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Jiang Y, Zhang X, Zhang X, Zhao K, Zhang J, Yang C, Chen Y. Comprehensive Analysis of the Transcriptome-Wide m6A Methylome in Pterygium by MeRIP Sequencing. Front Cell Dev Biol 2021; 9:670528. [PMID: 34249924 PMCID: PMC8267473 DOI: 10.3389/fcell.2021.670528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/04/2021] [Indexed: 01/08/2023] Open
Abstract
Aim Pterygium is a common ocular surface disease, which is affected by a variety of factors. Invasion of the cornea can cause severe vision loss. N6-methyladenosine (m6A) is a common post-transcriptional modification of eukaryotic mRNA, which can regulate mRNA splicing, stability, nuclear transport, and translation. To our best knowledge, there is no current research on the mechanism of m6A in pterygium. Methods We obtained 24 pterygium tissues and 24 conjunctival tissues from each of 24 pterygium patients recruited from Shanghai Yangpu Hospital, and the level of m6A modification was detected using an m6A RNA Methylation Quantification Kit. Expression and location of METTL3, a key m6A methyltransferase, were identified by immunostaining. Then we used m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq), RNA sequencing (RNA-seq), and bioinformatics analyses to compare the differential expression of m6A methylation in pterygium and normal conjunctival tissue. Results We identified 2,949 dysregulated m6A peaks in pterygium tissue, of which 2,145 were significantly upregulated and 804 were significantly downregulated. The altered m6A peak of genes were found to play a key role in the Hippo signaling pathway and endocytosis. Joint analyses of MeRIP-seq and RNA-seq data identified 72 hypermethylated m6A peaks and 15 hypomethylated m6A peaks in mRNA. After analyzing the differentially methylated m6A peaks and synchronously differentially expressed genes, we searched the Gene Expression Omnibus database and identified five genes related to the development of pterygium (DSP, MXRA5, ARHGAP35, TMEM43, and OLFML2A). Conclusion Our research shows that m6A modification plays an important role in the development of pterygium and can be used as a potential new target for the treatment of pterygium in the future.
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Affiliation(s)
- Yaping Jiang
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xin Zhang
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoyan Zhang
- Department of Ophthalmology, Huashan Hospital, Fudan University, Shanghai, China
| | - Kun Zhao
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chuanxi Yang
- Department of Cardiology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yihui Chen
- Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
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Alternative transcription of a shorter, non-anti-angiogenic thrombospondin-2 variant in cancer-associated blood vessels. Oncogene 2018; 37:2573-2585. [PMID: 29467494 PMCID: PMC5945577 DOI: 10.1038/s41388-018-0129-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 12/12/2022]
Abstract
Thrombospondin-2 (TSP2) is an anti-angiogenic matricellular protein that inhibits tumor growth and angiogenesis. Tumor-associated blood vascular endothelial cells (BECs) were isolated from human invasive bladder cancers and from matched normal bladder tissue by immuno-laser capture microdissection. Exon expression profiling analyses revealed a particularly high expression of a short TSP2 transcript containing only the last 9 (3′) exons of the full-length TSP2 transcript. Using 5′ and 3′ RACE (rapid amplification of cDNA ends) and Sanger sequencing, we confirmed the existence of the shorter transcript of TSP2 (sTSP2) and determined its sequence which completely lacked the anti-angiogenic thrombospondin type 1 repeats domain. The largest open reading frame predicted within the transcript comprises 209 amino acids and matches almost completely the C-terminal lectin domain of full-length TSP2. We produced recombinant sTSP2 and found that unlike the full-length TSP2, sTSP2 did not inhibit vascular endothelial growth factor-A-induced proliferation of cultured human BECs, but in contrast when combined with TSP2 blocked the inhibitory effects of TSP2 on BEC proliferation. In vivo studies with stably transfected A431 squamous cell carcinoma cells revealed that full-length TSP2, but not sTSP2, inhibited tumor growth and angiogenesis. This study reveals that the transcriptional program of tumor stromal cells can change to transcribe a new version of an endogenous angiogenesis inhibitor that has lost its anti-angiogenic activity.
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Tamaki T, Kamatsuka K, Sato T, Morooka S, Otsuka K, Hattori M, Sugiyama T. A novel transmembrane protein defines the endoplasmic reticulum stress-induced cell death pathway. Biochem Biophys Res Commun 2017; 486:149-155. [DOI: 10.1016/j.bbrc.2017.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/07/2017] [Indexed: 12/13/2022]
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4
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FAM172A is a tumor suppressor in colorectal carcinoma. Tumour Biol 2015; 37:6501-10. [DOI: 10.1007/s13277-015-4166-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 09/27/2015] [Indexed: 10/22/2022] Open
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Xiao S, Chen YC, Betenbaugh MJ, Martin SE, Shiloach J. MiRNA mimic screen for improved expression of functional neurotensin receptor from HEK293 cells. Biotechnol Bioeng 2015; 112:1632-43. [PMID: 25676429 DOI: 10.1002/bit.25567] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/23/2015] [Accepted: 02/05/2015] [Indexed: 01/17/2023]
Abstract
Obtaining adequate quantities of functional mammalian membrane proteins has been a bottleneck in their structural and functional studies because the expression of these proteins from mammalian cells is relatively low. To explore the possibility of enhancing expression of these proteins using miRNA, a stable T-REx-293 cell line expressing the neurotensin receptor type 1 (NTSR1), a hard-to-express G protein-coupled receptor (GPCR), was constructed. The cell line was then subjected to human miRNA mimic library screening. In parallel, an HEK293 cell line expressing luciferase was also screened with the same human miRNA mimic library. Five microRNA mimics: hsa-miR-22-5p, hsa-miR-18a-5p, hsa-miR-22-3p, hsa-miR-429, and hsa-miR-2110were identified from both screens. They led to 48% increase in the expression of functional NTSR1 and to 239% increase of luciferase expression. These miRNAs were also effective in enhancing the expression of secretedglypican-3 hFc-fusion protein from HEK293 cells.The results indicate that these molecules may have a wide role in enhancing the production of proteins with biomedical interest.
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Affiliation(s)
- Su Xiao
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892.,Departments of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Yu-Chi Chen
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of health, Rockville, Maryland, 20850
| | - Michael J Betenbaugh
- Departments of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Scott E Martin
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of health, Rockville, Maryland, 20850.
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892.
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Identification of cellular proteins that interact with human cytomegalovirus immediate-early protein 1 by protein array assay. Viruses 2013; 6:89-105. [PMID: 24385082 PMCID: PMC3917433 DOI: 10.3390/v6010089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/10/2013] [Accepted: 12/20/2013] [Indexed: 12/13/2022] Open
Abstract
Human cytomegalovirus (HCMV) gene expression during infection is characterized as a sequential process including immediate-early (IE), early (E), and late (L)-stage gene expression. The most abundantly expressed gene at the IE stage of infection is the major IE (MIE) gene that produces IE1 and IE2. IE1 has been the focus of study because it is an important protein, not only for viral gene expression but also for viral replication. It is believed that IE1 plays important roles in viral gene regulation by interacting with cellular proteins. In the current study, we performed protein array assays and identified 83 cellular proteins that interact with IE1. Among them, seven are RNA-binding proteins that are important in RNA processing; more than half are nuclear proteins that are involved in gene regulations. Tumorigenesis-related proteins are also found to interact with IE1, implying that the role of IE1 in tumorigenesis might need to be reevaluated. Unexpectedly, cytoplasmic proteins, such as Golgi autoantigen and GGA1 (both related to the Golgi trafficking protein), are also found to be associated with IE1. We also employed a coimmunoprecipitation assay to test the interactions of IE1 and some of the proteins identified in the protein array assays and confirmed that the results from the protein array assays are reliable. Many of the proteins identified by the protein array assay have not been previously reported. Therefore, the functions of the IE1-protein interactions need to be further explored in the future.
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Savoy RM, Ghosh PM. The dual role of filamin A in cancer: can't live with (too much of) it, can't live without it. Endocr Relat Cancer 2013; 20:R341-56. [PMID: 24108109 PMCID: PMC4376317 DOI: 10.1530/erc-13-0364] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Filamin A (FlnA) has been associated with actin as cytoskeleton regulator. Recently its role in the cell has come under scrutiny for FlnA's involvement in cancer development. FlnA was originally revealed as a cancer-promoting protein, involved in invasion and metastasis. However, recent studies have also found that under certain conditions, it prevented tumor formation or progression, confusing the precise function of FlnA in cancer development. Here, we try to decipher the role of FlnA in cancer and the implications for its dual role. We propose that differences in subcellular localization of FlnA dictate its role in cancer development. In the cytoplasm, FlnA functions in various growth signaling pathways, such as vascular endothelial growth factor, in addition to being involved in cell migration and adhesion pathways, such as R-Ras and integrin signaling. Involvement in these pathways and various others has shown a correlation between high cytoplasmic FlnA levels and invasive cancers. However, an active cleaved form of FlnA can localize to the nucleus rather than the cytoplasm and its interaction with transcription factors has been linked to a decrease in invasiveness of cancers. Therefore, overexpression of FlnA has a tumor-promoting effect, only when it is localized to the cytoplasm, whereas if FlnA undergoes proteolysis and the resulting C-terminal fragment localizes to the nucleus, it acts to suppress tumor growth and inhibit metastasis. Development of drugs to target FlnA and cause cleavage and subsequent localization to the nucleus could be a new and potent field of research in treating cancer.
