Draft Sequence Of Human Genome Research Articles

Lessons from the human genome: transitions between euchromatin and heterochromatin.

The publication of the human genome draft sequence provides, for the first time, a global view of the structural properties of the human genome. Initial sequence analysis, in combination with previous published reports, reveals that more than half of the transition regions between euchromatin and centromeric heterochromatin contain duplicated segments. The individual duplications originate from diverse euchromatic regions of the human genome, often containing intron-exon structure of known genes. Multiple duplicons are concatenated together to form larger blocks of wall-to-wall duplications. For a single chromosome, these paralogous segments can span >1 Mb of sequence and define a buffer zone between unique sequence and tandemly repeated satellite sequences. Unusual pericentromeric interspersed repeat elements have been identified at the junctions of many of these duplications. Phylogenetic and comparative studies of pericentromeric sequences suggest that this peculiar genome organization has emerged within the last 30 million years of human evolution and is a source of considerable genomic variation between closely related primate species. Interestingly, not all human pericentromeric regions show this proclivity to duplicate and transpose genomic sequence, suggesting at least two different models for the organization of these regions.

The genetics of type 2 diabetes.

Type 2 diabetes mellitus is not a single disease but a genetically heterogeneous group of metabolic disorders sharing glucose intolerance. The precise underlying biochemical defects are unknown and almost certainly include impairments of both insulin secretion and action. The rapidly increasing prevalence of T2D world wide makes it a major cause of morbidity and mortality. Understanding the genetic aetiology of T2D will facilitate its diagnosis, treatment and prevention. The results of linkage and association studies to date demonstrate that, as with other common diseases, multiple genes are involved in the susceptibility to T2D, each making a modest contribution to the overall risk. The completion of the draft human genome sequence and a brace of novel tools for genomic analysis promise to accelerate progress towards a more complete molecular description of T2D.

Molecular cloning and characterization of human WNT5B on chromosome 12p13.3 region.

WNT signaling pathway plays a key role in carcinogenesis and embryogenesis. We have cloned and characterized the human WNT5B. Overlapping WNT5B cDNAs, containing 1080-bp ORF, were isolated. WNT5B encoded a 359-amino-acid polypeptide with the N-terminal signal peptide, four N-linked glycosylation sites, and consensus amino-acid residues conserved among the WNT family. WNT5B showed 80.5% total-amino-acid identity with WNT5A. Comparison between nucleotide sequence of WNT5B cDNA and human genome draft sequences revealed that the WNT5B gene, consisting of 4 exons, was located on human chromosome 12p13.3 region. Northern blot analyses with W5B2 probe detected the 2.8- and 2.4-kb WNT5B mRNAs. WNT5B was moderately expressed in adult prostate and fetal brain, and weakly expressed in fetal lung, kidney, adult liver, ovary, and small intestine. Among human cancer cell lines, WNT5B was expressed in gastric cancer cell lines MKN7, MKN45, KATO-III, and a teratocarcinoma cell line NT2. WNT5B might be implicated in human carcinogenesis through activation of the WNT-beta-catenin-TCF signaling pathway, just like Wnt5a.

FRAT1 and FRAT2, clustered in human chromosome 10q24.1 region, are up-regulated in gastric cancer.

FRAT1 and FRAT2 are cancer-associated genes encoding GSK-3beta-binding proteins. Over-expression of FRAT1 or FRAT2 lead to carcinogenesis through activation of WNT--beta-catenin--TCF signaling pathway. We have previously cloned and characterized FRAT2. Here, we found that FRAT1 and FRAT2 genes were clustered in the human chromosome 10q24.1 region. Blast search revealed that FRAT1 and FRAT2 genes, consisting of a single exon, were located together on human genome draft sequences AC006098.1 and AL355490.7, corresponding to the human chromosome 10q24.1 region. FRAT1 and FRAT2 genes were clustered in a tail to tail manner with an interval of about 10.7 kb. The 2.7-kb FRAT1 mRNA was relatively highly expressed in fetal brain, adult spleen, pancreas, HeLa S3 (cervical cancer), and K-562 (chronic myelogenous leukemia). FRAT1 and FRAT2 were co-expressed in 7 gastric cancer cell lines and 10 cases of primary gastric cancer, and were up-regulated together in gastric cancer cell line TMK1 and 2 cases of primary gastric cancer. These results indicated that FRAT1 and FRAT2 genes were up-regulated together in several cases of human gastric cancer. Up-regulation of FRAT1 and FRAT2 in gastric cancer might lead to carcinogenesis through activation of WNT--beta-catenin--TCF signaling pathway.

Genome-wide detection of alternative splicing in expressed sequences of human genes.

