An expression-independent catalog of genes from human chromosome 22.

Trofatter, James A.; Long, Kimberly R.; Murrell, Jill R.; Stotler, Christy; Gusella, James F.; Buckler, Alan

doi:10.1101/gr.5.3.214

Cited by 25 publications

(19 citation statements)

References 43 publications

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“…An output rate of 0.8 unique exon per cosmid was similar to other long range exon trapping. 12,16 The background of vector-derived false positive pAMP subclones varied between 20-45% in different trapping pools as seen by oligonucleotide hybridization (not shown), a similar background to that observed in previous experiments. 12 The frequency of repetitive sequences in the trapped exons was 6.7% (19 of 285) in this experiment, compared to the 8.9% reported by Chen et al 12 There were 194 exons Ͼ70 bp and these were used in the mapping experiments; 123 were successfully mapped to chromosome 18 and of these 60 were mapped to 18q21.…”

Section: Discussionsupporting

confidence: 55%

Gene identification using exon amplification on human chromosome 18q21: implications for bipolar disorder

et al. 2000

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We previously reported linkage between bipolar disorder and a region on human chromosome (HC) 18q21. To identify genes in this region, exon trapping was performed on cosmids isolated from an HC18-specific cosmid library (LL18NC02) using 47 sequence tagged site (STS) markers from 18q21 as hybridization probes. A total of 285 unique sequences (exons) were obtained from 850 sequenced clones. Homology searching of the databases using NCBI's BLAST algorithms revealed that 31 exons have identity to known genes and/or ESTs, seven are identical to regions of finished genomic sequences in the 18q21 region, 20 have significant similarity (Ͼ30% sequence identity) to genes from human and/or other species, 19 were repetitive sequences, and 208 sequences (72%) are novel. Seventy per cent of the trapped sequences were predicted to be derived from genes using library screening and RT-PCR analyses. This represents an initial stage in characterizing genes in a susceptibility region for further study in bipolar disorder or other diseases that map to this region. Molecular Psychiatry (2000) 5, 502-509.

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Section: Discussionsupporting

confidence: 55%

Gene identification using exon amplification on human chromosome 18q21: implications for bipolar disorder

et al. 2000

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“…This ®nding was con®rmed by examination of 15 ESTs that matched BRL with high homology. Among these, a particular sequence (Accession No H55108) had been derived by exon ampli®cation from a cosmid sequence (Trofatter et al, 1995) previously mapped to human chromosome 22. This EST corresponds to bases 1492 ± 1648 of the BRL sequence.…”

Section: Chromosomal Mappingmentioning

confidence: 99%

The cloning, mapping and expression of a novel gene, BRL, related to the AF10 leukaemia gene

McCullagh¹,

Chaplin²,

Meerabux³

et al. 1999

Oncogene

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The MLL gene is reciprocally translocated with one of a number of di erent partner genes in a proportion of human acute leukaemias. The precise mechanism of oncogenic transformation is unclear since most of the partner genes encode unrelated proteins. However, two partner genes, AF10 and AF17 are related through the presence of a cysteine rich region and a leucine zipper. The identi®cation of other proteins with these structures will aid our understanding of their role in normal and leukaemic cells. We report the cloning of a novel human gene (BRL) which encodes a protein containing a cysteine rich region related to that of AF10 and AF17 and is overall most closely related to the previously known protein BR140. BRL maps to chromosome 22q13 and shows high levels of expression in testis and several cell lines. The deduced protein sequence also contains a bromodomain, four potential LXXLL motifs and four predicted nuclear localization signals. A monoclonal antibody raised to a BRL peptide sequence con®rmed its widespread expression as a 120 Kd protein and demonstrated localization to the nucleus within spermatocytes.

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“…This is similar to other longrange exon trapping studies . 2,3 The size distribution of the exons ranged from 25 to 533 bp (mean ¼ 130, median ¼ 116 bp), similar to the size range of exons analyzed in the human genome . 20,21 Two methods were used to confirm that the trapped exons arose from HC18.…”

Section: Resultsmentioning

confidence: 92%

“…It has proved to be very useful for the isolation of novel transcribed sequences, and been used for large-scale gene identification on chromosomes 21,22, and other regions in the human genome. [2][3][4][5][6][7][8][9][10][11][12][13] Since exon trapping does not rely on expression to identify genes, novel genes represented by trapped exons can be a substantial addition to the human gene content.…”

Section: Introductionmentioning

confidence: 99%

“…14,15 Using selected cosmid clones from the region, we isolated 285 exons and mapped 60 of them to this region of 18q21. 5 We have now extended exon trapping to the entire chromosome for several reasons: (1) additional loci on chromosome 18, including loci on 18p and 18q21.3-23, have been linked to bipolar disorder ; [16][17][18][19] (2) the complete set of genes on this chromosome is probably not yet established, even though the analysis of the human genome sequence provided preliminary evidence in silico only that there are approximately 800 genes on this chromosome; 20,21 (3) published data showed that there was only 20% overlap in the sets of predicted novel genes between public and Celera databases, 22 suggesting that any single method may not be sufficient to identify all human genes. Here we report the trapping, mapping, and sequence analysis of 1138 exons on chromosome 18, which could contribute to the gene content on this chromosome.…”

Section: Introductionmentioning

confidence: 99%

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Trapping and sequence analysis of 1138 putative exons from human chromosome 18

et al. 2003

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In a search for novel genes on chromosome 18 (HC18), on which several regions have been linked to bipolar disorder, we applied exon trapping to HC18-specific cosmids. Among the 1138 exons trapped, 1052 of them have been mapped to HC18, and the remaining 86 have not been localized. No exons were localized to genomic regions other than HC18. BLAST database search revealed that 190 exons were identical to 98 Unigenes on HC18; 98 identical to additional 82 clusters of ESTs not present in the HC18 Unigene set; 39 homologous to genes from human and other species (eo10 À3 ); and the remaining 811 exons had no significant homology to transcripts in public databases. The mapped exons were compared to the 867 annotated genes on HC18 in the Celera databases; 216 exons were identical to 104 Celera 'genes' and the remaining 836 exons were not found in the Celera databases. On average, there were two exons for a matched transcript (known genes and ESTs). Therefore, the 850 novel exons may represent hundreds of novel genes on chromosome 18.

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An expression-independent catalog of genes from human chromosome 22.

Cited by 25 publications

References 43 publications

Gene identification using exon amplification on human chromosome 18q21: implications for bipolar disorder

Gene identification using exon amplification on human chromosome 18q21: implications for bipolar disorder

The cloning, mapping and expression of a novel gene, BRL, related to the AF10 leukaemia gene

Trapping and sequence analysis of 1138 putative exons from human chromosome 18

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