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Affiliation(s)
- Rosalinda M Savoy
- Department of Urology, University of California Davis School of Medicine, University of California, 4860 Y Street, Suite 3500, Sacramento, California 95817, USA VA Northern California Health Care System, Mather, California, USA
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Uenishi H, Morozumi T, Toki D, Eguchi-Ogawa T, Rund LA, Schook LB. Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence. BMC Genomics 2012; 13:581. [PMID: 23150988 PMCID: PMC3499286 DOI: 10.1186/1471-2164-13-581] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 08/09/2012] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Along with the draft sequencing of the pig genome, which has been completed by an international consortium, collection of the nucleotide sequences of genes expressed in various tissues and determination of entire cDNA sequences are necessary for investigations of gene function. The sequences of expressed genes are also useful for genome annotation, which is important for isolating the genes responsible for particular traits. RESULTS We performed a large-scale expressed sequence tag (EST) analysis in pigs by using 32 full-length-enriched cDNA libraries derived from 28 kinds of tissues and cells, including seven tissues (brain, cerebellum, colon, hypothalamus, inguinal lymph node, ovary, and spleen) derived from pigs that were cloned from a sow subjected to genome sequencing. We obtained more than 330,000 EST reads from the 5'-ends of the cDNA clones. Comparison with human and bovine gene catalogs revealed that the ESTs corresponded to at least 15,000 genes. cDNA clones representing contigs and singlets generated by assembly of the EST reads were subjected to full-length determination of inserts. We have finished sequencing 31,079 cDNA clones corresponding to more than 12,000 genes. Mapping of the sequences of these cDNA clones on the draft sequence of the pig genome has indicated that the clones are derived from about 15,000 independent loci on the pig genome. CONCLUSIONS ESTs and cDNA sequences derived from full-length-enriched libraries are valuable for annotation of the draft sequence of the pig genome. This information will also contribute to the exploration of promoter sequences on the genome and to molecular biology-based analyses in pigs.
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Affiliation(s)
- Hirohide Uenishi
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
- Division of Animal Sciences, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
- Animal Genome Research Program, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Takeya Morozumi
- Animal Genome Research Program, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
- Animal Research Division, Japan Institute of Association for Techno-innovation in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan
| | - Daisuke Toki
- Animal Genome Research Program, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
- Animal Research Division, Japan Institute of Association for Techno-innovation in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan
| | - Tomoko Eguchi-Ogawa
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
- Animal Genome Research Program, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Lauretta A Rund
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Lawrence B Schook
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
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Eguchi-Ogawa T, Toki D, Wertz N, Butler JE, Uenishi H. Structure of the genomic sequence comprising the immunoglobulin heavy constant (IGHC) genes from Sus scrofa. Mol Immunol 2012; 52:97-107. [DOI: 10.1016/j.molimm.2012.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 04/27/2012] [Accepted: 05/01/2012] [Indexed: 11/29/2022]
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Ohte S, Kokabu S, Iemura SI, Sasanuma H, Yoneyama K, Shin M, Suzuki S, Fukuda T, Nakamura Y, Jimi E, Natsume T, Katagiri T. Identification and functional analysis of Zranb2 as a novel Smad-binding protein that suppresses BMP signaling. J Cell Biochem 2012; 113:808-14. [PMID: 22021003 DOI: 10.1002/jcb.23408] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Smads 1/5/8 transduce the major intracellular signaling of bone morphogenetic proteins (BMPs). In the present study, we analyzed Smad1-binding proteins in HEK293T cells using a proteomic technique and identified the protein, zinc-finger, RAN-binding domain-containing protein 2 (ZRANB2). Zranb2 interacted strongly with Smad1, Smad5, and Smad8 and weakly with Smad4. The overexpression of Zranb2 inhibited BMP activities in C2C12 myoblasts in vitro, and the injection of Zranb2 mRNA into zebrafish embryos induced weak dorsalization. Deletion analyses of Zranb2 indicated that the serine/arginine-rich (SR) domain and the glutamine-rich domain were required for the inhibition of BMP activity and the interaction with Smad1, respectively. Zranb2 was found to be localized in the nucleus; however, the SR domain-deleted mutant localized to the cytoplasm. The knockdown of endogenous Zranb2 in C2C12 cells enhanced BMP activity. Zranb2 suppressed Smad transcriptional activity without affecting Smad phosphorylation, nuclear localization, or DNA binding. Taken together, these findings suggested that Zranb2 is a novel BMP suppressor that forms a complex with Smads in the nucleus.
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Affiliation(s)
- Satoshi Ohte
- Division of Pathophysiology, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama, 350-1241, Japan
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11
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Identification of a 7-gene signature that predicts relapse and survival for early stage patients with cervical carcinoma. Med Oncol 2012; 29:2911-8. [DOI: 10.1007/s12032-012-0166-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 01/09/2012] [Indexed: 11/27/2022]
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A rapid and cost-effective method for sequencing pooled cDNA clones by using a combination of transposon insertion and Gateway technology. Biotechniques 2012; 51:195-7. [PMID: 21906043 DOI: 10.2144/000113737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/14/2011] [Indexed: 11/23/2022] Open
Abstract
Large-scale cDNA-sequencing projects require an efficient strategy for mass sequencing. Here we describe a method for sequencing pooled cDNA clones using a combination of transposon insertion and Gateway technology. Our method reduces the number of shotgun clones that are unsuitable for reconstruction of cDNA sequences, and has the advantage of reducing the total costs of the sequencing project.
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Bonnet C, Grati M, Marlin S, Levilliers J, Hardelin JP, Parodi M, Niasme-Grare M, Zelenika D, Délépine M, Feldmann D, Jonard L, El-Amraoui A, Weil D, Delobel B, Vincent C, Dollfus H, Eliot MM, David A, Calais C, Vigneron J, Montaut-Verient B, Bonneau D, Dubin J, Thauvin C, Duvillard A, Francannet C, Mom T, Lacombe D, Duriez F, Drouin-Garraud V, Thuillier-Obstoy MF, Sigaudy S, Frances AM, Collignon P, Challe G, Couderc R, Lathrop M, Sahel JA, Weissenbach J, Petit C, Denoyelle F. Complete exon sequencing of all known Usher syndrome genes greatly improves molecular diagnosis. Orphanet J Rare Dis 2011; 6:21. [PMID: 21569298 PMCID: PMC3125325 DOI: 10.1186/1750-1172-6-21] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Accepted: 05/11/2011] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Usher syndrome (USH) combines sensorineural deafness with blindness. It is inherited in an autosomal recessive mode. Early diagnosis is critical for adapted educational and patient management choices, and for genetic counseling. To date, nine causative genes have been identified for the three clinical subtypes (USH1, USH2 and USH3). Current diagnostic strategies make use of a genotyping microarray that is based on the previously reported mutations. The purpose of this study was to design a more accurate molecular diagnosis tool. METHODS We sequenced the 366 coding exons and flanking regions of the nine known USH genes, in 54 USH patients (27 USH1, 21 USH2 and 6 USH3). RESULTS Biallelic mutations were detected in 39 patients (72%) and monoallelic mutations in an additional 10 patients (18.5%). In addition to biallelic mutations in one of the USH genes, presumably pathogenic mutations in another USH gene were detected in seven patients (13%), and another patient carried monoallelic mutations in three different USH genes. Notably, none of the USH3 patients carried detectable mutations in the only known USH3 gene, whereas they all carried mutations in USH2 genes. Most importantly, the currently used microarray would have detected only 30 of the 81 different mutations that we found, of which 39 (48%) were novel. CONCLUSIONS Based on these results, complete exon sequencing of the currently known USH genes stands as a definite improvement for molecular diagnosis of this disease, which is of utmost importance in the perspective of gene therapy.
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Affiliation(s)
- Crystel Bonnet
- Unité de Génétique Médicale, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Unité de Génétique et Physiologie de l'Audition, INSERM UMRS 587, UPMC, Institut Pasteur, Paris, France
| | - M'hamed Grati
- Unité de Génétique Médicale, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Unité de Génétique et Physiologie de l'Audition, INSERM UMRS 587, UPMC, Institut Pasteur, Paris, France
- NIDCD, NIH, Bethesda, MD 20894, USA
| | - Sandrine Marlin
- Unité de Génétique Médicale, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jacqueline Levilliers
- Unité de Génétique et Physiologie de l'Audition, INSERM UMRS 587, UPMC, Institut Pasteur, Paris, France
| | - Jean-Pierre Hardelin
- Unité de Génétique et Physiologie de l'Audition, INSERM UMRS 587, UPMC, Institut Pasteur, Paris, France
| | - Marine Parodi
- Service de Biochimie et de Biologie Moléculaire, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, AP-HP, Paris, France
| | - Magali Niasme-Grare
- Service de Biochimie et de Biologie Moléculaire, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, AP-HP, Paris, France
| | | | | | - Delphine Feldmann
- Unité de Génétique Médicale, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Service de Biochimie et de Biologie Moléculaire, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, AP-HP, Paris, France
| | - Laurence Jonard
- Unité de Génétique Médicale, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Service de Biochimie et de Biologie Moléculaire, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, AP-HP, Paris, France
| | - Aziz El-Amraoui
- Unité de Génétique et Physiologie de l'Audition, INSERM UMRS 587, UPMC, Institut Pasteur, Paris, France
| | - Dominique Weil
- Unité de Génétique et Physiologie de l'Audition, INSERM UMRS 587, UPMC, Institut Pasteur, Paris, France
| | - Bruno Delobel
- Centre de Génétique, Hôpital St-Antoine, Lille, France
| | | | - Hélène Dollfus
- Service de Génétique médicale, Hôpital de Hautepierre, Strasbourg, France
| | | | - Albert David
- Service de Génétique, Hôtel Dieu, Nantes, France
| | | | | | | | - Dominique Bonneau
- Centre de Référence des Maladies Neurogénétiques, Centre Hospitalier Universitaire d'Angers, France
| | - Jacques Dubin
- Service ORL, Centre Hospitalier Universitaire d'Angers, France
| | | | | | | | - Thierry Mom
- Service ORL, Hôtel-Dieu, Clermont-Ferrand, France
| | - Didier Lacombe
- Centre de Génétique, Hôpital Pellegrin, Bordeaux, France
| | | | | | | | - Sabine Sigaudy
- Service de Génétique Médicale, Hôpital de la Timone, Marseille, France
| | - Anne-Marie Frances
- Service de Génétique Médicale, Hôpital intercommunal de Font-Pré, Toulon La Seyne sur Mer, France
| | - Patrick Collignon
- Service de Génétique Médicale, Hôpital intercommunal de Font-Pré, Toulon La Seyne sur Mer, France
| | - Georges Challe
- Departement d'Ophtalmologie et de Médecine Interne, Hôpital de la Salpêtrière, AP-HP, France
| | - Rémy Couderc
- Unité de Génétique Médicale, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Service de Biochimie et de Biologie Moléculaire, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, AP-HP, Paris, France
| | - Mark Lathrop
- Centre National de Génotypage, CEA, Evry, France
| | | | - Jean Weissenbach
- CEA, DSV, IG, Genoscope, CNRS-UMR 8030, UEVE, Université d'Evry, Evry, France
| | - Christine Petit
- Unité de Génétique et Physiologie de l'Audition, INSERM UMRS 587, UPMC, Institut Pasteur, Paris, France
- Collège de France, Paris, France
| | - Françoise Denoyelle
- Unité de Génétique et Physiologie de l'Audition, INSERM UMRS 587, UPMC, Institut Pasteur, Paris, France
- Service d'ORL et de Chirurgie Cervico-faciale, INSERM UMRS 587, Hôpital d'Enfants Armand-Trousseau, AP-HP, UPMC, Paris, France
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Palmer E, Freeman T. Investigation into the use of C- and N-terminal GFP fusion proteins for subcellular localization studies using reverse transfection microarrays. Comp Funct Genomics 2010; 5:342-53. [PMID: 18629169 PMCID: PMC2447460 DOI: 10.1002/cfg.405] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2003] [Revised: 03/05/2004] [Accepted: 03/05/2004] [Indexed: 11/07/2022] Open
Abstract
Reverse transfection microarrays were described recently as a high throughput
method for studying gene function. We have investigated the use of this technology for
determining the subcellular localization of proteins. Genes encoding 16 proteins with
a variety of functions were placed in Gateway expression constructs with 3′ or 5′ green
fluorescent protein (GFP) tags. These were then packaged in transfection reagent and
spotted robotically onto a glass slide to form a reverse transfection array. HEK293T
cells were grown over the surface of the array until confluent and GFP fluorescence
visualized by confocal microscopy. All C-terminal fusion proteins localized to cellular
compartments in accordance with previous studies and/or bioinformatic predictions.