We have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with approximately 2.1 million human mRNA and EST sequences, we mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. A large fraction (47%) of these were observed multiple times, indicating that they comprise a substantial fraction of the mRNA species. The vast majority of the detected alternative forms appear to be novel, and produce highly specific, biologically meaningful control of function in both known and novel human genes, e.g. specific removal of the lysosomal targeting signal from HLA-DM beta chain, replacement of the C-terminal transmembrane domain and cytoplasmic tail in an FC receptor beta chain homolog with a different transmembrane domain and cytoplasmic tail, likely modulating its signal transduction activity. Our data indicate that a large proportion of human genes, probably 42% or more, are alternatively spliced, but that this appears to be observed mainly in certain types of molecules (e.g. cell surface receptors) and systemic functions, particularly the immune system and nervous system. These results provide a comprehensive dataset for understanding the role of alternative splicing in the human genome, accessible at http://www.bioinformatics.ucla.edu/HASDB.

Up-regulation of Frizzled-7 (FZD7) in human gastric cancer

Human Frizzled-7 (FZD7) and human FzE3, showing 98.8% nucleotide identity, encode almost identical WNT receptors with nine amino-acid substitutions. FzE3 is claimed to be expressed specifically in esophageal cancer. We determined the structure of the FZD7 gene and the FZD7 cDNA expressed in esophageal cancer. The FZD7 gene without intron and the FZD7 cDNAs isolated from esophageal cancer cell lines TE4 and TE5 were found to encode WNT receptor identical to FZD7, but not to FzE3. Nucleotide sequence of FzE3 was not identified on the human genome draft sequence. Thus, we could not obtain any data suggesting the existence of FzE3. Expression profile of FZD7 was also investigated. FZD7 was expressed throughout normal gastrointestinal tract, from esophagus to rectum. Among human esophageal and gastric cancer cell lines, expression level of FZD7 was relatively lower in esophageal cancer cell lines, and was highest in the gastric cancer cell line MKN7. FZD7 was up-regulated in one out of six cases of human primary gastric cancer. As over-expression of Frizzled-7 leads to activation of the WNT-beta-catenin-TCF pathway, up-regulation of FZD7 in human gastric cancer might play key roles in carcinogenesis through activation of the WNT-beta-catenin-TCF pathway.

Wellcome Trust discourages Celera subscriptions

Following the controversy over publication of the draft human genome sequence earlier this year by Celera Genomics, the Wellcome Trust have added further fuel to the fire by preventing any Wellcome Trust grant funding from being used to subscribe to the human genome data resources produced by Celera. Access to the Celera sequence is available free to academic users on completion of a Public Access Agreement, but there is a restriction on how the data may be used subsequently. Celera also have a subscription-based analysis package, the ‘Celera Discovery System’, that incorporates the human sequence data with genome sequence data from Drosophila and from the recent Celera mouse genome sequence, as well as giving single nucleotide polymorphism information. Having been involved in the funding of the public human genome sequencing effort, principally through funding of the Sanger Centre in Cambridge, UK, it is unsurprising that the Trust would ask its grant awardees to use the public sequence information. The Director of the Wellcome Trust, Mike Dexter, was reported in Nature as saying: ‘There is no evidence that Celera's database offers any scientific advantage. This is not a ban: we are just trying to get the best value for trust money.’ Wellcome urges its researchers to make themselves aware of the publicly available data before entering into agreements with Celera. DS

What does the human genome sequence mean to you?

For a thorough and independent analysis of the meaning and importance of the February publications of the draft human genome sequences, visit http://news.bmn.com/hmsbeagle/96/notes/feature3. To mark the importance of the event, we are pre-publishing a number of Trends articles about these publications in our free, online magazine, HMS Beagle. You cannot afford to miss these up-to-the-minute commentaries, opinions and updates, written by leading players from across the whole of biology. And they're free!

What does the human genome sequence mean to you?

For a thorough and independent analysis of the meaning and importance of the February publications of the draft human genome sequences, visit http://news.bmn.com/hmsbeagle/96/notes/feature3. To mark the importance of the event, we are pre-publishing a number of Trends articles on these publications in our free, online magazine, HMS Beagle. You cannot afford to miss these up-to-the-minute commentaries, opinions and updates, written by leading players from across the whole of biology. And they're free!http://tibs.trends.com

What does the human genome sequence mean to you?

For a thorough and independent analysis of the meaning and importance of the February publications of the draft human genome sequences, visit http://news.bmn.com/hmsbeagle/96/notes/feature3. To mark the importance of the event, we are pre-publishing a number of Trends articles on these publications in our free, online magazine, HMS Beagle. You cannot afford to miss these up-to-the-minute commentaries, opinions and updates, written by leading players from across the whole of biology. And they're free!

What does the human genome sequence mean to you?

For a thorough and independent analysis of the meaning and importance of the February publications of the draft human genome sequences, visit http://news.bmn.com/hmsbeagle/96/notes/feature3. To mark the importance of the event, we are pre-publishing a number of Trends articles on these publications in our free, online magazine, HMS Beagle. You can't afford to miss these up-to-the-minute commentaries, opinions and updates, written by leading players from across the whole of biology. And they're free!

What does the human genome sequence mean to you?

