Automated DNA sequencing and analysis of 106 kilobases from human chromosome 19q13.3

Martin-Gallardo, Antonia; McCombie, W. Richard; Gocayne, Jeannine D.; FitzGerald, Michael G.; Wallace, Susan; Lee, B. M. B.; Lamerdin, Jane E.; Trapp, Susan; Kelley, Jenny M.; Liu, L. I.; Dubnick, Melvin J.; Johnston-Dow, L; Kerlavage, Anthony R.; Jong, Pieter J. de; Carrano, A.V.; Fields, Christopher J.; Venter, J. Craig

doi:10.1038/ng0492-34

Cited by 86 publications

(27 citation statements)

References 39 publications

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“…The 3© end of the cDNA was also determined by RACE using essentially the same protocol except that the dT anchor primer was used rather than oligo(dT) to prime the first-strand cDNA. The appropriate cDNA sequence-specific primers were designed from the published sequence corresponding to the open reading frame (ORF) of ASE-1 (Van Duin et al 1989;Martin-Gallardo et al 1992).…”

Section: Methodsmentioning

confidence: 99%

“…This autoantigen is localized to the FCs of the nucleolus during interphase and the NORs of the chromosomes during cell division. This cDNA encompasses a previously identified open reading frame, ASE-1 (Van Duin et al 1989;Martin-Gallardo et al 1992), which is positioned in an antisense orientation to and overlaps the gene for the DNA excision repair enzyme ERCC-1 (Van Duin et al 1986). …”

Section: Introductionmentioning

confidence: 98%

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ASE-1: a novel protein of the fibrillar centres of the nucleolus and nucleolus organizer region of mitotic chromosomes

et al. 1997

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A novel nucleolar component has been identified and cloned using a human autoimmune serum. This antigen, as inferred from the cDNA sequence, is an Mr 55000 protein. Immuno blot analysis, however, of both the native protein and the in vitro translation products of the cDNA showed that they migrate on SDS-PAGE at an apparent molecular mass of 90000 A BLAST search using the cDNA sequence indicated that it is in an antisense orientation to and overlaps the gene of the DNA repair enzyme ERCC-1. An open reading frame, without a translational start site, had been observed by others in this region of the chromosome 19 (19q13.3) and the putative protein was termed ASE-1 (Anti-Sense to ERCC-1). Our cDNA is a full-length equivalent of that open reading frame. ASE-1 was found to contain two domains that are present in a number of nucleolar specific proteins originating from a variety of organisms: a glycine-, arginine- and phenylalanine-rich putative nucleotide interaction domain and an alternating basic/acidic region. Indirect immunofluorescence analysis using antibodies generated to cloned regions of ASE-1 indicated that this protein occurs at the fibrillar centres of the nucleolus in interphase, the putative sites of rDNA transcription, and during cell division it is localized to the nucleolus organizer regions of the chromosomes. ASE-1 co-localises with the RNA polymerase I transcription initiation factor UBF/NOR-90 throughout all stages of the cell cycle and these two proteins associate with each other in vitro.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 98%

ASE-1: a novel protein of the fibrillar centres of the nucleolus and nucleolus organizer region of mitotic chromosomes

et al. 1997

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“…The Huntington disease region in chromosome 4p16.3 showed 26 islands in w740 kb, which gives an average of 1 every -28 kb (20,29,30). An analysis of the ERCCI locus of human chromosome 19q13.3 has detected 6 islands in 106 kb of DNA, representing an average of about 1 in 18 kb (19). Another 6 islands have been mapped in a 180-kb region in human chromosome 10q11.2 at a region tightly linked to the gene responsible for multiple endocrine neoplasia type 2A.…”

Section: Methodsmentioning

confidence: 99%

“…Our estimate depends on the assumption that each CpG island identifies a gene. While it is possible that some are not associated with genes (18), the number is likely to be small, as gene mapping studies across long chromosome regions have shown that novel CpG islands are usually associated with transcripts (19,20). In a few cases genes with two associated CpG islands have been reported (5).…”

Section: Methodsmentioning

confidence: 99%

Number of CpG islands and genes in human and mouse.

Antequera

Bird

1993

Proc. Natl. Acad. Sci. U.S.A.

