About: Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression

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About: Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
Creator	Baric, Ralph Gralinski, Lisa Whitmore, Alan Morrison, Juliet Peng, Xinxia Xiong, Hao Heise, Mark Tisoncik-Go, Jennifer Green, Richard Ferris, Martin Schroth, Gary Katze, Michael Pardo-Manuel De Villena, Fernando Thomas, Matthew
Source	Medline; PMC
abstract	Genetic variation between diverse mouse species is well-characterized, yet existing knowledge of the mouse transcriptome comes largely from one mouse strain (C57BL/6J). As such, it is unlikely to reflect the transcriptional complexity of the mouse species. Gene transcription is dynamic and condition-specific; therefore, to better understand the mouse transcriptional response to respiratory virus infection, we infected the eight founder strains of the Collaborative Cross with either influenza A virus or severe acute respiratory syndrome coronavirus and sequenced lung RNA samples at 2 and 4 days after infection. We found numerous instances of transcripts that were not present in the C57BL/6J reference annotation, indicating that a nontrivial proportion of the mouse genome is transcribed but poorly annotated. Of these novel transcripts, 2150 could be aligned to human or rat genomes, but not to existing mouse genomes, suggesting functionally conserved sequences not yet recorded in mouse genomes. We also found that respiratory virus infection induced differential expression of 4287 splicing junctions, resulting in strain-specific isoform expression. Of these, 59 were influenced by strain-specific mutations within 2 base pairs of key intron–exon boundaries, suggesting cis-regulated expression. Our results reveal the complexity of the transcriptional response to viral infection, previously undocumented genomic elements, and extensive diversity in the response across mouse strains. These findings identify hitherto unexplored transcriptional patterns and undocumented transcripts in genetically diverse mice. Host genetic variation drives the complexity and diversity of the host response by eliciting starkly different transcriptional profiles in response to a viral infection.
has issue date	2014-06-05(xsd:dateTime)
bibo:doi	10.1534/g3.114.011759
bibo:pmid	24902603
has license	cc-by
sha1sum (hex)	4c9d7e3db46a6026e1554f2fa3df4f93645381e1
schema:url	https://doi.org/10.1534/g3.114.011759
resource representing a document's title	Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
has PubMed Central identifier	PMC4132174
has PubMed identifier	24902603
schema:publication	G3 (Bethesda)
resource representing a document's body	covid:4c9d7e3db46a6026e1554f2fa3df4f93645381e1#body_text
is schema:about of	named entity 'C57BL/6J' named entity 'complexity' named entity 'annotated' named entity 'patterns' named entity 'recorded' named entity 'Respiratory' named entity 'SPECIFIC' named entity 'MOUSE STRAINS' named entity 'RESPIRATORY VIRUSES' named entity 'COLLABORATIVE' named entity 'ELEMENTS' named entity 'VIRAL INFECTION' named entity 'TRANSCRIBED' named entity 'FINDINGS' named entity 'FOUNDER' named entity 'BETTER' named entity 'MOUSE' named entity 'RESPONSE' covid:arg/4c9d7e3db46a6026e1554f2fa3df4f93645381e1 named entity 'RESULTS' named entity 'SEQUENCES' named entity 'GENETIC VARIATION' named entity 'RAT' named entity 'KEY' named entity 'RNA' named entity 'SPLICING' named entity 'UNLIKELY' named entity 'PREVIOUSLY' named entity 'STRAIN' named entity 'GENE TRANSCRIPTION' named entity 'RESULTING IN' named entity 'EITHER' named entity 'HOST RESPONSE' named entity 'CROSS' named entity 'STRAIN' named entity 'INFECTION' named entity 'ISOFORM' named entity 'INFLUENZA A VIRUS' named entity 'INTRON' named entity 'CONSERVED' named entity 'CROSS' named entity 'OUR' named entity 'CHARACTERIZED' named entity 'ISOFORM' named entity 'NOVEL' named entity 'INFECTED' named entity 'TRANSCRIPTS' named entity 'RELATED' named entity 'GENOMIC PROFILING' named entity 'GENE' named entity 'EXPRESSION' named entity 'DIFFERENTIAL EXPRESSION' named entity 'DIVERSITY' named entity 'NOT PRESENT' named entity 'GENOMES' named entity 'DYNAMIC' named entity 'INDICATING' named entity 'COMES' named entity 'COLLABORATIVE' named entity 'EXTENSIVE' named entity 'GENOMIC' named entity 'DRIVES' named entity 'DAYS' named entity 'ALIGNED TO' named entity 'BASE PAIRS' named entity 'REFLECT' named entity 'KNOWLEDGE' named entity 'FOUNDER'

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