Ian Dunham

..We obtained clones representing 70% of genes on human chromosome 22, whereas searching available cDNA clone collections found at best 48% from a single collection and 60% for all collections combined...

..There are several theories to account for how the mechanism evolved including the hypothesis that it was driven by the evolution of X-inactivation, or that it arose from an ancestrally imprinted chromosome...

..4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome...

..The sequence of the human genome should be completed in 2003. The next steps are to obtain accurate annotation of the genes within the sequence and to begin to define the sequences of multiple human genomes...

..Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project...

..Positive correlations are observed between replication timing and a number of genomic features including GC content, repeat content and transcriptional activity...

..Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types...

..We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing...

..These relationships have never been reported in mammalian systems for any transcription factor...

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..We suggest that our revised annotation criteria provide a paradigm for future annotation of the human genome...

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..While these gaps constitute only approximately 1% of the sequence, knowledge of the full complement of human genes and regulatory elements is incomplete without their sequences...

..Additionally, our experiments have revealed a novel candidate for Dgcr8-independent microRNA genesis and highlighted the challenges currently facing miRNA annotation...

..Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue...

..We show a positive correlation, both genome-wide and at a high resolution, between replication timing and a range of genome parameters including GC content, gene density and transcriptional activity...

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..SAM is also being used at various other laboratories...

..We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection...

..By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones...

..This approach has allowed us to resolve the previous cDNA and mapping information relating to GGT and link it to the physical map of 22q11...

..Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome...

..Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb...

..This study demonstrates the feasibility of developing genome-wide maps of LD...

..The knockdown phenotype is rescued by expression of Hes6 cDNA resistant to siRNA. These results define a novel role for Hes6 in actin cytoskeletal dynamics in post mitotic myoblasts...

..One known and two putative genes are located within this region but none of these genes shows tylosis-specific mutations within their protein-coding regions. Alternative mechanisms of disease gene action must therefore be considered...

..Here, we studied sequence polymorphisms in 23 Mb on chromosome 10p12-q11, including the putative IDDM10 region, to identify genes associated with T1D...

..These results provide an overview of the functional relationship among histone modifications and gene expression in human cells...

..These experiments confirmed 92% of the potential variants in a panel of 92 individuals. [Details of the SNPs and RFLP assays can be found at http://www.sanger.ac.uk and in dbSNP.]..

..Recent studies also demonstrate that some miRNAs have important roles in reprogramming somatic cells to induced pluripotent stem cells (iPSCs)...

..We have conducted a careful examination of off-target effects during an siRNA screen for novel regulators of the TRAIL apoptosis induction pathway(s)...

..Our data suggests that a similar approach could be used for the in vivo characterization of all predicted/uncharacterized TF and that the analysis could be scaled to the whole genome...

..Tissue-specific expression of these genes in a variety of cell lines, along with other evidence, suggests a role for these enzymes in growth or cell cycle control...

..This finding has important implications for efforts to finish the human genome sequence, complicates comparative sequence analysis of duplicon families, and could profoundly influence the tempo of gene-family evolution...

..dfci.harvard.edu). This expansion of the original ORFeome resource greatly increases the potential experimental search space for large-scale proteomics studies, which will lead to the generation of more comprehensive datasets...

..We confirmed the high frequency of chromosome 6 deletions in AA and GB, and identified two novel commonly deleted regions that may harbour TSGs...

..To accelerate the identification of genes, we sequenced the entire contig of approximately 1.1 Mb. Seven genes were identified within the region of allele loss between D6S264 and D6S149...

..Furthermore, comprehensive epigenetic profiling of 22q-located genes and high-resolution analysis of replication timing across the entire chromosome can be studied using our array...

..The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated...

..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...

..The precise locations of such modified histones may be involved in controlling the colinear expression of genes from the cluster...

..All data will be deposited with the ENCODE consortium as soon as it is shown to be reliable by replication and preliminary analysis. ..