846

452

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Estimation of gene number in mammals is difficult due to the high proportion of noncoding DNA within the nucleus. In this study, we provide a direct measurement of the number of genes in human and mouse. We have taken advantage of the fact that many mammalian genes are associated with CpG islands whose distinctive properties allow their physical separation from bulk DNA. Our results suggest that there are =45,000 CpG islands per haploid genome in humans and 37,000 in the mouse. Sequence comparison confirms that about 20% of the human CpG islands are absent from the homologous mouse genes. Analysis of a selection of genes suggests that both human and mouse are losing CpG islands over evolutionary time due to de novo methylation in the germ line followed by CpG loss through mutation. This process appears to be more rapid in rodents. Combining the number of CpG islands with the proportion of island-associated genes, we estimate that the total number of genes per haploid genome is 40,000 in both organisms. (see refs. 4-6 for reviews). CpG islands constitute a distinctive fraction of the genome because, unlike bulk DNA, they are nonmethylated and contain the dinucleotide CpG at its expected frequency. Another notable property of CpG islands is that their G+C content is significantly higher than that of non-island DNA. This facilitates their identification even in cloned DNA, where the native methylation pattern has been erased (7).In this study, we have exploited these properties to separate CpG islands from the rest of the genome and determineThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. their absolute number in human and mouse. A previous approach to the number of CpG islands was carried out in mouse by quantitation of end-labeled restriction fragments generated upon digestion of total genomic DNA with the methyl-sensitive restriction endonuclease Hpa II (8). An approximate figure of30,000 CpG islands per haploid genome was suggested. Our results show significant differences between mouse and human that are relevant to our understanding of the origin and maintenance of CpG islands.Because not all genes have CpG islands, the total number of genes cannot be deduced directly from their number. We have taken the study further by establishing the proportion of genes that are CpG island-associated. Combining the number of CpG islands per genome and the percentage of CpG island-associated genes, we obtain a direct estimate of the total number of genes in human and mouse. MATERIALS AND METHODSCell Culture Conditions. The human lymphoblastoid PES cell line (9) was grown in RPMI 1640 medium containing 10% tryptose phosphate broth and supplemented with 10% fetal bovine serum. The mouse embryo stem-cell line EFC-1 (10) was grown in Glasgow minimal essential medium supplemented with 10%o fetal bovine serum, 0.1 mM 2-mercaptoethanol, and 1 mM nonessential am...

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“…1B for the case of the 32 pairs of complementary trinucleotides in the 68-kb GenBank sequence HUMMMDBC (Martin-Gallardo et al 1992). The frequency of one member of each of the pairs is plotted relative to the Y-axis and the frequency of the corresponding member relative to the X-axis.…”

Section: Methodsmentioning

confidence: 99%

Relative roles of primary sequence and (G + C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species

Forsdyke

1995

J Mol Evol

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To an approximation Chargaff's rule (%A = %T; %G = %C) applies to single-stranded DNA. In long sequences, not only complementary bases but also complementary oligonucleotides are present in approximately equal frequencies. This applies to all species studied. However, species usually differ in base composition. With the goal of understanding the evolutionary forces involved, I have compared the frequencies of trinucleotides in long sequences and their shuffled counterparts. Among the 32 complementary trinucleotide pairs there is a hierarchy of frequencies which is influenced both by base composition (not affected by shuffling the order of the bases) and by base order (affected by shuffling). The influence of base order is greatest in DNA of 50% G + C and seems to reflects a more fundamental hierarchy of dinucleotide frequencies. Thus if TpA is at low frequency, all eight TpA-containing trinucleotides are at low frequency. Mammals and their viruses share similar hierarchies, with intra-and intergenomic differences being mainly associated with differences in base composition (percentage G + C). E. coli and, to a lesser extent, Drosophila melanogaster hierarchies differ from mammalian hierarchies; this is associated with differences both in base composition and in base order. It is proposed that Chargaff's rule applies to single-stranded DNA because there has been an evolutionary selection pressure favoring mutations that generate complementary oligonucleotides in close proximity, thus creating a potential to form stem-loops. These are dispersed throughout genomes and are rate-limiting in recombination. Differences in (G + C)% between species would impair interspecies recombination by interfering with stem-loop interactions.

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Automated DNA sequencing and analysis of 106 kilobases from human chromosome 19q13.3

Cited by 86 publications

References 39 publications

ASE-1: a novel protein of the fibrillar centres of the nucleolus and nucleolus organizer region of mitotic chromosomes

ASE-1: a novel protein of the fibrillar centres of the nucleolus and nucleolus organizer region of mitotic chromosomes

Number of CpG islands and genes in human and mouse.

Relative roles of primary sequence and (G + C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species

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