title: Conserved features of an RNA promoter for RNA polymerase II determined from sequence heterogeneity of a hepatitis delta virus population.
abstract: The right terminal domain of genomic hepatitis delta virus (HDV) RNA is involved in viral replication by recruiting host RNA polymerase II. To identify conserved features of this region, we performed high-throughput 454 sequencing of an HDV population actively replicating in cells. We generated 473,139 sequences representing 2351 new HDV variants of this region and investigated nucleotide conservation and positions of covariation in the population. We found that the sequence is heterogeneous and the rod-like conformation is conserved for both polarities of the HDV RNA genome at this location. Additionally, we identified conserved nucleotides near the previously reported initiation site of transcription, and corroborated our finding with sequences from HDV variants isolated in various hosts. Our analysis highlights the importance of both a conserved sequence at the tip of the rod-like structure and the RNA secondary structure upstream of the tip, which are likely important for HDV replication.
authors: Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Room 4111 A, Ottawa, Ontario, Canada, K1H 8M5.
authors: Yasnee
authors: Y
authors: Beeharry
authors: Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Room 4111 A, Ottawa, Ontario, Canada, K1H 8M5.
authors: Lynda
authors: L
authors: Rocheleau
authors: Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Room 4111 A, Ottawa, Ontario, Canada, K1H 8M5. Electronic address: mpelchat@uottawa.ca.
authors: Martin
authors: M
authors: Pelchat
mesh_terms: D001483:Base Sequence; D002460:Cell Line; D017124:Conserved Sequence; D014644:Genetic Variation; D003699:Hepatitis D / Q000821:virology*; D003698:Hepatitis Delta Virus / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics* / Q000378:metabolism; D014764:Viral Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D014764:Viral Proteins; D012319:RNA Polymerase II
keywords: Hepatitis delta virus; High-throughput sequencing; RNA covariation; Secondary structure alignment; Sequence analysis; Viral quasi-species