Abstract - 理化学研究所予防医療・診断技術開発プログラム

第 37 回日本分子生物学会年会フォーラム
国際 FANTOM プロジェクトの最新情報
～プロモーター／エンハンサーのダイナミクスでみる細胞活性～
日時：11 月 25 日（火）19：15-20：45
会場：パシフィコ横浜
第 37 回日本分子生物学会年会
オーガナイザー：林崎良英（理化学研究所
第 8 会場（会議センター3F 315）
予防医療・診断技術開発プログラム）
Piero Carninci（理化学研究所
ライフサイエンス技術基盤研究センター）
FANTOM は、20 か国、114 機関の 261 人の研究者が参加する理化学研究所主催の国際コンソーシア
ムです。今回のフォーラムでは、細胞分化の過程におけるプロモーター／エンハンサーの動的変化を
観測することにより、細胞活性を記述した最近の成果をまとめて紹介します。次世代シーケンサーの
一般化にともない、ゲノムワイドなアプローチは、研究の対象にかかわらず重要な意味を持つように
なってきました。オミックス研究に携わる研究者はもちろん、
「分野が違う」と思う若手の研究者や学
生の方にとっても有意義なものとなるでしょう。
一部は英語での講演となります。
19：15-19：20
開会にあたって
林崎良英（理化学研究所予防医療・診断技術開発プログラム）
19：20-19：25
ヘリスコープ一分子シーケンサーによる CAGE 解析法
伊藤昌可（理化学研究所予防医療・診断技術開発プログラム）
19：25-19：45
哺乳類におけるプロモーター単位でのゲノムワイドな発現地図と、
これを収録したデータベースシステム
川路英哉（理化学研究所予防医療・診断技術開発プログラム）
19：45-20：05
ヒト細胞および組織におけるエンハンサー活性地図
Albin Sandelin（コペンハーゲン大学）
20：05-20：25
哺乳類細胞の活性化および分化の過程におけるエンハンサー/
プロモーター活性のダイナミクス
Erik Arner
（理化学研究所ライフサイエンス技術基盤研究センター）
20：25-20：35
FANTOM の展望：長鎖 non-coding RNA の機能とネットワーク
Piero Carninci
（理化学研究所ライフサイエンス技術基盤研究センター）
20：35-20：45
FANTOM の展望：疾患のネットワークの理解とバイオマーカー探索
林崎良英（理化学研究所予防医療・診断技術開発プログラム）
林崎
良英
独立行政法人理化学研究所
予防医療・診断技術開発プログラム
プログラムディレクター
Omics for Medical Treatment
FANTOM の展望：疾患のネットワークの理解とバイオマーカー探索
要旨：
The “omics” approach integrates genomics, transcriptomics into single data set and can
lead to the identification of unknown genomic elements and their regulatory networks
involved in the diversity, developmental pathways and spatial organization of the
hundreds of cell types that make up a mammal.
In 2000, RIKEN has launched FANTOM (Functional Annotation of Mammalian Genome),
an international consortium, which is leading transcriptome research in the world.
Whereas the human genome project mapped every gene in the human genome, the
FANTOM project has been mapping which genes are “active”. At the fifth stage of the
project, FANTOM has released the data which provides the first overview of the networks
regulating transcription across all cell types.
Over 250 experts in primary cell biology and bioinformatics from 114 institutions based in
more than 20 countries and regions worked as part of FANTOM5. Cap Analysis of Gene
Expression (CAGE), the central technology used
during FANTOM5,
provides
genome-wide overview of transcription start sites and their usage in a cell. With this
original technology, we identified 180,000 promoters and 44000 enhancers on the genome
across over 180 human primary cells. In-depth analysis of the obtained data led to the
new knowledge that the activity of the large majority of these transcriptional regulation
regions is highly specific to cell type.
Our next research target is application of omics data to medical treatment. CAGE
analysis of cancer cells enable reclassification of cancer cells and lead to subsequent
biomarker discovery to identify patient subgroups with the highest unmet medical need.
Furthermore, CAGE data can identify a group of transcription factors that regulates each
transcripts.