However, less than half of the N-terminal fusion proteins localized correctly. Of those
that were not in concordance with the C-terminal tagged proteins, half did not exhibit
expression and the remainder had differing subcellular localizations to the C-terminal
fusion protein. This data indicates that N-terminal tagging with GFP adversely affects
the protein localization in reverse transfection assays, whereas tagging with GFP at
the C-terminal is generally better in preserving the localization of the native protein.
We discuss these results in the context of developing high-throughput subcellular
localization assays based on the reverse transfection array technology.
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15
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USP32 is an active, membrane-bound ubiquitin protease overexpressed in breast cancers. Mamm Genome 2010; 21:388-97. [DOI: 10.1007/s00335-010-9268-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 05/21/2010] [Indexed: 01/20/2023]
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16
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Huerfano S, Zíla V, Boura E, Spanielová H, Stokrová J, Forstová J. Minor capsid proteins of mouse polyomavirus are inducers of apoptosis when produced individually but are only moderate contributors to cell death during the late phase of viral infection. FEBS J 2010; 277:1270-83. [PMID: 20121946 DOI: 10.1111/j.1742-4658.2010.07558.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Minor structural proteins of mouse polyomavirus (MPyV) are essential for virus infection. To study their properties and possible contributions to cell death induction, fusion variants of these proteins, created by linking enhanced green fluorescent protein (EGFP) to their C- or N-termini, were prepared and tested in the absence of other MPyV gene products, namely the tumor antigens and the major capsid protein, VP1. The minor proteins linked to EGFP at their C-terminus (VP2-EGFP, VP3-EGFP) were found to display properties similar to their nonfused, wild-type versions: they killed mouse 3T3 cells quickly when expressed individually. Carrying nuclear localization signals at their common C-terminus, the minor capsid proteins were detected in the nucleus. However, a substantial subpopulation of both VP2 and VP3 proteins, as well as of the fusion proteins VP2-EGFP and VP3-EGFP, was detected in the cytoplasm, co-localizing with intracellular membranes. Truncated VP3 protein, composed of 103 C-terminal amino acids, exhibited reduced affinity for intracellular membranes and cytotoxicity. Biochemical studies proved each of the minor proteins to be a very potent inducer of apoptosis, which was dependent on caspase activation. Immuno-electron microscopy showed the minor proteins to be associated with damaged membranes of the endoplasmic reticulum, nuclear envelope and mitochondria as soon as 5 h post-transfection. Analysis of apoptotic markers and cell death kinetics in cells transfected with the wild-type MPyV genome and the genome mutated in both VP2 and VP3 translation start codons revealed that the minor proteins contribute moderately to apoptotic processes in the late phase of infection and both are dispensable for cell destruction at the end of the virus replication cycle.
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Affiliation(s)
- Sandra Huerfano
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
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17
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Chen H, Patterson N, Reich D. Population differentiation as a test for selective sweeps. Genome Res 2010; 20:393-402. [PMID: 20086244 DOI: 10.1101/gr.100545.109] [Citation(s) in RCA: 480] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Selective sweeps can increase genetic differentiation among populations and cause allele frequency spectra to depart from the expectation under neutrality. We present a likelihood method for detecting selective sweeps that involves jointly modeling the multilocus allele frequency differentiation between two populations. We use Brownian motion to model genetic drift under neutrality, and a deterministic model to approximate the effect of a selective sweep on single nucleotide polymorphisms (SNPs) in the vicinity. We test the method with extensive simulated data, and demonstrate that in some scenarios the method provides higher power than previously reported approaches to detect selective sweeps, and can provide surprisingly good localization of the position of a selected allele. A strength of our technique is that it uses allele frequency differentiation between populations, which is much more robust to ascertainment bias in SNP discovery than methods based on the allele frequency spectrum. We apply this method to compare continentally diverse populations, as well as Northern and Southern Europeans. Our analysis identifies a list of loci as candidate targets of selection, including well-known selected loci and new regions that have not been highlighted by previous scans for selection.
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Affiliation(s)
- Hua Chen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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18
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Maruyama Y, Wakamatsu A, Kawamura Y, Kimura K, Yamamoto JI, Nishikawa T, Kisu Y, Sugano S, Goshima N, Isogai T, Nomura N. Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. Nucleic Acids Res 2009; 37:D762-6. [PMID: 19073703 PMCID: PMC2686585 DOI: 10.1093/nar/gkn872] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Completion of human genome sequencing has greatly accelerated functional genomic research. Full-length cDNA clones are essential experimental tools for functional analysis of human genes. In one of the projects of the New Energy and Industrial Technology Development Organization (NEDO) in Japan, the full-length human cDNA sequencing project (FLJ project), nucleotide sequences of approximately 30 000 human cDNA clones have been analyzed. The Gateway system is a versatile framework to construct a variety of expression clones for various experiments. We have constructed 33 275 human Gateway entry clones from full-length cDNAs, representing to our knowledge the largest collection in the world. Utilizing these clones with a highly efficient cell-free protein synthesis system based on wheat germ extract, we have systematically and comprehensively produced and analyzed human proteins in vitro. Sequence information for both amino acids and nucleotides of open reading frames of cDNAs cloned into Gateway entry clones and in vitro expression data using those clones can be retrieved from the Human Gene and Protein Database (HGPD, http://www.HGPD.jp). HGPD is a unique database that stores the information of a set of human Gateway entry clones and protein expression data and helps the user to search the Gateway entry clones.
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Affiliation(s)
- Yukio Maruyama
- Japan Biological Informatics Consortium, Aomi, Koto-ku, Tokyo 135-8073, Japan
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19
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Schulze JO, Quedenau C, Roske Y, Adam T, Schüler H, Behlke J, Turnbull AP, Sievert V, Scheich C, Mueller U, Heinemann U, Büssow K. Structural and functional characterization of human Iba proteins. FEBS J 2008; 275:4627-40. [DOI: 10.1111/j.1742-4658.2008.06605.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Kohl T, Schmidt C, Wiemann S, Poustka A, Korf U. Automated production of recombinant human proteins as resource for proteome research. Proteome Sci 2008; 6:4. [PMID: 18226205 PMCID: PMC2266735 DOI: 10.1186/1477-5956-6-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 01/28/2008] [Indexed: 02/01/2023] Open
Abstract
Background An arbitrary set of 96 human proteins was selected and tested to set-up a fully automated protein production strategy, covering all steps from DNA preparation to protein purification and analysis. The target proteins are encoded by functionally uncharacterized open reading frames (ORF) identified by the German cDNA consortium. Fusion proteins were produced in E. coli with four different fusion tags and tested in five different purification strategies depending on the respective fusion tag. The automated strategy relies on standard liquid handling and clone picking equipment. Results A robust automated strategy for the production of recombinant human proteins in E. coli was established based on a set of four different protein expression vectors resulting in NusA/His, MBP/His, GST and His-tagged proteins. The yield of soluble fusion protein was correlated with the induction temperature and the respective fusion tag. NusA/His and MBP/His fusion proteins are best expressed at low temperature (25°C), whereas the yield of soluble GST fusion proteins was higher when protein expression was induced at elevated temperature. In contrast, the induction of soluble His-tagged fusion proteins was independent of the temperature. Amylose was not found useful for affinity-purification of MBP/His fusion proteins in a high-throughput setting, and metal chelating chromatography is recommended instead. Conclusion Soluble fusion proteins can be produced in E. coli in sufficient qualities and μg/ml culture quantities for downstream applications like microarray-based assays, and studies on protein-protein interactions employing a fully automated protein expression and purification strategy. Future applications might include the optimization of experimental conditions for the large-scale production of soluble recombinant proteins from libraries of open reading frames.
