PMID- 27330868
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20160622
LR  - 20200930
IS  - 2167-8359 (Print)
IS  - 2167-8359 (Electronic)
IS  - 2167-8359 (Linking)
VI  - 4
DP  - 2016
TI  - Different RNA splicing mechanisms contribute to diverse infective outcome of 
      classical swine fever viruses of differing virulence: insights from the deep 
      sequencing data in swine umbilical vein endothelial cells.
PG  - e2113
LID - 10.7717/peerj.2113 [doi]
LID - e2113
AB  - Molecular mechanisms underlying RNA splicing regulation in response to viral 
      infection are poorly understood. Classical swine fever (CSF), one of the most 
      economically important and highly contagious swine diseases worldwide, is caused 
      by classical swine fever virus (CSFV). Here, we used high-throughput sequencing 
      to obtain the digital gene expression (DGE) profile in swine umbilical vein 
      endothelial cells (SUVEC) to identify different response genes for CSFV by using 
      both Shimen and C strains. The numbers of clean tags obtained from the libraries 
      of the control and both CSFV-infected libraries were 3,473,370, 3,498,355, and 
      3,327,493 respectively. In the comparison among the control, CSFV-C, and 
      CSFV-Shimen groups, 644, 158, and 677 differentially expressed genes (DEGs) were 
      confirmed in the three groups. Pathway enrichment analysis showed that many of 
      these DEGs were enriched in spliceosome, ribosome, proteasome, ubiquitin-mediated 
      proteolysis, cell cycle, focal adhesion, Wnt signalling pathway, etc., where the 
      processes differ between CSFV strains of differing virulence. To further 
      elucidate important mechanisms related to the differential infection by the CSFV 
      Shimen and C strains, we identified four possible profiles to assess the 
      significantly expressed genes only by CSFV Shimen or CSFV C strain. GO analysis 
      showed that infection with CSFV Shimen and C strains disturbed 'RNA splicing' of 
      SUVEC, resulting in differential 'gene expression' in SUVEC. Mammalian target of 
      rapamycin (mTOR) was identified as a significant response regulator contributed 
      to impact on SUVEC function for CSFV Shimen. This computational study suggests 
      that CSFV of differing virulence could induce alterations in RNA splicing 
      regulation in the host cell to change cell metabolism, resulting in acute 
      haemorrhage and pathological damage or infectious tolerance.
FAU - Ning, Pengbo
AU  - Ning P
AD  - College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi; 
      School of Life Science and Technology, Xidian University, Xi'an, China.
FAU - Zhou, Yulu
AU  - Zhou Y
AD  - College of Science, Northwest A&F University , Yangling , China.
FAU - Liang, Wulong
AU  - Liang W
AD  - College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi.
FAU - Zhang, Yanming
AU  - Zhang Y
AD  - College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi.
LA  - eng
PT  - Journal Article
DEP - 20160608
PL  - United States
TA  - PeerJ
JT  - PeerJ
JID - 101603425
PMC - PMC4906664
OTO - NOTNLM
OT  - CSFV C
OT  - CSFV Shimen
OT  - RNA splicing
OT  - SUVEC
OT  - mTOR
COIS- The authors declare that there are no competing interests.
EDAT- 2016/06/23 06:00
MHDA- 2016/06/23 06:01
PMCR- 2016/06/08
CRDT- 2016/06/23 06:00
PHST- 2016/02/03 00:00 [received]
PHST- 2016/05/17 00:00 [accepted]
PHST- 2016/06/23 06:00 [entrez]
PHST- 2016/06/23 06:00 [pubmed]
PHST- 2016/06/23 06:01 [medline]
PHST- 2016/06/08 00:00 [pmc-release]
AID - 2113 [pii]
AID - 10.7717/peerj.2113 [doi]
PST - epublish
SO  - PeerJ. 2016 Jun 8;4:e2113. doi: 10.7717/peerj.2113. eCollection 2016.