略歴：
Yoshihide Hayashizaki is Director of the Preventive Medicine & Diagnosis Innovation
Program. He obtained his M.D. and Ph.D. from Osaka University Medical School in 1982
and 1986, respectively. In 1992, he joined RIKEN, and was appointed Project Director for
the RIKEN Genome Project in 1995. Since then he has been taking a transversal
data-driven approach to analyse transcriptomes by developing unique technologies
including a series of full-length cDNA technologies. This activity was followed by the
organization of FANTOM (Functional Annotation of Mammalian Genome), an
international consortium, originally to annotate a large number of cDNA and
subsequently expanded to transcriptome and network analysis. His research interests
are focused on the understanding of biological phenomena as systems at the molecular
level and its application to preventive medical care.
Piero Carninci
独立行政法人理化学研究所
ライフサイエンス技術基盤研究センター
機能性ゲノム解析部門部門長
FANTOM Future: long non-coding RNAs functions and networks
FANTOM の展望：長鎖 non-coding RNA の機能とネットワーク
要旨:
We have developed cap-analysis gene expression (CAGE) to simultaneously map mRNAs
and non-coding RNAs transcription starting sites (TSSs) and measure their expression at
each different promoters. Since CAGE shows single nucleotide resolution, we can use this
technology to comprehensively measure gene expression at each TSSs. Due to this
unprecedented resolution, we have learned that promoters use different regulatory
elements in different cells and tissues. Using CAGE, we can also infer the transcriptional
networks that regulate gene expression in each different cell type. For its high resolution
to map TSSs, CAGE has been used extensively in the ENCODE and modENCODE
projects.
In the FANTOM5 project, we have applied CAGE on a comprehensive panel of human
and mouse primary cells and other tissues, resulting in a very broad map the
promoterome and regulatory networks. Our map reveals the existence of more than
180,000 promoters and 45,000 enhancers, which are often tissue specific. The FANTOM5
database is one of the broadest expression database available to the community
(http://fantom.gsc.riken.jp/5/). Additionally, we have determined the pattern of
expression of retrotransposon elements (RE), which are likely to have a regulatory role.
As example, some families of LTR retrotransposon elements are specifically expressed in
ES and iPS cells, where they have a role in maintenance of pluripotency. Future
FANTOM projects will be focusing to broadly understand the function and the interaction
with cell regulatory networks of these RNAs in several primary cells, with the purpose to
create the broadest database of functional lncRNAs.
略歴：
Born and Educated in Italy he obtained his doctoral degree at the University of Trieste in
1989. From 1990 to 1995 he developed technologies for DNA extraction and DNA
sequencing at Talent, a spin-off biotech.
He moved to Japan in 1995 at RIKEN, Tsukuba Life Science center and became tenure
researcher in 1997. He has been developing technologies to capture full-length cDNAs,
which were used for the construction of the Fantom projects. Between 2008 and 2013, he
was a Team and Unit Leader and a Deputy Project Director at the RIKEN Omics Science
Center in Yokohama. He has developed technologies to analyze the transcribed part of the
genome (transcriptome), such as the cap-trapper and the CAGE. These technologies have
been broadly used in the RIKEN Fantom projects and allowed identifying non-coding
RNAs as are the major output of the mammalian genome and providing comprehensive
maps of the mammalian promoters. Additionally he developed a miniaturization of CAGE,
in order to approach biological problems that for which there is limited amount of starting
material.
From April in 2013, he is a Director of the Division Genomics Technologies and a Deputy
Director of Center for Life Science Technologies, RIKEN.
He has published more than 230 papers and book chapters, edited books and is a member
of editorial boards of various scientific journals.
伊藤
昌可
独立行政法人理化学研究所
予防医療・診断技術開発プログラム
コーディネーター
Cap analysis of gene expression on single molecule sequencer, HeliScope
genetic analysis system
ヘリスコープ一分子シーケンサーによる CAGE 解析法
要旨：
Cap Analysis of Gene Expression (CAGE) is the method to investigate transcription start
sites comprehensively, based on cap-trapper technology. The original protocol involved
various problematic steps and difficult to be used widely in research field. We have been
working on the simplification of the protocol, and optimization for single molecule
sequencer, HeliScope, because the single molecule sequencing technology can eliminate
any biases caused by amplification, ligation or another enzymatic processes. The
established CAGE protocol for single molecule sequencer, HeliScope CAGE was applied
on automatization, then finally we succeeded to achieve high-throughput CAGE library
production system.