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21
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Kishimoto A, Ono Y, Murakawa K, Ishibashi T, Wakamatsu A, Kanehori K, Nomura N, Isogai T, Yohda M, Sugano S. Classification and characterization of human full-length cDNA clones that are difficult to sequence. CHEM-BIO INFORMATICS JOURNAL 2008. [DOI: 10.1273/cbij.8.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Yukio Ono
- Hitachi Science Systems
- Hitachi High-Tech Manufacturing & Service Corporation
| | | | - Tadashi Ishibashi
- Hitachi Science Systems
- Hitachi High-Tech Manufacturing & Service Corporation
| | - Ai Wakamatsu
- Helix Research Institute
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | | | | | - Takao Isogai
- Helix Research Institute
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | | | - Sumio Sugano
- The Institute of Medical Science, The University of Tokyo
- Laboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo
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22
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Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda JI, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo MDF, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 2007; 36:D793-9. [PMID: 18089548 PMCID: PMC2238988 DOI: 10.1093/nar/gkm999] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.
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Affiliation(s)
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- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan
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23
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Bechtel S, Rosenfelder H, Duda A, Schmidt CP, Ernst U, Wellenreuther R, Mehrle A, Schuster C, Bahr A, Blöcker H, Heubner D, Hoerlein A, Michel G, Wedler H, Köhrer K, Ottenwälder B, Poustka A, Wiemann S, Schupp I. The full-ORF clone resource of the German cDNA Consortium. BMC Genomics 2007; 8:399. [PMID: 17974005 PMCID: PMC2213676 DOI: 10.1186/1471-2164-8-399] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Accepted: 10/31/2007] [Indexed: 11/24/2022] Open
Abstract
Background With the completion of the human genome sequence the functional analysis and characterization of the encoded proteins has become the next urging challenge in the post-genome era. The lack of comprehensive ORFeome resources has thus far hampered systematic applications by protein gain-of-function analysis. Gene and ORF coverage with full-length ORF clones thus needs to be extended. In combination with a unique and versatile cloning system, these will provide the tools for genome-wide systematic functional analyses, to achieve a deeper insight into complex biological processes. Results Here we describe the generation of a full-ORF clone resource of human genes applying the Gateway cloning technology (Invitrogen). A pipeline for efficient cloning and sequencing was developed and a sample tracking database was implemented to streamline the clone production process targeting more than 2,200 different ORFs. In addition, a robust cloning strategy was established, permitting the simultaneous generation of two clone variants that contain a particular ORF with as well as without a stop codon by the implementation of only one additional working step into the cloning procedure. Up to 92 % of the targeted ORFs were successfully amplified by PCR and more than 93 % of the amplicons successfully cloned. Conclusion The German cDNA Consortium ORFeome resource currently consists of more than 3,800 sequence-verified entry clones representing ORFs, cloned with and without stop codon, for about 1,700 different gene loci. 177 splice variants were cloned representing 121 of these genes. The entry clones have been used to generate over 5,000 different expression constructs, providing the basis for functional profiling applications. As a member of the recently formed international ORFeome collaboration we substantially contribute to generating and providing a whole genome human ORFeome collection in a unique cloning system that is made freely available in the community.
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Affiliation(s)
- Stephanie Bechtel
- Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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24
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Starkuviene V, Pepperkok R, Erfle H. Transfected cell microarrays: an efficient tool for high-throughput functional analysis. Expert Rev Proteomics 2007; 4:479-89. [PMID: 17705706 DOI: 10.1586/14789450.4.4.479] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transfected cell microarrays are considered to be a breakthrough methodology for high-throughput and high-content functional genomics. Here, recent advances in the cell microarray field are reviewed, along with its potential to increase the speed of determining gene function. These advances, combined with an increasing number and diversity of gene perturbing systems, such as RNAi and ectopic gene expression, provide tools for expanding our understanding of biology at the systems level.
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Affiliation(s)
- Vytaute Starkuviene
- European Molecular Biology Laboratory, Cell Biology & Cell Biophysics Unit, Heidelberg, Germany.
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25
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Starkuviene V, Pepperkok R. The potential of high-content high-throughput microscopy in drug discovery. Br J Pharmacol 2007; 152:62-71. [PMID: 17603554 PMCID: PMC1978277 DOI: 10.1038/sj.bjp.0707346] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Fluorescence microscopy is a powerful method to study protein function in its natural habitat, the living cell. With the availability of the green fluorescent protein and its spectral variants, almost any gene of interest can be fluorescently labelled in living cells opening the possibility to study protein localization, dynamics and interactions. The emergence of automated cellular systems allows rapid visualization of large groups of cells and phenotypic analysis in a quantitative manner. Here, we discuss recent advances in high-content high-throughput microscopy and its potential application to several steps of the drug discovery process.
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Affiliation(s)
- V Starkuviene
- Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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26
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del Val C, Ernst P, Falkenhahn M, Fladerer C, Glatting KH, Suhai S, Hotz-Wagenblatt A. ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. Nucleic Acids Res 2007; 35:W444-50. [PMID: 17526514 PMCID: PMC1933246 DOI: 10.1093/nar/gkm364] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The wealth of transcript information that has been made publicly available in recent years has led to large pools of individual web sites offering access to bioinformatics software. However, finding out which services exist, what they can or cannot do, how to use them and how to feed results from one service to the next one in the right format can be very time and resource consuming, especially for non-experts. Automating this task, we present a suite of protein annotation pipelines (tasks) developed at the German Cancer Research Centre (DKFZ) oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep). The aim of these tasks is to perform an exhaustive structural and functional analysis employing a wide variety of methods in combination with the most updated public databases. The three servers are available for academic users at the HUSAR open server http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar/
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Affiliation(s)
- C del Val
- DKFZ, German Cancer Research Center, Division of Molecular Biophysics, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.
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27
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Sakakibara Y, Irie T, Suzuki Y, Yamashita R, Wakaguri H, Kanai A, Chiba J, Takagi T, Mizushima-Sugano J, Hashimoto SI, Nakai K, Sugano S. Intrinsic promoter activities of primary DNA sequences in the human genome. DNA Res 2007; 14:71-7. [PMID: 17522093 PMCID: PMC2779894 DOI: 10.1093/dnares/dsm006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In order to understand an overview of promoter activities intrinsic to primary DNA sequences in the human genome within a particular cell type, we carried out systematic quantitative luciferase assays of DNA fragments corresponding to putative promoters for 472 human genes which are expressed in HEK (human embryonic kidney epithelial) 293 cells. We observed the promoter activities of them were distributed in a bimodal manner; putative promoters belonging to the first group (with strong promoter activities) were designated as P1 and the latter (with weak promoter activities) as P2. The frequencies of the TATA-boxes, the CpG islands, and the overall G + C-contents were significantly different between these two populations, indicating there are two separate groups of promoters. Interestingly, similar analysis using 251 randomly isolated genomic DNA fragments showed that P2-type promoter occasionally occurs within the human genome. Furthermore, 35 DNA fragments corresponding to putative promoters of non-protein-coding transcripts (ncRNAs) shared similar features with the P2 in both promoter activities and sequence compositions. At least, a part of ncRNAs, which have been massively identified by full-length cDNA projects with no functional relevance inferred, may have originated from those sporadic promoter activities of primary DNA sequences inherent to the human genome.
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Affiliation(s)
- Yuta Sakakibara
- Graduate School of Frontier Sciences, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
- Faculty of Industrial Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
| | - Takuma Irie
- Graduate School of Frontier Sciences, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
- To whom correspondence should be addressed. Tel/Fax. +81 4-7136-3607. E-mail:
| | - Riu Yamashita
- Human Genome Center, The Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
| | - Hiroyuki Wakaguri
- Graduate School of Frontier Sciences, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
| | - Akinori Kanai
- Graduate School of Frontier Sciences, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
| | - Joe Chiba
- Faculty of Industrial Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
| | - Toshihisa Takagi
- Graduate School of Frontier Sciences, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
| | - Junko Mizushima-Sugano
- Graduate School of Frontier Sciences, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
- Laboratory of Viral Infection II, Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Sirokane Minato-ku, Tokyo 108-8641, Japan
| | - Shin-ichi Hashimoto
- School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyoku, Tokyo 113-0033, Japan
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
| | - Sumio Sugano
- Graduate School of Frontier Sciences, the University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
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28
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Sauermann M, Hahne F, Schmidt C, Majety M, Rosenfelder H, Bechtel S, Huber W, Poustka A, Arlt D, Wiemann S. High-throughput flow cytometry-based assay to identify apoptosis-inducing proteins. ACTA ACUST UNITED AC 2007; 12:510-20. [PMID: 17478479 DOI: 10.1177/1087057107301271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
After sequencing the human genome, the challenge ahead is to systematically analyze the functions and disease relation of the proteins encoded. Here the authors describe the application of a flow cytometry-based high-throughput assay to screen for apoptosis-activating proteins in transiently transfected cells. The assay is based on the detection of activated caspase-3 with a specific antibody, in cells overexpressing proteins tagged C- or N-terminally with yellow fluorescent protein. Fluorescence intensities are measured using a flow cytometer integrated with a high-throughput autosampler. The applicability of this screen has been tested in a pilot screen with 200 proteins. The candidate proteins were all verified in an independent microscopy-based nuclear fragmentation assay, finally resulting in the identification of 6 apoptosis inducers.
