title: The transcriptional landscape of the mammalian genome.
abstract: This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
authors.forename: P
authors.initials: P
authors.lastname: Carninci
authors.forename: T
authors.initials: T
authors.lastname: Kasukawa
authors.forename: S
authors.initials: S
authors.lastname: Katayama
authors.forename: J
authors.initials: J
authors.lastname: Gough
authors.forename: M C
authors.initials: MC
authors.lastname: Frith
authors.forename: N
authors.initials: N
authors.lastname: Maeda
authors.forename: R
authors.initials: R
authors.lastname: Oyama
authors.forename: T
authors.initials: T
authors.lastname: Ravasi
authors.forename: B
authors.initials: B
authors.lastname: Lenhard
authors.forename: C
authors.initials: C
authors.lastname: Wells
authors.forename: R
authors.initials: R
authors.lastname: Kodzius
authors.forename: K
authors.initials: K
authors.lastname: Shimokawa
authors.forename: V B
authors.initials: VB
authors.lastname: Bajic
authors.forename: S E
authors.initials: SE
authors.lastname: Brenner
authors.forename: S
authors.initials: S
authors.lastname: Batalov
authors.forename: A R R
authors.initials: AR
authors.lastname: Forrest
authors.forename: M
authors.initials: M
authors.lastname: Zavolan
authors.forename: M J
authors.initials: MJ
authors.lastname: Davis
authors.forename: L G
authors.initials: LG
authors.lastname: Wilming
authors.forename: V
authors.initials: V
authors.lastname: Aidinis
authors.forename: J E
authors.initials: JE
authors.lastname: Allen
authors.forename: A
authors.initials: A
authors.lastname: Ambesi-Impiombato
authors.forename: R
authors.initials: R
authors.lastname: Apweiler
authors.forename: R N
authors.initials: RN
authors.lastname: Aturaliya
authors.forename: T L
authors.initials: TL
authors.lastname: Bailey
authors.forename: M
authors.initials: M
authors.lastname: Bansal
authors.forename: L
authors.initials: L
authors.lastname: Baxter
authors.forename: K W
authors.initials: KW
authors.lastname: Beisel
authors.forename: T
authors.initials: T
authors.lastname: Bersano
authors.forename: H
authors.initials: H
authors.lastname: Bono
authors.forename: A M
authors.initials: AM
authors.lastname: Chalk
authors.forename: K P
authors.initials: KP
authors.lastname: Chiu
authors.forename: V
authors.initials: V
authors.lastname: Choudhary
authors.forename: A
authors.initials: A
authors.lastname: Christoffels
authors.forename: D R
authors.initials: DR
authors.lastname: Clutterbuck
authors.forename: M L
authors.initials: ML
authors.lastname: Crowe
authors.forename: E
authors.initials: E
authors.lastname: Dalla
authors.forename: B P
authors.initials: BP
authors.lastname: Dalrymple
authors.forename: B
authors.initials: B
authors.lastname: de Bono
authors.forename: G
authors.initials: G
authors.lastname: Della Gatta
authors.forename: D
authors.initials: D
authors.lastname: di Bernardo
authors.forename: T
authors.initials: T
authors.lastname: Down
authors.forename: P
authors.initials: P
authors.lastname: Engstrom
authors.forename: M
authors.initials: M
authors.lastname: Fagiolini
authors.forename: G
authors.initials: G
authors.lastname: Faulkner
authors.forename: C F
authors.initials: CF
authors.lastname: Fletcher
authors.forename: T
authors.initials: T
authors.lastname: Fukushima
authors.forename: M
authors.initials: M
authors.lastname: Furuno
authors.forename: S
authors.initials: S
authors.lastname: Futaki
authors.forename: M
authors.initials: M
authors.lastname: Gariboldi
authors.forename: P
authors.initials: P
authors.lastname: Georgii-Hemming
authors.forename: T R
authors.initials: TR
authors.lastname: Gingeras
authors.forename: T
authors.initials: T
authors.lastname: Gojobori
authors.forename: R E
authors.initials: RE
authors.lastname: Green
authors.forename: S
authors.initials: S
authors.lastname: Gustincich
authors.forename: M
authors.initials: M
authors.lastname: Harbers
authors.forename: Y
authors.initials: Y
authors.lastname: Hayashi
authors.forename: T K
authors.initials: TK