略歴：
Masayoshi Itoh is coordinator of the Preventive Medicine & Diagnosis Innovation
Program. He obtained his Ph.D. from Gifu University in 1995. In 1996, he joined RIKEN
as a postdoctoral fellow in Genome Science Laboratory. From 1998 to 2000, he was
employed as a RIKEN special postdoctoral fellow, then signed as a stuff scientist of
Genome Science Laboratory in 2001. He has been working on the technology development
for large scale sequencing. The achievements were the large scale plasmid preparation
system for full-length cDNA project, and CAGE technology standardization and
automatization for single molecule sequencer, HeliScope, for Mouse Encyclopedia and
following FANTOM projects. Now, he has intended to apply CAGE technology on various
medical uses.
川路
英哉
独立行政法人理化学研究所
予防医療・診断技術開発プログラム
コーディネーター
A promoter level mammalian expression atlas and its web resource
哺乳類におけるプロモーター単位でのゲノムワイドな発現地図と、
これを収録したデータベースシステム
要旨：
哺乳類の発生経路や生体を構成する数百万の細胞種の空間的構成は、写の制御によってコントロ
ールされる。1 分子 CAGE 法を用いて、
Regulated transcription controls the diversity, developmental pathways and spatial
organization of the hundreds of cell types that make up a mammal. Using single-molecule
cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human
and mouse primary cells, cell lines and tissues to produce a comprehensive overview of
mammalian gene expression across the human body. We find that few genes are truly
‘housekeeping’, whereas many mammalian promoters are composite entities composed of
several closely separated TSSs, with independent cell-type-specific expression profiles.
TSSs specific to different cell types evolve at different rates, whereas promoters of
broadly expressed genes are the most conserved. Promoter-based expression analysis
reveals key transcription factors defining cell states and links them to binding-site motifs.
The functions of identified novel transcripts can be predicted by coexpression and sample
ontology enrichment analyses. The functional annotation of the mammalian genome 5
(FANTOM5) project provides comprehensive expression profiles and functional
annotation of mammalian cell-type-specific transcriptomes with wide applications in
biomedical research.
To facilitate the exploration of the large-scale data, we assembled it into a centralized
data resource with an open-access on-line interface. Descriptions of individual samples
are carefully curated manually and an application ontology that uses classes from
established ontologies for cell types, anatomy, and diseases is developed to group related
samples systematically based on sample types. Web-based databases, and visualization
tools (SSTAR, ZENBU, BioLayout Express3D, TET, BioMart) are provided to allow
research scientists to search, navigate, and extract data related to samples, genes,
promoter activity, and transcription factor gene regulation across the entire FANTOM5
atlas. We also exposed the data via trackHub of the UCSC Genome Browser, plugin of
BioGPS, and as nanopublication in the LinkedData community for further integration
with other datasets. This combination of software tools, curated databases and
systematic sample annotation gives the scientific community powerful tools to explore,
examine and extract data in multiple ways. Here we introduce the online resources, their
underlying data structure and discuss potential impacts in cell, genome and molecular
biology.
略歴：
理化学研究所予防医療診断技術開発プログラムコーディネーター。情報基盤センター予防
医療・ゲノミクス応用開発ユニットユニットリーダーを兼務する。
2003 年大阪大学にて博士号を取得。2007 年、理化学研究所入所。一連の計算科学的手法お
よびリソース（データベース）の開発、大規模な生物学的データ解析（とくに転写開始、そ
の制御、small RNA、エピジェネティクス）に携わる。研究分野は、計算生物学および分子
生物学を基礎とするゲノミックスから、医療に資するトランスレーショナルリサーチにまで
及ぶ。
Hideya Kawaji is a coordinator of RIKEN Preventive Medicine and Diagnosis Innovation
Program, and the leader of preventive medicine and applied genomics unit in RIKEN
Advanced Center for Computing and Communication. He obtained his Ph.D. from Osaka
University in 2003. After joining RIKEN in 2007, he developed a series of computational
methods and resource (databases), and performed data analysis to interpret a large set of
biological data, in particular about transcriptome including transcription initiation, its
regulation, small RNAs and epigenetics. His research interests ranges from genomics
based on computational and molecular biology to translational research contributing
medical care.
