TY - JOUR
T1 - Redefining the genetics of murine gammaherpesvirus 68 via transcriptome-based annotation
AU - Johnson, L. Steven
AU - Willert, Erin K.
AU - Virgin, Herbert W.
N1 - Funding Information:
We would like to thank the Washington University Microarray Core facility for running the tiled arrays, Seth Crosby's assistance on the original tiled array design, and members of the Virgin lab for reading the manuscript. This work was supported by U54AI057160 ARRA Administrative Supplement (to H.W.V.). L.S.J. and E.P.W. were supported by NIH TP32AI007163.
PY - 2010/6/17
Y1 - 2010/6/17
N2 - Viral genetic studies typically focus on large open reading frames (ORFs) identified during genome annotation (ORF-based annotation). Here we describe tools for examining viral gene expression nucleotide by nucleotide across the genome. Using these tools on the 119,450 base pair (bp) genome of murine gammaherpesvirus 68 (γHV68) allowed us to establish that γHV68 RNA expression was significantly more complex than predicted from ORF-based annotation, including over 73,000 nucleotides of unexpected transcriptionwithin 30 expressedgenomic regions (EGRs). Approximately 90% of this RNA expression was antisense to genomic regions containing known large ORFs. We verified the existence of previously undefined transcripts in three EGRs and determined which parts of the transcriptome depend on protein or viral DNA synthesis. This study redefines the genetic map of γHV68, indicating that herpesviruses contain significantly more genetic complexity than predicted from ORF-based genome annotations, and provides alternative tools and approaches for viral genetic studies.
AB - Viral genetic studies typically focus on large open reading frames (ORFs) identified during genome annotation (ORF-based annotation). Here we describe tools for examining viral gene expression nucleotide by nucleotide across the genome. Using these tools on the 119,450 base pair (bp) genome of murine gammaherpesvirus 68 (γHV68) allowed us to establish that γHV68 RNA expression was significantly more complex than predicted from ORF-based annotation, including over 73,000 nucleotides of unexpected transcriptionwithin 30 expressedgenomic regions (EGRs). Approximately 90% of this RNA expression was antisense to genomic regions containing known large ORFs. We verified the existence of previously undefined transcripts in three EGRs and determined which parts of the transcriptome depend on protein or viral DNA synthesis. This study redefines the genetic map of γHV68, indicating that herpesviruses contain significantly more genetic complexity than predicted from ORF-based genome annotations, and provides alternative tools and approaches for viral genetic studies.
UR - http://www.scopus.com/inward/record.url?scp=77956548303&partnerID=8YFLogxK
U2 - 10.1016/j.chom.2010.05.005
DO - 10.1016/j.chom.2010.05.005
M3 - Article
C2 - 20542255
AN - SCOPUS:77956548303
SN - 1931-3128
VL - 7
SP - 516
EP - 526
JO - Cell Host and Microbe
JF - Cell Host and Microbe
IS - 6
ER -