authors.lastname: Hensch
authors.forename: N
authors.initials: N
authors.lastname: Hirokawa
authors.forename: D
authors.initials: D
authors.lastname: Hill
authors.forename: L
authors.initials: L
authors.lastname: Huminiecki
authors.forename: M
authors.initials: M
authors.lastname: Iacono
authors.forename: K
authors.initials: K
authors.lastname: Ikeo
authors.forename: A
authors.initials: A
authors.lastname: Iwama
authors.forename: T
authors.initials: T
authors.lastname: Ishikawa
authors.forename: M
authors.initials: M
authors.lastname: Jakt
authors.forename: A
authors.initials: A
authors.lastname: Kanapin
authors.forename: M
authors.initials: M
authors.lastname: Katoh
authors.forename: Y
authors.initials: Y
authors.lastname: Kawasawa
authors.forename: J
authors.initials: J
authors.lastname: Kelso
authors.forename: H
authors.initials: H
authors.lastname: Kitamura
authors.forename: H
authors.initials: H
authors.lastname: Kitano
authors.forename: G
authors.initials: G
authors.lastname: Kollias
authors.forename: S P T
authors.initials: SP
authors.lastname: Krishnan
authors.forename: A
authors.initials: A
authors.lastname: Kruger
authors.forename: S K
authors.initials: SK
authors.lastname: Kummerfeld
authors.forename: I V
authors.initials: IV
authors.lastname: Kurochkin
authors.forename: L F
authors.initials: LF
authors.lastname: Lareau
authors.forename: D
authors.initials: D
authors.lastname: Lazarevic
authors.forename: L
authors.initials: L
authors.lastname: Lipovich
authors.forename: J
authors.initials: J
authors.lastname: Liu
authors.forename: S
authors.initials: S
authors.lastname: Liuni
authors.forename: S
authors.initials: S
authors.lastname: McWilliam
authors.forename: M
authors.initials: M
authors.lastname: Madan Babu
authors.forename: M
authors.initials: M
authors.lastname: Madera
authors.forename: L
authors.initials: L
authors.lastname: Marchionni
authors.forename: H
authors.initials: H
authors.lastname: Matsuda
authors.forename: S
authors.initials: S
authors.lastname: Matsuzawa
authors.forename: H
authors.initials: H
authors.lastname: Miki
authors.forename: F
authors.initials: F
authors.lastname: Mignone
authors.forename: S
authors.initials: S
authors.lastname: Miyake
authors.forename: K
authors.initials: K
authors.lastname: Morris
authors.forename: S
authors.initials: S
authors.lastname: Mottagui-Tabar
authors.forename: N
authors.initials: N
authors.lastname: Mulder
authors.forename: N
authors.initials: N
authors.lastname: Nakano
authors.forename: H
authors.initials: H
authors.lastname: Nakauchi
authors.forename: P
authors.initials: P
authors.lastname: Ng
authors.forename: R
authors.initials: R
authors.lastname: Nilsson
authors.forename: S
authors.initials: S
authors.lastname: Nishiguchi
authors.forename: S
authors.initials: S
authors.lastname: Nishikawa
authors.forename: F
authors.initials: F
authors.lastname: Nori
authors.forename: O
authors.initials: O
authors.lastname: Ohara
authors.forename: Y
authors.initials: Y
authors.lastname: Okazaki
authors.forename: V
authors.initials: V
authors.lastname: Orlando
authors.forename: K C
authors.initials: KC
authors.lastname: Pang
authors.forename: W J
authors.initials: WJ
authors.lastname: Pavan
authors.forename: G
authors.initials: G
authors.lastname: Pavesi
authors.forename: G
authors.initials: G
authors.lastname: Pesole
authors.forename: N
authors.initials: N
authors.lastname: Petrovsky
authors.forename: S
authors.initials: S
authors.lastname: Piazza
authors.forename: J
authors.initials: J
authors.lastname: Reed
authors.forename: J F
authors.initials: JF
authors.lastname: Reid
authors.forename: B Z
authors.initials: BZ
authors.lastname: Ring
authors.forename: M
authors.initials: M
authors.lastname: Ringwald
authors.forename: B
authors.initials: B
authors.lastname: Rost
authors.forename: Y
authors.initials: Y
authors.lastname: Ruan
authors.forename: S L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: A
authors.initials: A
authors.lastname: Sandelin
authors.forename: C