Albin Sandelin
コペンハーゲン大学
生物・バイオロジー研究開発センター
コンピューター・RNA 生物学部門教授
The FANTOM5 enhancer atlas
ヒト細胞および組織におけるエンハンサー活性地図
要旨：
Enhancers control the correct temporal and cell-type-specific activation of gene
expression in multicellular eukaryotes. Knowing their properties, regulatory activity and
targets is crucial to understand the regulation of differentiation and homeostasis. Recent
findings indicate that enhancers emit RNAs once they are active. Exploiting this fact, we
have used the FANTOM5 panel of samples, covering the majority of human tissues and
cell types, to produce an atlas of active, in vivo-transcribed enhancers.
We show that enhancers share properties with CpG-poor messenger RNA promoters but
produce bidirectional, exosome-sensitive, unspliced RNAs, the generation of which is
strongly related to enhancer activity. The atlas was used to compare regulatory programs
between different cells at unprecedented depth, to identify disease-associated regulatory
single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous
enhancers. The online FANTOM5 enhancer atlas represents a unique resource for studies
on cell-type-specific enhancers and gene regulation.
I this talk, I will give a brief overview of the FANTOM5 enhancer atlas, but also show our
current work in enhancer detection in medical samples and intuitive computational tools
for tissue-specific enhancer selection.
略歴：
Albin Sandelin is a Professor at the Department of Biology and BRIC, Copenhagen
University. He obtained his MSc in Molecular Biology in 2000 from Stockholm University
and his PhD from Karolinska Institute in 2004. His most noted work from that period
was the JASPAR DNA motif database, now a standard tool in bioinformatics. During his
postdoctoral period at RIKEN, he was one of the key analysts of 5’ end data from the
FANTOM project. As a principal investigator at Copenhagen University, he has used the
same technique in combination with computational methods to investigate the biology of
gene regulation, and is now extending this into inflammatory disease. A recent highlight
was an atlas of enhancer regions and their usage over the human body.
Erik Arner
独立行政法人理化学研究所
ライフサイエンス技術基盤研究センター
機能性ゲノム解析部門ＬＳＡ要素技術研究グループ
ゲノム情報解析チーム副チームリーダー
Dynamics of enhancer and promoter activity during mammalian cellular
activation and differentiation
哺乳類細胞の活性化および分化の過程におけるエンハンサー／プロモーター活性の
ダイナミクス
要旨：
Cellular differentiation requires the coordinated induction of genes needed in the new
cellular state, and down-regulation of those no longer required in the previous one. The
dynamic regulation of promoters and enhancers by transcription factors facilitates this
state change. Here, using Cap Analysis of Gene Expression (CAGE) we measured
enhancer and promoter activity for 20 human and 14 mouse time courses covering a wide
range of cell types and biological stimuli. The data further expand the functional
identification of enhancers and promoters in the mammalian genome and extend our
knowledge of their dynamic regulation and likely function. We demonstrate that
enhancer RNAs dominate the earliest expression responses in every time course studied,
followed by mRNAs encoding transcription factors and then by other transcripts in
successive waves. Early activated genes and enhancers are typically time-course specific.
The induction of enhancer RNA expression precedes or occurs concurrently with changes
in expression of candidate target genes in their vicinity. In any one system, the binding
sites for the same key transcription factors are over-represented in both active enhancers
and promoters. These results support a model in which enhancers, like known immediate
early promoters, exist in a poised state and are the key targets of early signal
transduction in any cellular transition.
略歴：
Erik Arner is a Senior Research Scientist at RIKEN, Japan. He is an expert in
bioinformatics. After finishing a Master’s degree in engineering biotechnology at Uppsala
University he obtained his Ph.D. from Karolinska Institutet in 2006, and joined RIKEN
in 2007. His research interest is in applying genome wide technologies to basic questions
in biology, aswell as to disease questions with clinical focus.

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