Genome-Wide Reverse Genetics Framework to Identify Novel Functions of the Vertebrate Secretome
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{"title"=>"Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome", "type"=>"journal", "authors"=>[{"first_name"=>"Michael A.", "last_name"=>"Pickart", "scopus_author_id"=>"35746864800"}, {"first_name"=>"Eric W.", "last_name"=>"Klee", "scopus_author_id"=>"16022162600"}, {"first_name"=>"Aubrey L.", "last_name"=>"Nielsen", "scopus_author_id"=>"8752046500"}, {"first_name"=>"Sridhar", "last_name"=>"Sivasubbu", "scopus_author_id"=>"8752046300"}, {"first_name"=>"Eric M.", "last_name"=>"Mendenhall", "scopus_author_id"=>"9741377300"}, {"first_name"=>"Brent R.", "last_name"=>"Bill", "scopus_author_id"=>"16243883200"}, {"first_name"=>"Eleanor", "last_name"=>"Chen", "scopus_author_id"=>"55057276000"}, {"first_name"=>"Craig E.", "last_name"=>"Eckfeldt", "scopus_author_id"=>"6507708270"}, {"first_name"=>"Michelle", "last_name"=>"Knowlton", "scopus_author_id"=>"23485504500"}, {"first_name"=>"Mara E.", "last_name"=>"Robu", "scopus_author_id"=>"16403450200"}, {"first_name"=>"Jon D.", "last_name"=>"Larson", "scopus_author_id"=>"7202866557"}, {"first_name"=>"Yun", "last_name"=>"Deng", "scopus_author_id"=>"57197040017"}, {"first_name"=>"Lisa A.", "last_name"=>"Schimmenti", "scopus_author_id"=>"6701347868"}, {"first_name"=>"Lynda B.M.", "last_name"=>"Ellis", "scopus_author_id"=>"7202635746"}, {"first_name"=>"Catherine M.", "last_name"=>"Verfaillie", "scopus_author_id"=>"7004524257"}, {"first_name"=>"Matthias", "last_name"=>"Hammerschmidt", "scopus_author_id"=>"7006962776"}, {"first_name"=>"Steven A.", "last_name"=>"Farber", "scopus_author_id"=>"35902565200"}, {"first_name"=>"Stephen C.", "last_name"=>"Ekker", "scopus_author_id"=>"7003541150"}], "year"=>2006, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"34249732803", "doi"=>"10.1371/journal.pone.0000104", "pui"=>"352571150", "pmid"=>"17218990", "scopus"=>"2-s2.0-34249732803", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"d3d109e1-d305-3965-9cba-82a4cdf8c90a", "abstract"=>"BACKGROUND: Understanding the functional role(s) of the more than 20,000 proteins of the vertebrate genome is a major next step in the post-genome era. The approximately 4,000 co-translationally translocated (CTT) proteins - representing the vertebrate secretome - are important for such vertebrate-critical processes as organogenesis. However, the role(s) for most of these genes is currently unknown. RESULTS: We identified 585 putative full-length zebrafish CTT proteins using cross-species genomic and EST-based comparative sequence analyses. We further investigated 150 of these genes (Figure 1) for unique function using morpholino-based analysis in zebrafish embryos. 12% of the CTT protein-deficient embryos resulted in specific developmental defects, a notably higher rate of gene function annotation than the 2%-3% estimate from random gene mutagenesis studies. CONCLUSION: This initial collection includes novel genes required for the development of vascular, hematopoietic, pigmentation, and craniofacial tissues, as well as lipid metabolism, and organogenesis. This study provides a framework utilizing zebrafish for the systematic assignment of biological function in a vertebrate genome.", "link"=>"http://www.mendeley.com/research/genomewide-reverse-genetics-framework-identify-novel-functions-vertebrate-secretome", "reader_count"=>44, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>16, "Student > Master"=>6, "Other"=>2, "Student > Bachelor"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>16, "Student > Master"=>6, "Other"=>2, "Student > Bachelor"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>10, "Materials Science"=>1, "Medicine and Dentistry"=>2, "Agricultural and Biological Sciences"=>24, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>24}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"France"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/955318"], "description"=>"<p>(A) A bioinformatics pipeline was developed to determine the subset of N-terminally complete CTT homologs representing the testable putative proteins of the zebrafish secretome. (B) AMOD software was developed to standardize and increase the efficiency of the MO design process to allow more rapid screening. (C) A MO database, MODB, was developed to manage, share, and data mine all MO design and outcome information. (D) Following MO synthesis and distribution to the participating labs, MOs were investigated using a variety of assays in zebrafish embryos that allowed functional annotation of 18/150 of the putative CTT proteins investigated. Results of investigations were recorded in MODB for data mining. AMOD software was used to design a second sequence-independent MO to assess specificity of the initial MO tested.