Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs.
Identifieur interne : 000871 ( Ncbi/Curation ); précédent : 000870; suivant : 000872Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs.
Auteurs : Brandon S. Razooky [États-Unis] ; Benedikt Obermayer [Allemagne] ; Joshua Biggs O'May [États-Unis] ; Alexander Tarakhovsky [États-Unis]Source :
- Genes [ 2073-4425 ] ; 2017.
Abstract
Viral infection leads to a robust cellular response whereby the infected cell produces hundreds of molecular regulators to combat infection. Currently, non-canonical components, e.g., long noncoding RNAs (lncRNAs) have been added to the repertoire of immune regulators involved in the antiviral program. Interestingly, studies utilizing next-generation sequencing technologies show that a subset of the >10,000 lncRNAs in the mammalian genome contain small open reading frames (smORFs) associated with active translation, i.e., many lncRNAs are not noncoding. Here, we use genome-wide high-throughput methods to identify potential micropeptides in smORF-containing lncRNAs involved in the immune response. Using influenza as a viral infection model, we performed RNA-seq and ribosome profiling to track expression and translation of putative lncRNAs that may encode for peptides and identify tens of potential candidates. Interestingly, many of these peptides are highly conserved at the protein level, strongly suggesting biological relevance and activity. By perusing publicly available data sets, four potential peptides of interest seem common to stress induction and/or are highly conserved; potential peptides from the MMP24-AS1, ZFAS1, RP11-622K12.1, and MIR22HG genes. Interestingly, using an antibody against the potential peptide encoded by MIR22HG RNA, we show that the peptide is stably expressed in the absence of infection, and upregulated in response to infection, corroborating the prediction of the ribosome profiling results. These data show the utility of perturbation approaches in identifying potentially relevant novel molecules encoded in the genome.
DOI: 10.3390/genes8080206
PubMed: 28825667
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000313
- to stream PubMed, to step Curation: Pour aller vers cette notice dans l'étape Curation :000312
- to stream PubMed, to step Checkpoint: Pour aller vers cette notice dans l'étape Curation :000299
- to stream Ncbi, to step Merge: Pour aller vers cette notice dans l'étape Curation :000871
Links to Exploration step
pubmed:28825667Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs.</title>
<author><name sortKey="Razooky, Brandon S" sort="Razooky, Brandon S" uniqKey="Razooky B" first="Brandon S" last="Razooky">Brandon S. Razooky</name>
<affiliation wicri:level="2"><nlm:affiliation>Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065, USA. brazooky@gmail.com.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065</wicri:regionArea>
<placeName><region type="state">État de New York</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Obermayer, Benedikt" sort="Obermayer, Benedikt" uniqKey="Obermayer B" first="Benedikt" last="Obermayer">Benedikt Obermayer</name>
<affiliation wicri:level="3"><nlm:affiliation>Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany. benedikt.obermayer@mdc-berlin.de.</nlm:affiliation>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin</wicri:regionArea>
<placeName><region type="land" nuts="3">Berlin</region>
<settlement type="city">Berlin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="O May, Joshua Biggs" sort="O May, Joshua Biggs" uniqKey="O May J" first="Joshua Biggs" last="O'May">Joshua Biggs O'May</name>
<affiliation wicri:level="2"><nlm:affiliation>Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065, USA. brazooky@gmail.com.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065</wicri:regionArea>
<placeName><region type="state">État de New York</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Tarakhovsky, Alexander" sort="Tarakhovsky, Alexander" uniqKey="Tarakhovsky A" first="Alexander" last="Tarakhovsky">Alexander Tarakhovsky</name>
<affiliation wicri:level="2"><nlm:affiliation>Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY 10065, USA. tarakho@mail.rockefeller.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY 10065</wicri:regionArea>
<placeName><region type="state">État de New York</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2017">2017</date>
<idno type="RBID">pubmed:28825667</idno>
<idno type="pmid">28825667</idno>
<idno type="doi">10.3390/genes8080206</idno>
<idno type="wicri:Area/PubMed/Corpus">000313</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000313</idno>
