non-consensus) base pairs at the neutral rate, coupled with purifying selection on sites matching the splice site consensus 47 . Given the high level of neutral site divergence that has occurred between mammalian and chicken orthologous sequences (see neutral evolutionary rate, below), one would expect that orthologous mammalian-chicken splice sites should show a level of conservation no different from that of any unrelated pair of splice sites.…”

Section: Evolutionary Conservation Of Gene Componentsmentioning

confidence: 99%

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

2004

Nature

2,262

1,054

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“…Out of 123 models, only 2 spliced transcripts (1 Pro-Gen model and 1 GrailEXP model) were confirmed (1.7%). By using this RT-PCR methodology in other studies we documented transcripts of more than 98% of the human chromosome 21 genes, and discovered 19 additional transcripts 10,18 ; we also found 139 additional transcripts in the whole mouse genome 12 . All 26 ESTand 63 adjacent block models were also tested in the presence and absence of reverse transcriptase in hepatoma cell line and brain cDNA pools, to reveal possible unspliced non-coding RNAs.…”

mentioning

confidence: 68%

“…These threshold criteria are informative for the identification of important genomic functional elements 13,14 . From those 3,491 blocks, 1,229 correspond partly or fully to known exonic sequences and annotated pseudogenes of human chromosome 21 (denoted as known) 8,10,[15][16][17][18] , and the remaining 2,262 blocks have unknown function (denoted as unknown). When compared with each other they did not have significant similarity, indicating that they are not repeats or widespread structural features.…”

mentioning

confidence: 99%

Numerous potentially functional but non-genic conserved sequences on human chromosome 21

Dermitzakis

Reymond

Lyle

et al. 2002

Nature

Self Cite

223

145

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The use of comparative genomics to infer genome function relies on the understanding of how different components of the genome change over evolutionary time. The aim of such comparative analysis is to identify conserved, functionally transcribed sequences such as protein-coding genes and non-coding RNA genes, and other functional sequences such as regulatory regions, as well as other genomic features. Here, we have compared the entire human chromosome 21 with syntenic regions of the mouse genome, and have identified a large number of conserved blocks of unknown function. Although previous studies have made similar observations, it is unknown whether these conserved sequences are genes or not. Here we present an extensive experimental and computational analysis of human chromosome 21 in an effort to assign function to sequences conserved between human chromosome 21 (ref. 8) and the syntenic mouse regions. Our data support the presence of a large number of potentially functional non-genic sequences, probably regulatory and structural. The integration of the properties of the conserved components of human chromosome 21 to the rapidly accumulating functional data for this chromosome will improve considerably our understanding of the role of sequence conservation in mammalian genomes

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Nineteen Additional Unpredicted Transcripts from Human Chromosome 21

Cited by 46 publications

References 47 publications

Characterization of a First Domain of Human High Glycine-Tyrosine and High Sulfur Keratin-associated Protein (KAP) Genes on Chromosome 21q22.1

Characterization of a First Domain of Human High Glycine-Tyrosine and High Sulfur Keratin-associated Protein (KAP) Genes on Chromosome 21q22.1

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Numerous potentially functional but non-genic conserved sequences on human chromosome 21

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