</p>", "links"=>[], "tags"=>["mo"], "article_id"=>625590, "categories"=>["Biotechnology", "Genetics", "Developmental Biology", "Biological Sciences"], "users"=>["Michael A. Pickart", "Eric W. Klee", "Aubrey L. Nielsen", "Sridhar Sivasubbu", "Eric M. Mendenhall", "Brent R. Bill", "Eleanor Chen", "Craig E. Eckfeldt", "Michelle Knowlton", "Mara E. Robu", "Jon D. Larson", "Yun Deng", "Lisa A. Schimmenti", "Lynda B.M. Ellis", "Catherine M. Verfaillie", "Matthias Hammerschmidt", "Steven A. Farber", "Stephen C. Ekker"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000104.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_of_overall_MO_screen_/625590", "title"=>"Schematic of overall MO screen.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 13:04:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/955478"], "description"=>"<p>(A) Co-translationally translocated vertebrate protein sequences (CTT Proteins) were identified using an <i>in silico</i> prediction pipeline to create the reference CTT protein sequence sets. (B) Zebrafish Tentative Consequence (TC) sequences were compared to the reference protein sequence sets using BLASTX. Zebrafish TC sequences possessing highly homologous regions located near the reference protein sequence N-termini and possessing clear translational initiation sites were selected for further analysis. (C) The corresponding zebrafish TC peptides were then analyzed by the <i>in silico</i> prediction pipeline and sequences possessing a signal peptide selected for morpholino design. (D) E.g. zebrafish sequence SP1991 was selected on the basis of its strong homology to the N-terminus of reference protein gi_14768182. Analysis identified a strong translation initiation site near the 5′ end of the SP1991 nucleotide sequence and <i>in silico</i> predictions identified a clear signal peptide near the N-terminus of the translated peptide.</p>", "links"=>[], "tags"=>["genes", "mo"], "article_id"=>625751, "categories"=>["Biotechnology", "Genetics", "Developmental Biology", "Biological Sciences"], "users"=>["Michael A. Pickart", "Eric W. Klee", "Aubrey L. Nielsen", "Sridhar Sivasubbu", "Eric M. Mendenhall", "Brent R. Bill", "Eleanor Chen", "Craig E. Eckfeldt", "Michelle Knowlton", "Mara E. Robu", "Jon D. Larson", "Yun Deng", "Lisa A. Schimmenti", "Lynda B.M. Ellis", "Catherine M. Verfaillie", "Matthias Hammerschmidt", "Steven A. Farber", "Stephen C. Ekker"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000104.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selection_of_candidate_genes_for_MO_targeting_/625751", "title"=>"Selection of candidate genes for MO targeting.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 13:05:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/955692"], "description"=>"<p>(A) Normal vascular development observed in untreated Tg (fli-1:eGFP) embryos. (B, L) Decreases in the number of vascular sprouts (arrow heads) observed following injection of MO targeting Syndecan-2<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000104#pone.0000104-Chen1\" target=\"_blank\">[20]</a>. (C, M) Gaps within the caudal vein plexus (small arrow heads) observed following injection of MO targeting heparin sulfatetransferase-6-O 2-sulfotransferase (HSST6O-2)<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000104#pone.0000104-Chen2\" target=\"_blank\">[21]</a>. (D, N) Loss of integrity in the caudal vein plexus (arrow) observed following injection of MO targeting MAGP1<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000104#pone.0000104-Chen3\" target=\"_blank\">[22]</a>. Premature return in caudal vein flow shown by gata-1:dsRed expression to varying severities (arrowheads) following injection of MOs targeting Ephrin B2 (E,O), SPPL2b (F,P), predicted protein LOC407708 (G, Q), and C1q (H, R). Note: the premature return defects were not shown by fli-1:eGFP expression (E, F, G, H), however, were confirmed by other vascular markers (data not shown). (K) Normal blood development observed in untreated Tg (<i>gata-1:DsRed</i>) embryos. Decreased number of blood cells observed in 2 dpf embryos following injection with MO against Synaptotagmin13 (S) or Novel Protein similar to SLC27A2 (T). Accompanying panels (I) and (J) display no major vasculature defects for each of these genes respectively.</p>", "links"=>[], "tags"=>["vasculogenesis", "hematopoeisis", "observed", "tg", "embryos", "mo", "inactivation", "ctt"], "article_id"=>625952, "categories"=>["Biotechnology", "Genetics", "Developmental Biology", "Biological Sciences"], "users"=>["Michael A. Pickart", "Eric W. Klee", "Aubrey L. Nielsen", "Sridhar Sivasubbu", "Eric M. Mendenhall", "Brent R. Bill", "Eleanor Chen", "Craig E. Eckfeldt", "Michelle Knowlton", "Mara E. Robu", "Jon D. Larson", "Yun Deng", "Lisa A. Schimmenti", "Lynda B.M. Ellis", "Catherine M. Verfaillie", "Matthias Hammerschmidt", "Steven A. Farber", "Stephen C. Ekker"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000104.