Literature DB >> 21938627

CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks.

Hazuki Takahashi1, Sachi Kato, Mitsuyoshi Murata, Piero Carninci.   

Abstract

We provide here a protocol for the preparation of cap-analysis gene expression (CAGE) libraries, which allows for measuring the expression of eukaryotic capped RNAs and simultaneously map the promoter regions. The presented protocol simplifies the previously published ones and moreover produces tags that are 27 nucleotides long, which facilitates mapping to the genome. The protocol takes less than 5 days to complete and presents a notable improvement compared to previously published versions.

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Year:  2012        PMID： 21938627      PMCID： PMC4094367          DOI： 10.1007/978-1-61779-292-2_11

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  8 in total

1.  Cloning full-length, cap-trapper-selected cDNAs by using the single-strand linker ligation method.

Authors:  Y Shibata; P Carninci; A Watahiki; T Shiraki; H Konno; M Muramatsu; Y Hayashizaki
Journal:  Biotechniques       Date:  2001-06       Impact factor: 1.993

2.  Extra-long first-strand cDNA synthesis.

Authors:  P Carninci; T Shiraki; Y Mizuno; M Muramatsu; Y Hayashizaki
Journal:  Biotechniques       Date:  2002-05       Impact factor: 1.993

3.  Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer.

Authors:  Norihiro Maeda; Hiromi Nishiyori; Mari Nakamura; Chika Kawazu; Mitsuyoshi Murata; Hiromi Sano; Kengo Hayashida; Shiro Fukuda; Michihira Tagami; Akira Hasegawa; Kayoko Murakami; Kate Schroder; Katharine Irvine; David Hume; Yoshihide Hayashizaki; Piero Carninci; Harukazu Suzuki
Journal:  Biotechniques       Date:  2008-07       Impact factor: 1.993

4.  Genome-wide analysis of mammalian promoter architecture and evolution.

Authors:  Piero Carninci; Albin Sandelin; Boris Lenhard; Shintaro Katayama; Kazuro Shimokawa; Jasmina Ponjavic; Colin A M Semple; Martin S Taylor; Pär G Engström; Martin C Frith; Alistair R R Forrest; Wynand B Alkema; Sin Lam Tan; Charles Plessy; Rimantas Kodzius; Timothy Ravasi; Takeya Kasukawa; Shiro Fukuda; Mutsumi Kanamori-Katayama; Yayoi Kitazume; Hideya Kawaji; Chikatoshi Kai; Mari Nakamura; Hideaki Konno; Kenji Nakano; Salim Mottagui-Tabar; Peter Arner; Alessandra Chesi; Stefano Gustincich; Francesca Persichetti; Harukazu Suzuki; Sean M Grimmond; Christine A Wells; Valerio Orlando; Claes Wahlestedt; Edison T Liu; Matthias Harbers; Jun Kawai; Vladimir B Bajic; David A Hume; Yoshihide Hayashizaki
Journal:  Nat Genet       Date:  2006-04-28       Impact factor: 38.330

5.  High-efficiency full-length cDNA cloning by biotinylated CAP trapper.

Authors:  P Carninci; C Kvam; A Kitamura; T Ohsumi; Y Okazaki; M Itoh; M Kamiya; K Shibata; N Sasaki; M Izawa; M Muramatsu; Y Hayashizaki; C Schneider
Journal:  Genomics       Date:  1996-11-01       Impact factor: 5.736

6.  The regulated retrotransposon transcriptome of mammalian cells.

Authors:  Geoffrey J Faulkner; Yasumasa Kimura; Carsten O Daub; Shivangi Wani; Charles Plessy; Katharine M Irvine; Kate Schroder; Nicole Cloonan; Anita L Steptoe; Timo Lassmann; Kazunori Waki; Nadine Hornig; Takahiro Arakawa; Hazuki Takahashi; Jun Kawai; Alistair R R Forrest; Harukazu Suzuki; Yoshihide Hayashizaki; David A Hume; Valerio Orlando; Sean M Grimmond; Piero Carninci
Journal:  Nat Genet       Date:  2009-04-19       Impact factor: 38.330