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Affiliation(s)
- Mamatha Sauermann
- Division of Molecular Genome Analysis, German Cancer Research Centre, Heidelberg, Germany
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29
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Yuan J, Palioura S, Salazar JC, Su D, O'Donoghue P, Hohn MJ, Cardoso AM, Whitman WB, Söll D. RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc Natl Acad Sci U S A 2006; 103:18923-7. [PMID: 17142313 PMCID: PMC1748153 DOI: 10.1073/pnas.0609703104] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The trace element selenium is found in proteins as selenocysteine (Sec), the 21st amino acid to participate in ribosome-mediated translation. The substrate for ribosomal protein synthesis is selenocysteinyl-tRNA(Sec). Its biosynthesis from seryl-tRNA(Sec) has been established for bacteria, but the mechanism of conversion from Ser-tRNA(Sec) remained unresolved for archaea and eukarya. Here, we provide evidence for a different route present in these domains of life that requires the tRNA(Sec)-dependent conversion of O-phosphoserine (Sep) to Sec. In this two-step pathway, O-phosphoseryl-tRNA(Sec) kinase (PSTK) converts Ser-tRNA(Sec) to Sep-tRNA(Sec). This misacylated tRNA is the obligatory precursor for a Sep-tRNA:Sec-tRNA synthase (SepSecS); this protein was previously annotated as SLA/LP. The human and archaeal SepSecS genes complement in vivo an Escherichia coli Sec synthase (SelA) deletion strain. Furthermore, purified recombinant SepSecS converts Sep-tRNA(Sec) into Sec-tRNA(Sec) in vitro in the presence of sodium selenite and purified recombinant E. coli selenophosphate synthetase (SelD). Phylogenetic arguments suggest that Sec decoding was present in the last universal common ancestor. SepSecS and PSTK coevolved with the archaeal and eukaryotic lineages, but the history of PSTK is marked by several horizontal gene transfer events, including transfer to non-Sec-decoding Cyanobacteria and fungi.
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Affiliation(s)
- Jing Yuan
- Departments of *Molecular Biophysics and Biochemistry and
| | | | | | - Dan Su
- Departments of *Molecular Biophysics and Biochemistry and
| | | | | | | | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605
| | - Dieter Söll
- Departments of *Molecular Biophysics and Biochemistry and
- Chemistry, Yale University, New Haven, CT 06520-8114; and
- To whom correspondence should be addressed. E-mail:
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del Val C, Kuryshev VY, Glatting KH, Ernst P, Hotz-Wagenblatt A, Poustka A, Suhai S, Wiemann S. CAFTAN: a tool for fast mapping, and quality assessment of cDNAs. BMC Bioinformatics 2006; 7:473. [PMID: 17064411 PMCID: PMC1636072 DOI: 10.1186/1471-2105-7-473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Accepted: 10/25/2006] [Indexed: 11/10/2022] Open
Abstract
Background The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient use of large cDNA resources requires the development of strategies that are capable of a speedy selection of truly useful cDNAs from biological and experimental noise. To this end we have developed a new high-throughput analysis tool, CAFTAN, which simplifies these efforts and thus fills the gap between large-scale cDNA collections and their systematic annotation and application in functional genomics. Results CAFTAN is built around the mapping of cDNAs to the genome assembly, and the subsequent analysis of their genomic context. It uses sequence features like the presence and type of PolyA signals, inner and flanking repeats, the GC-content, splice site types, etc. All these features are evaluated in individual tests and classify cDNAs according to their sequence quality and likelihood to have been generated from fully processed mRNAs. Additionally, CAFTAN compares the coordinates of mapped cDNAs with the genomic coordinates of reference sets from public available resources (e.g., VEGA, ENSEMBL). This provides detailed information about overlapping exons and the structural classification of cDNAs with respect to the reference set of splice variants. The evaluation of CAFTAN showed that is able to correctly classify more than 85% of 5950 selected "known protein-coding" VEGA cDNAs as high quality multi- or single-exon. It identified as good 80.6 % of the single exon cDNAs and 85 % of the multiple exon cDNAs. The program is written in Perl and in a modular way, allowing the adoption of this strategy to other tasks like EST-annotation, or to extend it by adding new classification rules and new organism databases as they become available. We think that it is a very useful program for the annotation and research of unfinished genomes. Conclusion CAFTAN is a high-throughput sequence analysis tool, which performs a fast and reliable quality prediction of cDNAs. Several thousands of cDNAs can be analyzed in a short time, giving the curator/scientist a first quick overview about the quality and the already existing annotation of a set of cDNAs. It supports the rejection of low quality cDNAs and helps in the selection of likely novel splice variants, and/or completely novel transcripts for new experiments.
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Affiliation(s)
- Coral del Val
- DKFZ, German Cancer Research Center, Division Molecular Biophysics, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- DKFZ, German Cancer Research Center, Division of Molecular Genome Analysis, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Dept. Computer Science and Artificial Intelligence, ETSI Informatics University of Granada, C/Daniel Saucedo Aranda s/n 18071, Granada, Spain
| | - Vladimir Yurjevich Kuryshev
- DKFZ, German Cancer Research Center, Division of Molecular Genome Analysis, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Karl-Heinz Glatting
- DKFZ, German Cancer Research Center, Division Molecular Biophysics, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Peter Ernst
- DKFZ, German Cancer Research Center, Division Molecular Biophysics, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- DKFZ, German Cancer Research Center, Division Molecular Biophysics, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Annemarie Poustka
- DKFZ, German Cancer Research Center, Division of Molecular Genome Analysis, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Sandor Suhai
- DKFZ, German Cancer Research Center, Division Molecular Biophysics, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Stefan Wiemann
- DKFZ, German Cancer Research Center, Division of Molecular Genome Analysis, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
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Laketa V, Simpson JC, Bechtel S, Wiemann S, Pepperkok R. High-content microscopy identifies new neurite outgrowth regulators. Mol Biol Cell 2006; 18:242-52. [PMID: 17093056 PMCID: PMC1751310 DOI: 10.1091/mbc.e06-08-0666] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Neurons, with their long axons and elaborate dendritic arbour, establish the complex circuitry that is essential for the proper functioning of the nervous system. Whereas a catalogue of structural, molecular, and functional differences between axons and dendrites is accumulating, the mechanisms involved in early events of neuronal differentiation, such as neurite initiation and elongation, are less well understood, mainly because the key molecules involved remain elusive. Here we describe the establishment and application of a microscopy-based approach designed to identify novel proteins involved in neurite initiation and/or elongation. We identified 21 proteins that affected neurite outgrowth when ectopically expressed in cells. Complementary time-lapse microscopy allowed us to discriminate between early and late effector proteins. Localization experiments with GFP-tagged proteins in fixed and living cells revealed a further 14 proteins that associated with neurite tips either early or late during neurite outgrowth. Coexpression experiments of the new effector proteins provide a first glimpse on a possible functional relationship of these proteins during neurite outgrowth. Altogether, we demonstrate the potential of the systematic microscope-based screening approaches described here to tackle the complex biological process of neurite outgrowth regulation.
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Affiliation(s)
- Vibor Laketa
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory-Heidelberg, 69117 Heidelberg, Germany.
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Yamasaki C, Kawashima H, Todokoro F, Imamizu Y, Ogawa M, Tanino M, Itoh T, Gojobori T, Imanishi T. TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB. Nucleic Acids Res 2006; 34:W345-9. [PMID: 16845023 PMCID: PMC1538819 DOI: 10.1093/nar/gkl283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Transcriptome Auto-annotation Conducting Tool (TACT) is a newly developed web-based automated tool for conducting functional annotation of transcripts by the integration of sequence similarity searches and functional motif predictions. We developed the TACT system by integrating two kinds of similarity searches, FASTY and BLASTX, against protein sequence databases, UniProtKB (Swiss-Prot/TrEMBL) and RefSeq, and a unified motif prediction program, InterProScan, into the ORF-prediction pipeline originally designed for the ‘H-Invitational’ human transcriptome annotation project. This system successively applies these constituent programs to an mRNA sequence in order to predict the most plausible ORF and the function of the protein encoded. In this study, we applied the TACT system to 19 574 non-redundant human transcripts registered in H-InvDB and evaluated its predictive power by the degree of agreement with human-curated functional annotation in H-InvDB. As a result, the TACT system could assign functional description to 12 559 transcripts (64.2%), the remainder being hypothetical proteins. Furthermore, the overall agreement of functional annotation with H-InvDB, including those transcripts annotated as hypothetical proteins, was 83.9% (16 432/19 574). These results show that the TACT system is useful for functional annotation and that the prediction of ORFs and protein functions is highly accurate and close to the results of human curation. TACT is freely available at .
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Affiliation(s)
- Chisato Yamasaki
- Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumAIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyAIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hiroaki Kawashima
- Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumAIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
- DYNACOM Co., Ltd643 Mobara, Mobara-shi, Chiba 297-0026, Japan
| | - Fusano Todokoro
- DYNACOM Co., Ltd643 Mobara, Mobara-shi, Chiba 297-0026, Japan
| | | | - Makoto Ogawa
- DYNACOM Co., Ltd643 Mobara, Mobara-shi, Chiba 297-0026, Japan
| | - Motohiko Tanino
- Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumAIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyAIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Takeshi Itoh
- Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyAIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Genome Research Department, National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Takashi Gojobori
- Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyAIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies1111 Yata, Mishima Shizuoka 411-8540, Japan
| | - Tadashi Imanishi
- Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyAIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
- To whom correspondence should be addressed. Tel: +81 3 3599 8800; Fax: +81 3 3599 8801;
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Takeda JI, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V, Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T, Imanishi T. Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res 2006; 34:3917-28. [PMID: 16914452 PMCID: PMC1557807 DOI: 10.1093/nar/gkl507] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2006] [Revised: 07/03/2006] [Accepted: 07/03/2006] [Indexed: 11/12/2022] Open
Abstract
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56,419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37,670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants.
