Ontology type: schema:ScholarlyArticle Open Access: True
2022-05-09
AUTHORSDmitry E. Andreev, Gary Loughran, Alla D. Fedorova, Maria S. Mikhaylova, Ivan N. Shatsky, Pavel V. Baranov
ABSTRACTRecent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due to start codon plurality within the same RNA. This plurality is often due to the failure of some scanning ribosomes to recognize potential start codons leading to initiation downstream—a process termed leaky scanning. Codons other than AUG (non-AUG) are particularly leaky due to their inefficiency. Here we discuss our current understanding of non-AUG initiation. We argue for a near-ubiquitous role of non-AUG initiation in shaping the dynamic composition of mammalian proteomes. More... »
PAGES111
http://scigraph.springernature.com/pub.10.1186/s13059-022-02674-2
DOIhttp://dx.doi.org/10.1186/s13059-022-02674-2
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1147723623
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/35534899
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Animals",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Codon",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Codon, Initiator",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Mammals",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Peptide Chain Initiation, Translational",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Protein Biosynthesis",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "RNA, Messenger",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Ribosomes",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia",
"id": "http://www.grid.ac/institutes/grid.14476.30",
"name": [
"Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117997, Moscow, Russia",
"Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia"
],
"type": "Organization"
},
"familyName": "Andreev",
"givenName": "Dmitry E.",
"id": "sg:person.0602662304.16",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0602662304.16"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "School of Biochemistry and Cell Biology, University College Cork, T12 XF62, Cork, Ireland",
"id": "http://www.grid.ac/institutes/grid.7872.a",
"name": [
"School of Biochemistry and Cell Biology, University College Cork, T12 XF62, Cork, Ireland"
],
"type": "Organization"
},
"familyName": "Loughran",
"givenName": "Gary",
"id": "sg:person.0642070574.31",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0642070574.31"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "School of Biochemistry and Cell Biology, University College Cork, T12 XF62, Cork, Ireland",
"id": "http://www.grid.ac/institutes/grid.7872.a",
"name": [
"School of Biochemistry and Cell Biology, University College Cork, T12 XF62, Cork, Ireland"
],
"type": "Organization"
},
"familyName": "Fedorova",
"givenName": "Alla D.",
"id": "sg:person.013147113727.55",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013147113727.55"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia",
"id": "http://www.grid.ac/institutes/grid.14476.30",
"name": [
"Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia"
],
"type": "Organization"
},
"familyName": "Mikhaylova",
"givenName": "Maria S.",
"id": "sg:person.015515676461.79",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015515676461.79"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia",
"id": "http://www.grid.ac/institutes/grid.14476.30",
"name": [
"Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia"
],
"type": "Organization"
},
"familyName": "Shatsky",
"givenName": "Ivan N.",
"id": "sg:person.01154577247.83",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01154577247.83"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "School of Biochemistry and Cell Biology, University College Cork, T12 XF62, Cork, Ireland",
"id": "http://www.grid.ac/institutes/grid.7872.a",
"name": [
"School of Biochemistry and Cell Biology, University College Cork, T12 XF62, Cork, Ireland"
],
"type": "Organization"
},
"familyName": "Baranov",
"givenName": "Pavel V.",
"id": "sg:person.0634677755.62",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634677755.62"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1038/nature08034",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1026075248",
"https://doi.org/10.1038/nature08034"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nsmb.3464",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1091522400",
"https://doi.org/10.1038/nsmb.3464"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/224957a0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1015663377",
"https://doi.org/10.1038/224957a0"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41587-020-00806-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1134921088",
"https://doi.org/10.1038/s41587-020-00806-2"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41586-018-0258-0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1105150810",
"https://doi.org/10.1038/s41586-018-0258-0"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s12863-020-0828-7",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1125442451",
"https://doi.org/10.1186/s12863-020-0828-7"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/29703",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048134234",
"https://doi.org/10.1038/29703"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature21036",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003690889",
"https://doi.org/10.1038/nature21036"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature10913",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022866252",
"https://doi.org/10.1038/nature10913"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/sj.onc.1202032",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030648359",
"https://doi.org/10.1038/sj.onc.1202032"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nsmb.3010",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1019251158",
"https://doi.org/10.1038/nsmb.3010"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncomms11663",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033513939",
"https://doi.org/10.1038/ncomms11663"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/sj.onc.1206688",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005280160",
"https://doi.org/10.1038/sj.onc.1206688"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s12859-014-0380-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041540150",
"https://doi.org/10.1186/s12859-014-0380-4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nrm2838",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036173966",
"https://doi.org/10.1038/nrm2838"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13059-018-1602-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1110935399",
"https://doi.org/10.1186/s13059-018-1602-2"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nrm3083",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1026414037",
"https://doi.org/10.1038/nrm3083"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13059-015-0651-z",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1025122898",
"https://doi.org/10.1186/s13059-015-0651-z"
],
"type": "CreativeWork"
}
],
"datePublished": "2022-05-09",
"datePublishedReg": "2022-05-09",
"description": "Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due to start codon plurality within the same RNA. This plurality is often due to the failure of some scanning ribosomes to recognize potential start codons leading to initiation downstream\u2014a process termed leaky scanning. Codons other than AUG (non-AUG) are particularly leaky due to their inefficiency. Here we discuss our current understanding of non-AUG initiation. We argue for a near-ubiquitous role of non-AUG initiation in shaping the dynamic composition of mammalian proteomes.",
"genre": "article",
"id": "sg:pub.10.1186/s13059-022-02674-2",
"inLanguage": "en",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.9048876",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.9405373",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.9405579",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.8103153",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1023439",
"issn": [
"1474-760X",
"1465-6906"
],
"name": "Genome Biology",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "23"
}
],
"keywords": [
"non-AUG initiation",
"AUG translation initiation",
"non-canonical translation",
"potential start codons",
"non-coding RNA",
"protein coding regions",
"mammalian proteomes",
"translation initiation",
"proteogenomic studies",
"start codon",
"same RNA",
"scanning ribosomes",
"untranslated region",
"coding regions",
"leaky scanning",
"ubiquitous role",
"codon",
"extensive translation",
"RNA",
"current understanding",
"proteome",
"ribosomes",
"mammals",
"translation",
"initiation",
"mRNA",
"region",
"role",
"dynamic composition",
"understanding",
"composition",
"process",
"study",
"scanning",
"failure",
"inefficiency",
"plurality"
],
"name": "Non-AUG translation initiation in mammals",
"pagination": "111",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1147723623"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/s13059-022-02674-2"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"35534899"
]
}
],
"sameAs": [
"https://doi.org/10.1186/s13059-022-02674-2",
"https://app.dimensions.ai/details/publication/pub.1147723623"
],
"sdDataset": "articles",
"sdDatePublished": "2022-06-01T22:25",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220601/entities/gbq_results/article/article_934.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1186/s13059-022-02674-2"
}
]
Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13059-022-02674-2'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13059-022-02674-2'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-022-02674-2'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-022-02674-2'
This table displays all metadata directly associated to this object as RDF triples.
250 TRIPLES
22 PREDICATES
89 URIs
63 LITERALS
15 BLANK NODES