7.  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

8.  The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:  Harukazu Suzuki; Alistair R R Forrest; Erik van Nimwegen; Carsten O Daub; Piotr J Balwierz; Katharine M Irvine; Timo Lassmann; Timothy Ravasi; Yuki Hasegawa; Michiel J L de Hoon; Shintaro Katayama; Kate Schroder; Piero Carninci; Yasuhiro Tomaru; Mutsumi Kanamori-Katayama; Atsutaka Kubosaki; Altuna Akalin; Yoshinari Ando; Erik Arner; Maki Asada; Hiroshi Asahara; Timothy Bailey; Vladimir B Bajic; Denis Bauer; Anthony G Beckhouse; Nicolas Bertin; Johan Björkegren; Frank Brombacher; Erika Bulger; Alistair M Chalk; Joe Chiba; Nicole Cloonan; Adam Dawe; Josee Dostie; Pär G Engström; Magbubah Essack; Geoffrey J Faulkner; J Lynn Fink; David Fredman; Ko Fujimori; Masaaki Furuno; Takashi Gojobori; Julian Gough; Sean M Grimmond; Mika Gustafsson; Megumi Hashimoto; Takehiro Hashimoto; Mariko Hatakeyama; Susanne Heinzel; Winston Hide; Oliver Hofmann; Michael Hörnquist; Lukasz Huminiecki; Kazuho Ikeo; Naoko Imamoto; Satoshi Inoue; Yusuke Inoue; Ryoko Ishihara; Takao Iwayanagi; Anders Jacobsen; Mandeep Kaur; Hideya Kawaji; Markus C Kerr; Ryuichiro Kimura; Syuhei Kimura; Yasumasa Kimura; Hiroaki Kitano; Hisashi Koga; Toshio Kojima; Shinji Kondo; Takeshi Konno; Anders Krogh; Adele Kruger; Ajit Kumar; Boris Lenhard; Andreas Lennartsson; Morten Lindow; Marina Lizio; Cameron Macpherson; Norihiro Maeda; Christopher A Maher; Monique Maqungo; Jessica Mar; Nicholas A Matigian; Hideo Matsuda; John S Mattick; Stuart Meier; Sei Miyamoto; Etsuko Miyamoto-Sato; Kazuhiko Nakabayashi; Yutaka Nakachi; Mika Nakano; Sanne Nygaard; Toshitsugu Okayama; Yasushi Okazaki; Haruka Okuda-Yabukami; Valerio Orlando; Jun Otomo; Mikhail Pachkov; Nikolai Petrovsky; Charles Plessy; John Quackenbush; Aleksandar Radovanovic; Michael Rehli; Rintaro Saito; Albin Sandelin; Sebastian Schmeier; Christian Schönbach; Ariel S Schwartz; Colin A Semple; Miho Sera; Jessica Severin; Katsuhiko Shirahige; Cas Simons; George St Laurent; Masanori Suzuki; Takahiro Suzuki; Matthew J Sweet; Ryan J Taft; Shizu Takeda; Yoichi Takenaka; Kai Tan; Martin S Taylor; Rohan D Teasdale; Jesper Tegnér; Sarah Teichmann; Eivind Valen; Claes Wahlestedt; Kazunori Waki; Andrew Waterhouse; Christine A Wells; Ole Winther; Linda Wu; Kazumi Yamaguchi; Hiroshi Yanagawa; Jun Yasuda; Mihaela Zavolan; David A Hume; Takahiro Arakawa; Shiro Fukuda; Kengo Imamura; Chikatoshi Kai; Ai Kaiho; Tsugumi Kawashima; Chika Kawazu; Yayoi Kitazume; Miki Kojima; Hisashi Miura; Kayoko Murakami; Mitsuyoshi Murata; Noriko Ninomiya; Hiromi Nishiyori; Shohei Noma; Chihiro Ogawa; Takuma Sano; Christophe Simon; Michihira Tagami; Yukari Takahashi; Jun Kawai; Yoshihide Hayashizaki
Journal:  Nat Genet       Date:  2009-04-19       Impact factor: 38.330
  8 in total
  40 in total

Review 1.  Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.

Authors:  Molly Megraw; Jason S Cumbie; Maria G Ivanchenko; Sergei A Filichkin
Journal:  Plant Cell       Date:  2016-02-11       Impact factor: 11.277

2.  Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.

Authors:  Evgenia Ntini; Aino I Järvelin; Jette Bornholdt; Yun Chen; Mette Boyd; Mette Jørgensen; Robin Andersson; Ilka Hoof; Aleks Schein; Peter R Andersen; Pia K Andersen; Pascal Preker; Eivind Valen; Xiaobei Zhao; Vicent Pelechano; Lars M Steinmetz; Albin Sandelin; Torben Heick Jensen
Journal:  Nat Struct Mol Biol       Date:  2013-07-14       Impact factor: 15.369

Review 3.  Long Noncoding RNA Discovery in Cardiovascular Disease: Decoding Form to Function.

Authors:  Tamer Sallam; Jaspreet Sandhu; Peter Tontonoz
Journal:  Circ Res       Date:  2018-01-05       Impact factor: 17.367

4.  Unsupervised pattern discovery in human chromatin structure through genomic segmentation.

Authors:  Michael M Hoffman; Orion J Buske; Jie Wang; Zhiping Weng; Jeff A Bilmes; William Stafford Noble
Journal:  Nat Methods       Date:  2012-03-18       Impact factor: 28.547

5.  5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.

Authors:  Hazuki Takahashi; Timo Lassmann; Mitsuyoshi Murata; Piero Carninci
Journal:  Nat Protoc       Date:  2012-02-23       Impact factor: 13.491

6.  Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex.

Authors:  R Taylor Raborn; Ken Spitze; Volker P Brendel; Michael Lynch
Journal:  Genetics       Date:  2016-08-31       Impact factor: 4.562

Review 7.  A survey of transcripts generated by spinal muscular atrophy genes.

Authors:  Natalia N Singh; Eric W Ottesen; Ravindra N Singh
Journal:  Biochim Biophys Acta Gene Regul Mech       Date:  2020-05-06       Impact factor: 4.490

8.  Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites.

Authors:  María Katherine Mejía-Guerra; Wei Li; Narmer F Galeano; Mabel Vidal; John Gray; Andrea I Doseff; Erich Grotewold
Journal:  Plant Cell       Date:  2015-12-01       Impact factor: 11.277

Review 9.  The state of play in higher eukaryote gene annotation.

Authors:  Jonathan M Mudge; Jennifer Harrow
Journal:  Nat Rev Genet       Date:  2016-10-24       Impact factor: 53.242

Review 10.  Experimental approaches for gene regulatory network construction: the chick as a model system.

Authors:  Andrea Streit; Monica Tambalo; Jingchen Chen; Timothy Grocott; Maryam Anwar; Alona Sosinsky; Claudio D Stern
Journal:  Genesis       Date:  2012-12-19       Impact factor: 2.487
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