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Affiliation(s)
- Jun-ichi Takeda
- Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Mitsuteru Nakao
- Computational Biology Research Center, National Institute of Advanced Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
- Kazusa DNA Research Institute2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Roberto A. Barrero
- Center for Information Biology and DDBJ, National Institute of Genetics1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Kanako O. Koyanagi
- Graduate School of Information Science and Technology, Hokkaido UniversityNorth 14, West 9, Kita-ku, Sapporo, Hokkaido 060-0814, Japan
| | - Lihua Jin
- Center for Information Biology and DDBJ, National Institute of Genetics1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Chie Motono
- Computational Biology Research Center, National Institute of Advanced Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
| | - Hiroko Hata
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Takao Isogai
- Reverse Proteomics Research Institute, 2-6-7 Kazusa-KamatariKisarazu, Chiba 292-0818, Japan
- Helix Research Institute, Inc. 1532-3Yana, Kisarazu, Chiba 292-0812, Japan
| | - Keiichi Nagai
- Helix Research Institute, Inc. 1532-3Yana, Kisarazu, Chiba 292-0812, Japan
- Central Research Laboratory, Hitachi Ltd1-280, Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8601, Japan
| | - Tetsuji Otsuki
- Helix Research Institute, Inc. 1532-3Yana, Kisarazu, Chiba 292-0812, Japan
| | - Vladimir Kuryshev
- Division of Molecular Genome Analysis, German Cancer Research CenterIm Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Masafumi Shionyu
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Kei Yura
- Quantum Bioinformatics Team, Center for Computational Science and Engineering, Japan Atomic Energy Agency8-1 Umemidai, Kizu, Souraku, Kyoto 619-0215, Japan
- Core Research for Evolution Science and Technology, Japan Science and Technology AgencyJapan
| | - Mitiko Go
- Division of Molecular Genome Analysis, German Cancer Research CenterIm Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Ochanomizu University2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MD, USA
- Centre National de la Recherche Scientifique, Laboratoire de Physique MathematiqueMontpellier, France
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MD, USA
- Centre National de la Recherche Scientifique, Laboratoire de Physique MathematiqueMontpellier, France
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research CenterIm Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Nobuo Nomura
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Takashi Gojobori
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
- Center for Information Biology and DDBJ, National Institute of Genetics1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Tadashi Imanishi
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
- Graduate School of Information Science and Technology, Hokkaido UniversityNorth 14, West 9, Kita-ku, Sapporo, Hokkaido 060-0814, Japan
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Temple G, Lamesch P, Milstein S, Hill DE, Wagner L, Moore T, Vidal M. From genome to proteome: developing expression clone resources for the human genome. Hum Mol Genet 2006; 15 Spec No 1:R31-43. [PMID: 16651367 DOI: 10.1093/hmg/ddl048] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
cDNA clones have long been valuable reagents for studying the structure and function of proteins. With recent access to the entire human genome sequence, it has become possible and highly productive to compare the sequences of mRNAs to their genes, in order to validate the sequences and protein-coding annotations of each (1,2). Thus, well-characterized collections of human cDNAs are now playing an essential role in defining the structure and function of human genes and proteins. In this review, we will summarize the major collections of human cDNA clones, discuss some limitations common to most of these collections and describe several noteworthy proteomics applications, focusing on the detection and analysis of protein-protein interactions (PPI). These human cDNA collections contain principally two types of cDNA clones. The largest collections comprise cDNAs with full-length protein coding sequences (FL-CDS). Some but not all of these cDNA clones may represent the entire mRNA sequence, but many are missing considerable non-coding UTR sequence, usually at the 5' end. A second type of cDNA clone, a 'full-ORF' (F-ORF) expression clone, is one where the annotated protein-coding sequence, excised of 5' UTR and 3' UTR sequence, has been transferred to a vector designed to facilitate transfer to other vectors for protein expression.
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Affiliation(s)
- Gary Temple
- Mammalian Gene Collection, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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35
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Fleischer S, Wiemann S, Will H, Hofmann TG. PML-associated repressor of transcription (PAROT), a novel KRAB-zinc finger repressor, is regulated through association with PML nuclear bodies. Exp Cell Res 2006; 312:901-12. [PMID: 16412420 DOI: 10.1016/j.yexcr.2005.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Revised: 12/02/2005] [Accepted: 12/05/2005] [Indexed: 01/03/2023]
Abstract
Promyelocytic leukemia nuclear bodies (PML-NBs) are implicated in transcriptional regulation. Here we identify a novel transcriptional repressor, PML-associated repressor of transcription (PAROT), which is regulated in its repressor activity through recruitment to PML-NBs. PAROT is a Krüppel-associated box ( KRAB) zinc-finger (ZNF) protein, which comprises an amino terminal KRAB-A and KRAB-B box, a linker domain and 8 tandemly repeated C(2)H(2)-ZNF motifs at its carboxy terminus. Consistent with its domain structure, when tethered to DNA, PAROT represses transcription, and this is partially released by the HDAC inhibitor trichostatin A. PAROT colocalizes with members of the heterochromatin protein 1 (HP1) family and with transcriptional intermediary factor-1beta/KRAB-associated protein 1 (TIF-1beta/KAP1), a transcriptional corepressor for the KRAB-ZNF family. Interestingly, PML isoform IV, in contrast to PML-III, efficiently recruits PAROT and TIF-1beta from heterochromatin to PML-NBs. PML-NB recruitment of PAROT partially releases its transcriptional repressor activity, indicating that PAROT can be regulated through subnuclear compartmentalization. Taken together, our data identify a novel transcriptional repressor and provide evidence for its regulation through association with PML-NBs.
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Affiliation(s)
- Sandra Fleischer
- Heinrich-Pette-Institut für Experimentelle Virologie und Immunologie, Martinistrasse 52, 20251 Hamburg, Germany
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36
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Korf U, Wiemann S. Protein microarrays as a discovery tool for studying protein-protein interactions. Expert Rev Proteomics 2006; 2:13-26. [PMID: 15966849 DOI: 10.1586/14789450.2.1.13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Exploring the function of the genome and the encoded proteins has emerged as a new and exciting challenge in the postgenomic era. Novel technologies come into view that promise to be valuable for the investigation not only of single proteins, but of entire protein networks. Protein microarrays are the innovative assay platform for highly parallel in vitro studies of protein-protein interactions. Due to their flexibility and multiplexing capacity, protein microarrays benefit basic research, diagnosis and biomedicine. This review provides an overview on the basic principles of protein microarrays and their potential to multiplex protein-protein interaction studies.
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Affiliation(s)
- Ulrike Korf
- Division of Molecular Genome Analysis (B050), DKFZ Heidelberg, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
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37
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Kuryshev VY, Vorobyov E, Zink D, Schmitz J, Rozhdestvensky TS, Münstermann E, Ernst U, Wellenreuther R, Moosmayer P, Bechtel S, Schupp I, Horst J, Korn B, Poustka A, Wiemann S. An anthropoid-specific segmental duplication on human chromosome 1q22. Genomics 2006; 88:143-51. [PMID: 16545939 DOI: 10.1016/j.ygeno.2006.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 01/23/2006] [Accepted: 02/05/2006] [Indexed: 11/27/2022]
Abstract
Segmental duplications (SDs) play a key role in genome evolution by providing material for gene diversification and creation of variant or novel functions. They also mediate recombinations, resulting in microdeletions, which have occasionally been associated with human genetic diseases. Here, we present a detailed analysis of a large genomic region (about 240 kb), located on human chromosome 1q22, that contains a tandem SD, SD1q22. This duplication occurred about 37 million years ago in a lineage leading to anthropoid primates, after their separation from prosimians but before the Old and New World monkey split. We reconstructed the hypothetical unduplicated ancestral locus and compared it with the extant SD1q22 region. Our data demonstrate that, as a consequence of the duplication, new anthropoid-specific genetic material has evolved in the resulting paralogous segments. We describe the emergence of two new genes, whose new functions could contribute to the speciation of anthropoid primates. Moreover, we provide detailed information regarding structure and evolution of the SD1q22 region that is a prerequisite for future studies of its anthropoid-specific functions and possible linkage to human genetic disorders.
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Affiliation(s)
- Vladimir Yu Kuryshev
- Department of Molecular Genome Analysis, DKFZ-German Cancer Research Center, INF 580, D-69120 Heidelberg, Germany
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Seiler M, Mehrle A, Poustka A, Wiemann S. The 3of5 web application for complex and comprehensive pattern matching in protein sequences. BMC Bioinformatics 2006; 7:144. [PMID: 16542452 PMCID: PMC1523217 DOI: 10.1186/1471-2105-7-144] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Accepted: 03/16/2006] [Indexed: 11/16/2022] Open
Abstract
Background The identification of patterns in biological sequences is a key challenge in genome analysis and in proteomics. Frequently such patterns are complex and highly variable, especially in protein sequences. They are frequently described using terms of regular expressions (RegEx) because of the user-friendly terminology. Limitations arise for queries with the increasing complexity of patterns and are accompanied by requirements for enhanced capabilities. This is especially true for patterns containing ambiguous characters and positions and/or length ambiguities. Results We have implemented the 3of5 web application in order to enable complex pattern matching in protein sequences. 3of5 is named after a special use of its main feature, the novel n-of-m pattern type. This feature allows for an extensive specification of variable patterns where the individual elements may vary in their position, order, and content within a defined stretch of sequence. The number of distinct elements can be constrained by operators, and individual characters may be excluded. The n-of-m pattern type can be combined with common regular expression terms and thus also allows for a comprehensive description of complex patterns. 3of5 increases the fidelity of pattern matching and finds ALL possible solutions in protein sequences in cases of length-ambiguous patterns instead of simply reporting the longest or shortest hits. Grouping and combined search for patterns provides a hierarchical arrangement of larger patterns sets. The algorithm is implemented as internet application and freely accessible. The application is available at . Conclusion The 3of5 application offers an extended vocabulary for the definition of search patterns and thus allows the user to comprehensively specify and identify peptide patterns with variable elements. The n-of-m pattern type offers an improved accuracy for pattern matching in combination with the ability to find all solutions, without compromising the user friendliness of regular expression terms.
