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Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set.

ABSTRACT: The FANTOM2 cDNA sequence data set is an excellent model to demonstrate the power of large-scale cDNA sequencing, with the goal of providing a full-length transcript sequence for each mouse gene. This data set enhances the use of the mouse as a model for human disease. Here we identify mouse cDNA sequences in the FANTOM2 data set for a set of 67 human disease genes that as of May 2002 had no corresponding mouse cDNA annotated in the Mouse Genome Informatics (MGI) database. These 67 human disease genes include genes related to neurological and eye disorders and cancer. We also present a list of the human disease genes and their cloned mouse orthologs found in two public databases, LocusLink and MGI. Allelic variant and gene functional information available in MGI provides additional information relative to these mouse models, whereas computed sequence-based connections at NCBI support facile navigation through multiple genomes.

SUBMITTER: Schriml LM

PROVIDER: S-EPMC403698 | biostudies-literature | 2003 Jun

REPOSITORIES: biostudies-literature

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Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set.

Schriml Lynn M LM Hill David P DP Blake Judith A JA Bono Hidemasa H Wynshaw-Boris Anthony A Pavan William J WJ Ring Brian Z BZ Beisel Kirk K Setou Mitsutoshi M Okazaki Yasushi Y

Genome research 20030601 6B

The FANTOM2 cDNA sequence data set is an excellent model to demonstrate the power of large-scale cDNA sequencing, with the goal of providing a full-length transcript sequence for each mouse gene. This data set enhances the use of the mouse as a model for human disease. Here we identify mouse cDNA sequences in the FANTOM2 data set for a set of 67 human disease genes that as of May 2002 had no corresponding mouse cDNA annotated in the Mouse Genome Informatics (MGI) database. These 67 human disease ...[more]

PMID: 12819148

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Project description:We performed a systematic maximum density subgraph (MDS) detection of conserved sequence regions to discover new, biologically relevant motifs from a set of 21,050 conceptually translated mouse cDNA (FANTOM1) sequences. A total of 3202 candidate sequences, which shared similar regions over >20 amino acid residues, were screened against known conserved regions listed in Pfam, ProDom, and InterPro. The filtering procedure resulted in 139 FANTOM1 sequences belonging to 49 new motif candidates. Using annotations and multiple sequence alignment information, we removed by visual inspection 42 candidates whose members were found to be false positives because of sequence redundancy, alternative splicing, low complexity, transcribed retroviral repeat elements contained in the region of the predicted open reading frame, and reports in the literature. The remaining seven motifs have been expanded by hidden Markov model (HMM) profile searches of SWISS-PROT/TrEMBL from 28 FANTOM1 sequences to 164 members and analyzed in detail on sequence and structure level to elucidate the possible functions of motifs and members. The novel and conserved motif MDS00105 is specific for the mammalian inhibitor of growth (ING) family. Three submotifs MDS00105.1-3 are specific for ING1/ING1L, ING1-homolog, and ING3 subfamilies. The motif MDS00105 together with a PHD finger domain constitutes a module for ING proteins. Structural motif MDS00113 represents a leucine zipper-like motif. Conserved motif MDS00145 is a novel 1-acyl-SN-glycerol-3-phosphate acyltransferase (AGPAT) submotif containing a transmembrane domain that distinguishes AGPAT3 and AGPAT4 from all other acyltransferase domain-containing proteins. Functional motif MDS00148 overlaps with the kazal-type serine protease inhibitor domain but has been detected only in an extracellular loop region of solute carrier 21 (SLC21) (organic anion transporters) family members, which may regulate the specificity of anion uptake. Our motif discovery not only aided in the functional characterization of new mouse orthologs for potential drug targets but also allowed us to predict that at least 16 other new motifs are waiting to be discovered from the current SWISS-PROT/TrEMBL database.

Project description:We developed a reverse genetics system for infectious pancreatic necrosis virus (IPNV), a prototype virus of the Birnaviridae family, with the use of plus-stranded RNA transcripts derived from cloned cDNA. Full-length cDNA clones of the IPNV genome that contained the entire coding and noncoding regions of RNA segments A and B were constructed. Segment A encodes a 106-kDa precursor protein which is cleaved to yield mature VP2, nonstructural protease, and VP3 proteins, whereas segment B encodes the RNA-dependent RNA polymerase VP1. Plus-sense RNA transcripts of both segments were prepared by in vitro transcription of linearized plasmids with T7 RNA polymerase. Transfection of chinook salmon embryo (CHSE) cells with combined transcripts of segments A and B generated infectious IPNV particles 10 days posttransfection. Furthermore, a transfectant virus containing a genetically tagged sequence was generated to confirm the feasibility of this system. The presence and specificity of the recovered virus were ascertained by immunofluorescence staining of infected CHSE cells with rabbit anti-IPNV serum and by nucleotide sequence analysis. In addition, 3'-terminal sequence analysis of RNA from the recovered virus showed that extraneous nucleotides synthesized at the 3' end during in vitro transcription were precisely trimmed or excluded during replication, and hence these were not incorporated into the genome. An attempt was made to determine if RNA-dependent RNA polymerase of IPNV and infectious bursal disease virus (IBDV), another birnavirus, can support virus rescue in heterologous combinations. Thus, CHSE cells were transfected with transcripts derived from IPNV segment A and IBDV segment B and Vero cells were transfected with transcripts derived from IBDV segment A and IPNV segment B. In either case, no infectious IPNV or IBDV particles were generated even after a third passage in cell culture, suggesting that viral RNA-dependent RNA polymerase is species specific. However, the reverse genetics system for IPNV that we developed will greatly facilitate studies of viral replication and pathogenesis and the design of a new generation of live attenuated vaccines.

Dataset Information

Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set.

Publications

Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set.

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