<idno type="wicri:Area/PubMed/Curation">000312</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000312</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000299</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000299</idno>
<idno type="wicri:Area/Ncbi/Merge">000871</idno>
<idno type="wicri:Area/Ncbi/Curation">000871</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs.</title>
<author><name sortKey="Razooky, Brandon S" sort="Razooky, Brandon S" uniqKey="Razooky B" first="Brandon S" last="Razooky">Brandon S. Razooky</name>
<affiliation wicri:level="2"><nlm:affiliation>Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065, USA. brazooky@gmail.com.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065</wicri:regionArea>
<placeName><region type="state">État de New York</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Obermayer, Benedikt" sort="Obermayer, Benedikt" uniqKey="Obermayer B" first="Benedikt" last="Obermayer">Benedikt Obermayer</name>
<affiliation wicri:level="3"><nlm:affiliation>Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany. benedikt.obermayer@mdc-berlin.de.</nlm:affiliation>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin</wicri:regionArea>
<placeName><region type="land" nuts="3">Berlin</region>
<settlement type="city">Berlin</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="O May, Joshua Biggs" sort="O May, Joshua Biggs" uniqKey="O May J" first="Joshua Biggs" last="O'May">Joshua Biggs O'May</name>
<affiliation wicri:level="2"><nlm:affiliation>Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065, USA. brazooky@gmail.com.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065</wicri:regionArea>
<placeName><region type="state">État de New York</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Tarakhovsky, Alexander" sort="Tarakhovsky, Alexander" uniqKey="Tarakhovsky A" first="Alexander" last="Tarakhovsky">Alexander Tarakhovsky</name>
<affiliation wicri:level="2"><nlm:affiliation>Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY 10065, USA. tarakho@mail.rockefeller.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Laboratory of Virology and Infectious Diseases, The Rockefeller University, New York, NY 10065</wicri:regionArea>
<placeName><region type="state">État de New York</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">Genes</title>
<idno type="ISSN">2073-4425</idno>
<imprint><date when="2017" type="published">2017</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Viral infection leads to a robust cellular response whereby the infected cell produces hundreds of molecular regulators to combat infection. Currently, non-canonical components, e.g., long noncoding RNAs (lncRNAs) have been added to the repertoire of immune regulators involved in the antiviral program. Interestingly, studies utilizing next-generation sequencing technologies show that a subset of the >10,000 lncRNAs in the mammalian genome contain small open reading frames (smORFs) associated with active translation, i.e., many lncRNAs are not noncoding. Here, we use genome-wide high-throughput methods to identify potential micropeptides in smORF-containing lncRNAs involved in the immune response. Using influenza as a viral infection model, we performed RNA-seq and ribosome profiling to track expression and translation of putative lncRNAs that may encode for peptides and identify tens of potential candidates. Interestingly, many of these peptides are highly conserved at the protein level, strongly suggesting biological relevance and activity. By perusing publicly available data sets, four potential peptides of interest seem common to stress induction and/or are highly conserved; potential peptides from the MMP24-AS1, ZFAS1, RP11-622K12.1, and MIR22HG genes. Interestingly, using an antibody against the potential peptide encoded by MIR22HG RNA, we show that the peptide is stably expressed in the absence of infection, and upregulated in response to infection, corroborating the prediction of the ribosome profiling results. These data show the utility of perturbation approaches in identifying potentially relevant novel molecules encoded in the genome.</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/StressCovidV1/Data/Ncbi/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000871 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd -nk 000871 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= StressCovidV1 |flux= Ncbi |étape= Curation |type= RBID |clé= pubmed:28825667 |texte= Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Curation/RBID.i -Sk "pubmed:28825667" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Curation/biblio.hfd \ | NlmPubMed2Wicri -a StressCovidV1
This area was generated with Dilib version V0.6.33. |