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Affiliation(s)
- Markus Seiler
- Division of Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Alexander Mehrle
- Division of Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Annemarie Poustka
- Division of Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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Manjasetty BA, Büssow K, Fieber-Erdmann M, Roske Y, Gobom J, Scheich C, Götz F, Niesen FH, Heinemann U. Crystal structure of Homo sapiens PTD012 reveals a zinc-containing hydrolase fold. Protein Sci 2006; 15:914-20. [PMID: 16522806 PMCID: PMC2242484 DOI: 10.1110/ps.052037006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The human protein PTD012 is the longer product of an alternatively spliced gene and was described to be localized in the nucleus. The X-ray structure analysis at 1.7 A resolution of PTD012 through SAD phasing reveals a monomeric protein and a novel fold. The shorter splice form was also studied and appears to be unfolded and non-functional. The structure of PTD012 displays an alphabetabetaalpha four-layer topology. A metal ion residing between the central beta-sheets is partially coordinated by three histidine residues. X-ray absorption near-edge structure (XANES) analysis identifies the PTD012-bound ion as Zn(2+). Tetrahedral coordination of the ion is completed by the carboxylate oxygen atom of an acetate molecule taken up from the crystallization buffer. The binding of Zn(2+) to PTD012 is reminiscent of zinc-containing enzymes such as carboxypeptidase, carbonic anhydrase, and beta-lactamase. Biochemical assays failed to demonstrate any of these enzyme activities in PTD012. However, PTD012 exhibits ester hydrolase activity on the substrate p-nitrophenyl acetate.
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40
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Colwill K, Wells CD, Elder K, Goudreault M, Hersi K, Kulkarni S, Hardy WR, Pawson T, Morin GB. Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites. BMC Biotechnol 2006; 6:13. [PMID: 16519801 PMCID: PMC1421398 DOI: 10.1186/1472-6750-6-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Accepted: 03/06/2006] [Indexed: 11/26/2022] Open
Abstract
Background Recombinational systems have been developed to rapidly shuttle Open Reading Frames (ORFs) into multiple expression vectors in order to analyze the large number of cDNAs available in the post-genomic era. In the Creator system, an ORF introduced into a donor vector can be transferred with Cre recombinase to a library of acceptor vectors optimized for different applications. Usability of the Creator system is impacted by the ability to easily manipulate DNA, the number of acceptor vectors for downstream applications, and the level of protein expression from Creator vectors. Results To date, we have developed over 20 novel acceptor vectors that employ a variety of promoters and epitope tags commonly employed for proteomics applications and gene function analysis. We also made several enhancements to the donor vectors including addition of different multiple cloning sites to allow shuttling from pre-existing vectors and introduction of the lacZ alpha reporter gene to allow for selection. Importantly, in order to ameliorate any effects on protein expression of the loxP site between a 5' tag and ORF, we introduced a splicing event into our expression vectors. The message produced from the resulting 'Creator Splice' vector undergoes splicing in mammalian systems to remove the loxP site. Upon analysis of our Creator Splice constructs, we discovered that protein expression levels were also significantly increased. Conclusion The development of new donor and acceptor vectors has increased versatility during the cloning process and made this system compatible with a wider variety of downstream applications. The modifications introduced in our Creator Splice system were designed to remove extraneous sequences due to recombination but also aided in downstream analysis by increasing protein expression levels. As a result, we can now employ epitope tags that are detected less efficiently and reduce our assay scale to allow for higher throughput. The Creator Splice system appears to be an extremely useful tool for proteomics.
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Affiliation(s)
- Karen Colwill
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Clark D Wells
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Kelly Elder
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Marilyn Goudreault
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Kadija Hersi
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sarang Kulkarni
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - W Rod Hardy
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada
| | - Tony Pawson
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada
| | - Gregg B Morin
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
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41
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Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W, Glatting KH, Huber W, Pepperkok R, Poustka A, Wiemann S. The LIFEdb database in 2006. Nucleic Acids Res 2006; 34:D415-8. [PMID: 16381901 PMCID: PMC1347501 DOI: 10.1093/nar/gkj139] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
LIFEdb () integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an updated user interface with enhanced query capabilities, (ii) a configurable output table and the option to download search results in XML, (iii) the integration of data from cell-based screening assays addressing the influence of protein-overexpression on cell proliferation and (iv) the display of the relative expression (‘Electronic Northern’) of the genes under investigation using curated gene expression ontology information. LIFEdb enables researchers to systematically select and characterize genes and proteins of interest, and presents data and information via its user-friendly web-based interface.
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Affiliation(s)
- Alexander Mehrle
- Division Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.
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42
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Noda AO, Ikeo K, Gojobori T. Comparative genome analyses of nervous system-specific genes. Gene 2006; 365:130-6. [PMID: 16376029 DOI: 10.1016/j.gene.2005.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 06/17/2005] [Accepted: 09/07/2005] [Indexed: 10/25/2022]
Abstract
To elucidate the evolutionary process of the nervous system (NS) in metazoa, we examined the relationship between human genes specifically expressed in the NS (NS-specific genes) and the time of their evolutionary emergence. We obtained 255 human NS-specific genes from the gene expression data of the human full-length cDNA annotation invitational (H-invitational) database. To determine when these genes emerged for the first time during evolution, we searched for orthologues of the 255 NS-specific genes in 13 species (excluding human) by homology searches against their complete genome sequences. We found that 14% of the NS-specific orthologous genes had already emerged before the divergence between yeast and human. This finding suggests that a common ancestor, which should have no nervous system, already possessed a portion of the genes homologous to human NS-specific genes, implying that 14% of the NS-specific genes should have changed differentially their original functions during evolution. If this is the case, then the remaining 86% of the 255 NS-specific human genes have newly emerged during evolution. In particular, we found that the largest portion (24%) of the 255 NS-specific genes had emerged after divergence of urochordata and human but before divergence of fishes and human. These results suggest that the main cause of the NS evolution was the addition of new genes which took place most actively just before or at the evolutionary emergence of vertebrates.
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Affiliation(s)
- Akiko Ogura Noda
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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43
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Yamasaki C, Koyanagi KO, Fujii Y, Itoh T, Barrero R, Tamura T, Yamaguchi-Kabata Y, Tanino M, Takeda JI, Fukuchi S, Miyazaki S, Nomura N, Sugano S, Imanishi T, Gojobori T. Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene 2005; 364:99-107. [PMID: 16185827 DOI: 10.1016/j.gene.2005.05.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Revised: 04/06/2005] [Accepted: 05/30/2005] [Indexed: 10/25/2022]
Abstract
H-Invitational Database (H-InvDB; ) is a human transcriptome database, containing integrative annotation of 41,118 full-length cDNA clones originated from 21,037 loci. H-InvDB is a product of the H-Invitational project, an international collaboration to systematically and functionally validate human genes by analysis of a unique set of high quality full-length cDNA clones using automatic annotation and human curation under unified criteria. Here, 19,574 proteins encoded by these cDNAs were classified into 11,709 function-known and 7865 function-unknown hypothetical proteins by similarity with protein databases and motif prediction (InterProScan). The proportion of "hypothetical proteins" in H-InvDB was as high as 40.4%. In this study, we thus conducted data-mining in H-InvDB with the aim of assigning advanced functional annotations to those hypothetical proteins. First, by data-mining in the H-InvDB version of GTOP, we identified 337 SCOP domains within 7865 H-Inv hypothetical proteins. Second, by data-mining of predicted subcellular localization by SOSUI and TMHMM in H-InvDB, we found 1032 transmembrane proteins within H-Inv hypothetical proteins. These results clearly demonstrate that structural prediction is effective for functional annotation of proteins with unknown functions. All the data in H-InvDB are shown in two main views, the cDNA view and the Locus view, and five auxiliary databases with web-based viewers; DiseaseInfo Viewer, H-ANGEL, Clustering Viewer, G-integra and TOPO Viewer; the data also are provided as flat files and XML files. The data consists of descriptions of their gene structures, novel alternative splicing isoforms, functional RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs in relation with orphan diseases, gene expression profiling, and comparisons with mouse full-length cDNAs in the context of molecular evolution. This unique integrative platform for conducting in silico data-mining represents a substantial contribution to resources required for the exploration of human biology and pathology.
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Affiliation(s)
- Chisato Yamasaki
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
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44
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Hao Z, Li X, Qiao T, Zhang J, Shao X, Fan D. Distribution of CIAPIN1 in normal fetal and adult human tissues. J Histochem Cytochem 2005; 54:417-26. [PMID: 16314443 DOI: 10.1369/jhc.5a6753.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
CIAPIN1, a newly identified antiapoptotic molecule that plays an essential role in mouse definitive hematopoiesis, is considered a downstream effector of the receptor tyrosine kinase-Ras signaling pathway. Our previous studies have indicated that CIAPIN1 is involved in the development of multidrug resistance (MDR) in gastric cancer cells. However, the mechanism of CIAPIN1-mediated antiapoptosis and MDR has not been fully elucidated. To reveal the possible physiological role of CIAPIN1, we examined the expression and distribution of CIAPIN1 in fetal and adult human tissues using immunohistochemistry. We found that CIAPIN1 was ubiquitously distributed in fetal and adult tissues, and was localized in both the cytoplasm and the nucleus. The expression patterns of CIAPIN1 were similar in fetal and adult tissues, and was correlated with the previously described expression pattern of p21ras. These observations suggest that CIAPIN1 expression appears to be involved in cell differentiation, and that it might exert universal and possibly important physiological functions under the regulation of Ras in humans.
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Affiliation(s)
- Zhiming Hao
- State Key Laboratory of Cancer Biology, Institute of Digestive Diseases, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032 Shaanxi Province, China
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45
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Arlt D, Huber W, Liebel U, Schmidt C, Majety M, Sauermann M, Rosenfelder H, Bechtel S, Mehrle A, Bannasch D, Schupp I, Seiler M, Simpson JC, Hahne F, Moosmayer P, Ruschhaupt M, Guilleaume B, Wellenreuther R, Pepperkok R, Sültmann H, Poustka A, Wiemann S. Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle. Cancer Res 2005; 65:7733-42. [PMID: 16140941 DOI: 10.1158/0008-5472.can-05-0642] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cancer transcription microarray studies commonly deliver long lists of "candidate" genes that are putatively associated with the respective disease. For many of these genes, no functional information, even less their relevance in pathologic conditions, is established as they were identified in large-scale genomics approaches. Strategies and tools are thus needed to distinguish genes and proteins with mere tumor association from those causally related to cancer. Here, we describe a functional profiling approach, where we analyzed 103 previously uncharacterized genes in cancer relevant assays that probed their effects on DNA replication (cell proliferation). The genes had previously been identified as differentially expressed in genome-wide microarray studies of tumors. Using an automated high-throughput assay with single-cell resolution, we discovered seven activators and nine repressors of DNA replication. These were further characterized for effects on extracellular signal-regulated kinase 1/2 (ERK1/2) signaling (G1-S transition) and anchorage-independent growth (tumorigenicity). One activator and one inhibitor protein of ERK1/2 activation and three repressors of anchorage-independent growth were identified. Data from tumor and functional profiling make these proteins novel prime candidates for further in-depth study of their roles in cancer development and progression. We have established a novel functional profiling strategy that links genomics to cell biology and showed its potential for discerning cancer relevant modulators of the cell cycle in the candidate lists from microarray studies.
