FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi ,Toshio Kitamura ,Kaoru Kaida ,Atsutaka Kubosaki ,Anita Schwegmann ,Jun Takai ,Tsugumi Kawashima ,Alistair R.r Forrest ,Naoki Suzuki ,Takeya Kasukawa ,Mitsuhiro Endoh ,Kelly J Hitchens ,Michihira Tagami ,Marina Lizio ,Mutsumi Kanamori-Katayama ,Kenichi Nakazato ,Kelly J Morris ,Swati Pradhan-Bhatt ,T Gingeras ,Shiro Fukuda ,Juha Kere ,Michael Rehli ,Christine L Mummery ,Shigeo Koyasu ,Akiko Saka ,Jay W Shin ,Hiroshi Ohno ,Niklas Mejhert ,Yohei Yonekura ,Ernst J Wolvetang ,Linda Berg ,Alessandro Bonetti ,Weon-Ju Lee ,Masahide Hamaguchi ,Taeko Dohi ,Christine A Wells ,Louise N Winteringham ,Alan Mackay‐Sim ,Yoko Yamaguchi ,Carmelo Ferrai ,Harukazu Suzuki ,Meenhard Herlyn ,Chiyo Yanagi-Mizuochi ,Jun Kawai ,Soichi Ogishima ,Marcvande Wetering ,Haruhiko Koseki ,Dipti Vijayan ,Naoko Takahashi ,Hiroshi Tanaka ,B Albert S Edge ,Tomokatsu Ikawa ,Ana Pombo ,Eri Saijyo ,Yuki I Kawamura ,Mary C Farach-Carson ,Masanori Suzuki ,Ailsa J Carlisle ,Peter G Zhang ,Andru Tomoiu ,Timothy C Barnett ,Anna Ehrlund ,Matthias Edinger ,Toshiyuki Nakamura ,Alka Saxena ,Levon M Khachigian ,Hisashi Shimoji ,Daniel Goldowitz ,Ai Kaiho ,Afsaneh Eslami ,Hideya Kawaji ,Michael Detmar ,Jayson Harshbarger ,Atsushi Kondo ,Shigehiro Yoshida ,Daisuke Sugiyama ,Mitsuko Hara ,Hiroshi Kawamoto ,Fumi Hori ,Piero Carninci ,Chieko Kai ,Thomas Ha ,Alan J Knox ,Shohei Noma ,Valerio Orlando ,Sayaka Nagao-Sato ,Gundula Schulze‐Tanzil ,Naganari Ohkura ,Karl Ekwall ,Takaaki Sugiyama ,Patrizia Rizzu ,Hans Clevers ,Imad Abugessaisa ,Christian Schmidl ,Hozumi Motohashi ,Sven Guhl ,Anthony G Beckhouse ,Dmitry A Ovchinnikov ,S Zucchelli ,S Peter Klinken ,Serkan Sahin ,Stefano Gustincich ,Thierry Sengstag ,Robert Passier ,Masaaki Furuno ,Mitsuhiro Ohshima ,Antti Sajantila ,Peter Heutink ,Soichi Kojima ,Shoko Watanabe ,Rie Fujita ,Geoffrey J Faulkner ,Antje Blumenthal ,Claudio Schneider ,Akira Hasegawa ,Peter Arner ,J Kenneth Baillie ,Timo Lassmann ,Kazuyo Moro ,Carrie A Davis ,Hiroo Toyoda ,Sachi Ishikawa-Kato ,Fumio Nakahara ,Masayuki Yamamoto ,Suzana Savvi ,Richard Axton ,Guojun Sheng ,Andreas Lennartsson ,Misako Yoneda ,Shimon Sakaguchi ,Mizuho Sakai ,Reto Guler ,Takahiro Arakawa ,Yosuke Mizuno ,Miki Kojima ,Margaret Patrikakis ,Malcolm E Fisher ,Hideki Tatsukawa ,Mitsuru Morimoto ,Tomohiro Nozaki ,Carsten O Daub ,Frank Brombacher ,Yutaka Nakachi ,Yasushi Okazaki ,Magda Babina ,Lynsey Fairbairn ,Beatrice Bodega ,Tony J Kenna ,Hiromi Nishiyori-Sueki ,Noriko Ninomiya ,Teunis B H Geijtenbeek ,Mitsuyoshi Murata ,Hideki Enomoto ,David Hume ,Masayoshi Itoh ,Hironori Satoh ,Mariko Okada‐Hatakeyama ,James Briggs ,Ri Ichiroh Manabe ,Yuki Hasegawa ,Kim M Summers ,Judith S Kempfle ,Yuri Ishizu ,Lesley M Forrester ,Naoto Kondo ,Sarah Klein ,Christophe Simon ,Jun Furusawa ,Hiroki Sato ,Michela Fagiolini ,Hiromasa Morikawa ,Yukio Nakamura ,Jessica Severin ,Sugata Roy ,Xian Qin ,Roberto Verardo ,Yoshihide Hayashizaki

doi:10.1038/sdata.2017.112

Abstract

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

Highlights

Background & SummarySince the completion of the human genome sequencing, role of individual bases has been a central question
We focused on transitions of cell states by monitoring ‘time course’ samples, such as activations, differentiations, and developments at sequential time points[15]
Based on frequencies of the observed 5′ends of individual capped RNA molecules at a single base-pair resolution, we identified 201,802 and 158,966 peaks for human and mouse respectively, where promoters are defined as the sequence immediately upstream of the peaks and frequencies of observed CAGE reads reflect activities of the promoters

Summary

Introduction

Background & SummarySince the completion of the human genome sequencing, role of individual bases has been a central question. In the course of the two phases focused on ‘snapshot’ and ‘time course’ samples, we profiled 1,816 human and 1,016 mouse samples in total, and obtained approximately four millions of single-molecule reads successfully aligned to the genome per sample on average.

Results

Conclusion