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Defects_in_vasculogenesis_and_hematopoeisis_observed_in_Tg_fli_1_eGFP_green_or_Tg_gata_1_DsRed_red_embryos_following_MO_inactivation_of_select_CTT_genes_/625952", "title"=>"Defects in vasculogenesis and hematopoeisis observed in Tg (<i>fli-1:eGFP</i> (green)) or Tg (<i>gata-1:DsRed</i> (red)) embryos following MO inactivation of select CTT genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 13:07:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/955964"], "description"=>"<p>Embryos at the 1–8 cell stage were initially injected with a MO of interest. At 24 hpf, a fluorescent fatty acid (BODIPY-C12) was injected into the yolk. (A) 48 hpf embryo injected with BODIPY-C12 at 24 hpf. Embryos were then kept in the dark until 72 hpf when they were scored for morphologic phenotype. Embryos (4/tube) were homogenized in 50% methanol and extracted TLC plates were then scanned to reveal triacylglycerol (TG), diacylglycerol (DG), initial substrate (C12) and phospholipids (phosphatidylcholine (PC) and lysophosphatidylcholine (LPC)). Fluorescent intensities were quantified and the total fluorescence of all lipids was determined. (B) For each MO injected, data were expressed as a percent of total lipids and compared to a phenol red control to obtain the percent of control (C) A second experiment comparing BODIPY-C12 incorporation in control and Apo2c MO injected embryos. A given experiment represents a mean of at least three individual lipid extracts with 4 embryos each. * p<0.05 (D) Syntenic analysis indicates that the zebrafish EST sequence with homology to Apoc2, is the fish ortholog of that gene. (E,F) Morphology of embryos injected with apoC2 MO. Arrowheads indicate enlarged yolk.</p>", "links"=>[], "tags"=>["yolk", "lipid"], "article_id"=>626235, "categories"=>["Biotechnology", "Genetics", "Developmental Biology", "Biological Sciences"], "users"=>["Michael A. Pickart", "Eric W. Klee", "Aubrey L. Nielsen", "Sridhar Sivasubbu", "Eric M. Mendenhall", "Brent R. Bill", "Eleanor Chen", "Craig E. Eckfeldt", "Michelle Knowlton", "Mara E. Robu", "Jon D. Larson", "Yun Deng", "Lisa A. Schimmenti", "Lynda B.M. Ellis", "Catherine M. Verfaillie", "Matthias Hammerschmidt", "Steven A. Farber", "Stephen C. Ekker"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000104.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ApoC2_is_required_for_yolk_lipid_procesing_/626235", "title"=>"ApoC2 is required for yolk lipid procesing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 13:09:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/956199"], "description"=>"<p>(A, B) Otolith morphology observed in 2 dpf untreated embryos. (C, D) Absence of otoliths, in otherwise normal 2 dpf embryo, following injection of MO targeting CHCHD4. (B, D) Enlarged view of otic capsules; arrows denote normally formed (B) or absent (D) otoliths, respectively. (E, F) Eye morphology in 3 dpf embryos. (G, H) Abnormally small eyes observed in 3 dpf embryo following injection of MO targeting AMBP. (F, H) Enlarged view of histological sections of eye in un-affected (F) and affected (H) embryos. Note differences in both the size and tissue organization of the affected eye. (I) Wild-type morphology of 1 dpf embryo. (J) Ventral curvature phenotype observed in 1 dpf embryos injected with MO targeting SSRdelta. (K, L) Normal pigmentation observed in untreated 1 and 2 dpf embryos. Reduction in pigment observed in 1 and 2 dpf embryos, respectively, following injection of MO targeting ATP6V0C (M, N)<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000104#pone.0000104-Pickart1\" target=\"_blank\">[23]</a>, or junction adhesion molecule 2 (JAM2) (O, P), or UBX domain containing 2 (UBXD2) (Q, R)).</p>", "links"=>[], "tags"=>["defects", "observed", "mo", "inactivation", "ctt"], "article_id"=>626459, "categories"=>["Biotechnology", "Genetics", "Developmental Biology", "Biological Sciences"], "users"=>["Michael A. Pickart", "Eric W. Klee", "Aubrey L. Nielsen", "Sridhar Sivasubbu", "Eric M. Mendenhall", "Brent R. Bill", "Eleanor Chen", "Craig E. Eckfeldt", "Michelle Knowlton", "Mara E. Robu", "Jon D. Larson", "Yun Deng", "Lisa A. Schimmenti", "Lynda B.M. Ellis", "Catherine M. Verfaillie", "Matthias Hammerschmidt", "Steven A. Farber", "Stephen C. Ekker"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0000104.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Morphological_defects_observed_following_MO_inactivation_of_select_CTT_genes_/626459", "title"=>"Morphological defects observed following MO inactivation of select CTT genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 13:11:07"}

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Relative Metric

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