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Affiliation(s)
- Dorit Arlt
- Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
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46
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Roy M, Xu Q, Lee C. Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms. Nucleic Acids Res 2005; 33:5026-33. [PMID: 16147986 PMCID: PMC1201329 DOI: 10.1093/nar/gki792] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Revised: 07/19/2005] [Accepted: 08/09/2005] [Indexed: 02/01/2023] Open
Abstract
Alternative splicing is widespread in the human genome, and it appears that many genes display different splice forms in cancerous tissue than in normal human tissues. However, since cDNAs for many cancer-associated genes were originally cloned from tumor samples, it is important to ask whether this repertoire of cDNAs provides a complete or representative picture of the transcript isoforms found in normal tissues. To answer this, we used bioinformatics and RT-PCR to identify novel splice forms, focusing on in-frame exonskips, for a panel of 50 cancer-associated genes in normal tissue samples. These data show that in nearly two-thirds of the genes, normal tissues expressed previously unknown splice forms, of which 40% were normally a dominant splice form. Surprisingly, the tumor-associated splice forms were twice as likely to be represented in GenBank than their normal tissue-associated splice forms, most likely because 70% of the mRNAs in GenBank for these genes were cloned from tumor samples. As an example, we describe a novel normal splice form of IKBbeta, an important regulator of the NFkappaB pathway. Our data suggest that systematic re-evaluation of cancer genes' splice forms in normal tissue will yield insights into their distinct functions in normal tissues and in cancer. Our database contains 1308 novel normal splice forms, including many known cancer genes.
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Affiliation(s)
- Meenakshi Roy
- Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los AngelesLos Angeles, CA 90095-1570, USA
| | - Qiang Xu
- Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los AngelesLos Angeles, CA 90095-1570, USA
| | - Christopher Lee
- Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los AngelesLos Angeles, CA 90095-1570, USA
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47
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Wiemann S, Kolb-Kokocinski A, Poustka A. Alternative pre-mRNA processing regulates cell-type specific expression of the IL4l1 and NUP62 genes. BMC Biol 2005; 3:16. [PMID: 16029492 PMCID: PMC1198218 DOI: 10.1186/1741-7007-3-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Accepted: 07/19/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Given the complexity of higher organisms, the number of genes encoded by their genomes is surprisingly small. Tissue specific regulation of expression and splicing are major factors enhancing the number of the encoded products. Commonly these mechanisms are intragenic and affect only one gene. RESULTS Here we provide evidence that the IL4I1 gene is specifically transcribed from the apparent promoter of the upstream NUP62 gene, and that the first two exons of NUP62 are also contained in the novel IL4I1_2 variant. While expression of IL4I1 driven from its previously described promoter is found mostly in B cells, the expression driven by the NUP62 promoter is restricted to cells in testis (Sertoli cells) and in the brain (e.g., Purkinje cells). Since NUP62 is itself ubiquitously expressed, the IL4I1_2 variant likely derives from cell type specific alternative pre-mRNA processing. CONCLUSION Comparative genomics suggest that the promoter upstream of the NUP62 gene originally belonged to the IL4I1 gene and was later acquired by NUP62 via insertion of a retroposon. Since both genes are apparently essential, the promoter had to serve two genes afterwards. Expression of the IL4I1 gene from the "NUP62" promoter and the tissue specific involvement of the pre-mRNA processing machinery to regulate expression of two unrelated proteins indicate a novel mechanism of gene regulation.
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Affiliation(s)
- Stefan Wiemann
- Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany
| | - Anja Kolb-Kokocinski
- Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany
| | - Annemarie Poustka
- Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany
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48
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Büssow K, Scheich C, Sievert V, Harttig U, Schultz J, Simon B, Bork P, Lehrach H, Heinemann U. Structural genomics of human proteins--target selection and generation of a public catalogue of expression clones. Microb Cell Fact 2005; 4:21. [PMID: 15998469 PMCID: PMC1250228 DOI: 10.1186/1475-2859-4-21] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 07/05/2005] [Indexed: 11/12/2022] Open
Abstract
Background The availability of suitable recombinant protein is still a major bottleneck in protein structure analysis. The Protein Structure Factory, part of the international structural genomics initiative, targets human proteins for structure determination. It has implemented high throughput procedures for all steps from cloning to structure calculation. This article describes the selection of human target proteins for structure analysis, our high throughput cloning strategy, and the expression of human proteins in Escherichia coli host cells. Results and Conclusion Protein expression and sequence data of 1414 E. coli expression clones representing 537 different proteins are presented. 139 human proteins (18%) could be expressed and purified in soluble form and with the expected size. All E. coli expression clones are publicly available to facilitate further functional characterisation of this set of human proteins.
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Affiliation(s)
- Konrad Büssow
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Christoph Scheich
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Volker Sievert
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Ulrich Harttig
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- RZPD German Resource Center for Genome Research GmbH, Heubnerweg 6, 14059 Berlin, Germany
- DIFE, Arthur-Scheunert-Allee 114–116, 14558 Nuthetal, Germany
| | - Jörg Schultz
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
- Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Bernd Simon
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Peer Bork
- EMBL Heidelberg, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Hans Lehrach
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Planck-Institut für Molekulare Genetik, Ihnestr. 73, 14195 Berlin, Germany
| | - Udo Heinemann
- Protein Structure Factory, Heubnerweg 6, 14059 Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Institut für Chemie/Kristallographie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
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49
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Hong S, Pedersen PL. Mitochondrial ATP synthase: a bioinformatic approach reveals new insights about the roles of supernumerary subunits g and A6L. J Bioenerg Biomembr 2005; 36:515-23. [PMID: 15692730 DOI: 10.1007/s10863-004-8998-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The mitochondrial ATP synthase is a membrane protein complex which couples the proton gradient across the mitochondrial inner membrane to the synthesis of ATP from ADP+Pi. The complex is composed of essential subunits for its motor functions and supernumerary subunits, the roles of which remain to be elucidated. Subunits g and A6L are supernumerary subunits, and the specific roles of these subunits are still matters of debate. To gain insight into the functions of these two subunits, we carried out the alignment and the homolog search of the protein sequences of the subunits and found the following features: Subunit g appears to have isoforms in animals, and the transmembrane domain of the animal subunit g contains a completely conserved acidic residue in the middle of a helix on the conserved side of the transmembrane helix. This finding implicates the conserved acidic residue as important for the function of subunit g. The alignment of A6L protein sequences shows a conserved aromatic residue at the N-terminal domain with which the N-terminal MPQL sequence comprises a unique MPQLX4Ar motif that can signify the protein A6L. The conserved aromatic residue may also be important for the function of A6L.
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Affiliation(s)
- Sangjin Hong
- Department of Biological Chemistry, Johns Hopkins University, School of Medicine, 725 N. Wolfe Street, Baltimore, Maryland, 21205-2185, USA
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50
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Kakitani M, Oshima T, Horikoshi K, Yoshitome T, Ueda A, Kajikawa M, Iba Y, Ozone Y, Ijima Y, Yoshino T, Itoh M, Seki S, Aoki A, Ishihara T, Shionoya M, Makino U, Kitada R, Ohguma A, Ohta T, Yoshida Y, Kudoh H, Hanaoka K, Sibuya K, Ishida I, Kakeda M, Yagi M, Yoneya T, Tomizuka K. A novel transgenic chimaeric mouse system for the rapid functional evaluation of genes encoding secreted proteins. Nucleic Acids Res 2005; 33:e85. [PMID: 15914664 PMCID: PMC1140086 DOI: 10.1093/nar/gni083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A major challenge of the post-genomic era is the functional characterization of anonymous open reading frames (ORFs) identified by the Human Genome Project. In this context, there is a strong requirement for the development of technologies that enhance our ability to analyze gene functions at the level of the whole organism. Here, we describe a rapid and efficient procedure to generate transgenic chimaeric mice that continuously secrete a foreign protein into the systemic circulation. The transgene units were inserted into the genomic site adjacent to the endogenous immunoglobulin (Ig) κ locus by homologous recombination, using a modified mouse embryonic stem (ES) cell line that exhibits a high frequency of homologous recombination at the Igκ region. The resultant ES clones were injected into embryos derived from a B-cell-deficient host strain, thus producing chimaerism-independent, B-cell-specific transgene expression. This feature of the system eliminates the time-consuming breeding typically implemented in standard transgenic strategies and allows for evaluating the effect of ectopic transgene expression directly in the resulting chimaeric mice. To demonstrate the utility of this system we showed high-level protein expression in the sera and severe phenotypes in human EPO (hEPO) and murine thrombopoietin (mTPO) transgenic chimaeras.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hiroe Kudoh
- Molecular Embryology, Department of Biosciences, School of Science, Kitasato University1-15-1 Kitasato, Sagamihara-shi, Kanagawa, 228-8555, Japan
| | - Kazunori Hanaoka
- Molecular Embryology, Department of Biosciences, School of Science, Kitasato University1-15-1 Kitasato, Sagamihara-shi, Kanagawa, 228-8555, Japan
| | | | | | | | | | | | - Kazuma Tomizuka
- To whom correspondence should be addressed. Tel: +81 27 346 9934; Fax: +81 27 346 1971;
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