Literature DB >> 25505068

Characterization of novel transcripts of human papillomavirus type 16 using cap analysis gene expression technology.

Ayumi Taguchi1, Kazunori Nagasaka2, Kei Kawana2, Kosuke Hashimoto3, Rika Kusumoto-Matsuo4, Charles Plessy3, Miranda Thomas5, Hiroe Nakamura1, Alessandro Bonetti3, Katsutoshi Oda1, Iwao Kukimoto4, Piero Carninci3, Lawrence Banks5, Yutaka Osuga1, Tomoyuki Fujii1.   

Abstract

We have performed cap-analysis gene expression (CAGE) sequencing to identify the regulatory networks that orchestrate genome-wide transcription in human papillomavirus type 16 (HPV16)-positive cervical cell lines of different grades: W12E, SiHa, and CaSki. Additionally, a cervical intraepithelial neoplasia grade 1 (CIN1) lesion was assessed for identifying the transcriptome expression profile. Here we have precisely identified a novel antisense noncoding viral transcript in HPV16. In conclusion, CAGE sequencing should pave the way for understanding a diversity of viral transcript expression.
Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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Year:  2014        PMID： 25505068      PMCID： PMC4338893          DOI： 10.1128/JVI.03433-14

Source DB:  PubMed          Journal:  J Virol        ISSN： 0022-538X            Impact factor:   5.103


  31 in total

1.  A code for transcription initiation in mammalian genomes.

Authors:  Martin C Frith; Eivind Valen; Anders Krogh; Yoshihide Hayashizaki; Piero Carninci; Albin Sandelin
Journal:  Genome Res       Date:  2007-11-21       Impact factor: 9.043

2.  CAGE: cap analysis of gene expression.

Authors:  Rimantas Kodzius; Miki Kojima; Hiromi Nishiyori; Mari Nakamura; Shiro Fukuda; Michihira Tagami; Daisuke Sasaki; Kengo Imamura; Chikatoshi Kai; Matthias Harbers; Yoshihide Hayashizaki; Piero Carninci
Journal:  Nat Methods       Date:  2006-03       Impact factor: 28.547

3.  Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

Authors:  Eivind Valen; Giovanni Pascarella; Alistair Chalk; Norihiro Maeda; Miki Kojima; Chika Kawazu; Mitsuyoshi Murata; Hiromi Nishiyori; Dejan Lazarevic; Dario Motti; Troels Torben Marstrand; Man-Hung Eric Tang; Xiaobei Zhao; Anders Krogh; Ole Winther; Takahiro Arakawa; Jun Kawai; Christine Wells; Carsten Daub; Matthias Harbers; Yoshihide Hayashizaki; Stefano Gustincich; Albin Sandelin; Piero Carninci
Journal:  Genome Res       Date:  2008-12-11       Impact factor: 9.043

Review 4.  New roles for large and small viral RNAs in evading host defences.

Authors:  Christopher S Sullivan
Journal:  Nat Rev Genet       Date:  2008-05-20       Impact factor: 53.242

5.  Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.

Authors:  Charles Plessy; Nicolas Bertin; Hazuki Takahashi; Roberto Simone; Md Salimullah; Timo Lassmann; Morana Vitezic; Jessica Severin; Signe Olivarius; Dejan Lazarevic; Nadine Hornig; Valerio Orlando; Ian Bell; Hui Gao; Jacqueline Dumais; Philipp Kapranov; Huaien Wang; Carrie A Davis; Thomas R Gingeras; Jun Kawai; Carsten O Daub; Yoshihide Hayashizaki; Stefano Gustincich; Piero Carninci
Journal:  Nat Methods       Date:  2010-06-13       Impact factor: 28.547

6.  The E8--E2 gene product of human papillomavirus type 16 represses early transcription and replication but is dispensable for viral plasmid persistence in keratinocytes.

Authors:  Michael J Lace; James R Anson; Gregory S Thomas; Lubomir P Turek; Thomas H Haugen
Journal:  J Virol       Date:  2008-08-27       Impact factor: 5.103

7.  Functional mapping of the human papillomavirus type 16 E1 cistron.

Authors:  Michael J Lace; James R Anson; Lubomir P Turek; Thomas H Haugen
Journal:  J Virol       Date:  2008-08-27       Impact factor: 5.103

Review 8.  Human papillomavirus: gene expression, regulation and prospects for novel diagnostic methods and antiviral therapies.

Authors:  Sheila V Graham
Journal:  Future Microbiol       Date:  2010-10       Impact factor: 3.165

9.  The transcriptional landscape of the mammalian genome.

Authors:  P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728

10.  Fast and accurate long-read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2010-01-15       Impact factor: 6.937
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  4 in total

Review 1.  HPV16 and HPV18 Genome Structure, Expression, and Post-Transcriptional Regulation.

Authors:  Lulu Yu; Vladimir Majerciak; Zhi-Ming Zheng
Journal:  Int J Mol Sci       Date:  2022-04-29       Impact factor: 6.208

Review 2.  Deciphering the Multifactorial Susceptibility of Mucosal Junction Cells to HPV Infection and Related Carcinogenesis.

Authors:  Michael Herfs; Thing R Soong; Philippe Delvenne; Christopher P Crum
Journal:  Viruses       Date:  2017-04-20       Impact factor: 5.048

3.  Single-Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular Carcinoma.

Authors:  Kübra Altinel; Kosuke Hashimoto; Yu Wei; Christine Neuveut; Ishita Gupta; Ana Maria Suzuki; Alexandre Dos Santos; Pierrick Moreau; Tian Xia; Soichi Kojima; Sachi Kato; Yasuhiro Takikawa; Isao Hidaka; Masahito Shimizu; Tomokazu Matsuura; Akihito Tsubota; Hitoshi Ikeda; Sumiko Nagoshi; Harukazu Suzuki; Marie-Louise Michel; Didier Samuel; Marie Annick Buendia; Jamila Faivre; Piero Carninci
Journal:  J Virol       Date:  2016-11-14       Impact factor: 5.103

4.  Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages.

Authors:  Ayumi Taguchi; Kazunori Nagasaka; Charles Plessy; Hiroe Nakamura; Yoshiko Kawata; Sachi Kato; Kosuke Hashimoto; Takeshi Nagamatsu; Katsutoshi Oda; Iwao Kukimoto; Kei Kawana; Piero Carninci; Yutaka Osuga; Tomoyuki Fujii
Journal:  Sci Rep       Date:  2020-10-22       Impact factor: 4.379
  4 in total

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