For a thorough and independent analysis of the meaning and importance of the February publications of the draft human genome sequences, visit: http://news.bmn.com/hmsbeagle/96/notes/feature3To mark the importance of the event, we are pre-publishing a selection of Trends articles on these publications in our free, online magazine, HMS Beagle. You cannot afford to miss these up-to-the-minute commentaries, opinions and updates, written by leading players from across the whole of biology. And they're free!

A high-resolution radiation hybrid map of the human genome draft sequence.

We have constructed a physical map of the human genome by using a panel of 90 whole-genome radiation hybrids (the TNG panel) in conjunction with 40,322 sequence-tagged sites (STSs) derived from random genomic sequences as well as expressed sequences. Of 36,678 STSs on the TNG radiation hybrid map, only 3604 (9.8%) were absent from the unassembled draft sequence of the human genome. Of 20,030 STSs ordered on the TNG map as well as the assembled human genome draft sequence and the Celera assembled human genome sequence, 36% of the STSs had a discrepant order between the working draft sequence and the Celera sequence. The TNG map order was identical to one of the two sequence orders in 60% of these discrepant cases.

Integration of telomere sequences with the draft human genome sequence

Telomeres are the ends of linear eukaryotic chromosomes. To ensure that no large stretches of uncharacterized DNA remain between the ends of the human working draft sequence and the ends of each chromosome, we would need to connect the sequences of the telomeres to the working draft sequence. But telomeres have an unusual DNA sequence composition and organization that makes them particularly difficult to isolate and analyse. Here we use specialized linear yeast artificial chromosome clones, each carrying a large telomere-terminal fragment of human DNA, to integrate most human telomeres with the working draft sequence. Subtelomeric sequence structure appears to vary widely, mainly as a result of large differences in subtelomeric repeat sequence abundance and organization at individual telomeres. Many subtelomeric regions appear to be gene-rich, matching both known and unknown expressed genes. This indicates that human subtelomeric regions are not simply buffers of nonfunctional 'junk DNA' next to the molecular telomere, but are instead functional parts of the expressed genome.

Can sequencing shed light on cell cycling?

Every organism must have cells that can replicate indefinitely. Can the draft human genome sequence tell us how the cell cycle works and how it evolved? We studied two protein families--the cyclins and their partners the cyclin-dependent kinases (Cdks)--and a conserved regulatory circuit, the spindle checkpoint. Disappointingly, we discovered a few novel cyclins and no new Cdks or components of the spindle checkpoint, and could shed little light on the organization of the cell cycle.

Mining the draft human genome.

Now that the draft human genome sequence is available, everyone wants to be able to use it. However, we have perhaps become complacent about our ability to turn new genomes into lists of genes. The higher volume of data associated with a larger genome is accompanied by a much greater increase in complexity. We need to appreciate both the scale of the challenge of vertebrate genome analysis and the limitations of current gene prediction methods and understanding.

Genomics, the cytoskeleton and motility.

The draft human genome sequence is an important step in cataloguing the molecular hardware that supports the processes of life. Here I look at what we have learned from the draft sequence about our cytoskeletal and motility systems. Most cytoskeletal and motility proteins were discovered previously by biochemical isolation, traditional cloning methods or random sequences of complementary DNAs. The ongoing challenges of assembling and annotating genes for motor proteins with long, fragmented coding sequences emphasize the importance of expert knowledge of related proteins and confirmatory evidence from cDNA sequences.

Draft human genome sequence published

Draft human genome sequence published

Cancer and genomics.

Identification of the genes that cause oncogenesis is a central aim of cancer research. We searched the proteins predicted from the draft human genome sequence for paralogues of known tumour suppressor genes, but no novel genes were identified. We then assessed whether it was possible to search directly for oncogenic sequence changes in cancer cells by comparing cancer genome sequences against the draft genome. Apparently chimaeric transcripts (from oncogenic fusion genes generated by chromosomal translocations, the ends of which mapped to different genomic locations) were detected to the same degree in both normal and neoplastic tissues, indicating a significant level of false positives. Our experiment underscores the limited amount and variable quality of DNA sequence from cancer cells that is currently available.

Rank Aggregation Method for Biological Databases

After the first draft sequence of human genome is obtained, the next challenge will be to discover andunderstand the function and variation of genes and to understand how such qualities affect healthand disease. For the sake of this, several powerful techniques for collecting gene expression patternshave been developed, such as microarrays [3], SAGE [7], BodyMap [5] and MPSS [2]. Although thesetechniques certainly enable us to obtain expression profiles regarding enormous genes, each does notcompletely cover all the expression levels of human genes. For obtaining the expressions of as manygenes as possible, compensating the shortage of genes with other profiles and aggregating such theprofiles would be promising. The compensation and aggregation are, however, difficult because of thedifferences of distributions of the expression levels between the expression profiles. The method weshow enables us to aggregate such the expression profiles through gene ranking methods based onstatistical property.