authors.initials: C
authors.lastname: Schneider
authors.forename: C
authors.initials: C
authors.lastname: Schönbach
authors.forename: K
authors.initials: K
authors.lastname: Sekiguchi
authors.forename: C A M
authors.initials: CA
authors.lastname: Semple
authors.forename: S
authors.initials: S
authors.lastname: Seno
authors.forename: L
authors.initials: L
authors.lastname: Sessa
authors.forename: Y
authors.initials: Y
authors.lastname: Sheng
authors.forename: Y
authors.initials: Y
authors.lastname: Shibata
authors.forename: H
authors.initials: H
authors.lastname: Shimada
authors.forename: K
authors.initials: K
authors.lastname: Shimada
authors.forename: D
authors.initials: D
authors.lastname: Silva
authors.forename: B
authors.initials: B
authors.lastname: Sinclair
authors.forename: S
authors.initials: S
authors.lastname: Sperling
authors.forename: E
authors.initials: E
authors.lastname: Stupka
authors.forename: K
authors.initials: K
authors.lastname: Sugiura
authors.forename: R
authors.initials: R
authors.lastname: Sultana
authors.forename: Y
authors.initials: Y
authors.lastname: Takenaka
authors.forename: K
authors.initials: K
authors.lastname: Taki
authors.forename: K
authors.initials: K
authors.lastname: Tammoja
authors.forename: S L
authors.initials: SL
authors.lastname: Tan
authors.forename: S
authors.initials: S
authors.lastname: Tang
authors.forename: M S
authors.initials: MS
authors.lastname: Taylor
authors.forename: J
authors.initials: J
authors.lastname: Tegner
authors.forename: S A
authors.initials: SA
authors.lastname: Teichmann
authors.forename: H R
authors.initials: HR
authors.lastname: Ueda
authors.forename: E
authors.initials: E
authors.lastname: van Nimwegen
authors.forename: R
authors.initials: R
authors.lastname: Verardo
authors.forename: C L
authors.initials: CL
authors.lastname: Wei
authors.forename: K
authors.initials: K
authors.lastname: Yagi
authors.forename: H
authors.initials: H
authors.lastname: Yamanishi
authors.forename: E
authors.initials: E
authors.lastname: Zabarovsky
authors.forename: S
authors.initials: S
authors.lastname: Zhu
authors.forename: A
authors.initials: A
authors.lastname: Zimmer
authors.forename: W
authors.initials: W
authors.lastname: Hide
authors.forename: C
authors.initials: C
authors.lastname: Bult
authors.forename: S M
authors.initials: SM
authors.lastname: Grimmond
authors.forename: R D
authors.initials: RD
authors.lastname: Teasdale
authors.forename: E T
authors.initials: ET
authors.lastname: Liu
authors.forename: V
authors.initials: V
authors.lastname: Brusic
authors.forename: J
authors.initials: J
authors.lastname: Quackenbush
authors.forename: C
authors.initials: C
authors.lastname: Wahlestedt
authors.forename: J S
authors.initials: JS
authors.lastname: Mattick
authors.forename: D A
authors.initials: DA
authors.lastname: Hume
authors.forename: C
authors.initials: C
authors.lastname: Kai
authors.forename: D
authors.initials: D
authors.lastname: Sasaki
authors.forename: Y
authors.initials: Y
authors.lastname: Tomaru
authors.forename: S
authors.initials: S
authors.lastname: Fukuda
authors.forename: M
authors.initials: M
authors.lastname: Kanamori-Katayama
authors.forename: M
authors.initials: M
authors.lastname: Suzuki
authors.forename: J
authors.initials: J
authors.lastname: Aoki
authors.forename: T
authors.initials: T
authors.lastname: Arakawa
authors.forename: J
authors.initials: J
authors.lastname: Iida
authors.forename: K
authors.initials: K
authors.lastname: Imamura
authors.forename: M
authors.initials: M
authors.lastname: Itoh
authors.forename: T
authors.initials: T
authors.lastname: Kato
authors.forename: H
authors.initials: H
authors.lastname: Kawaji
authors.forename: N
authors.initials: N
authors.lastname: Kawagashira
authors.forename: T
authors.initials: T
authors.lastname: Kawashima
authors.forename: M
authors.initials: M
authors.lastname: Kojima
authors.forename: S
authors.initials: S
authors.lastname: Kondo
authors.forename: H
authors.initials: H
authors.lastname: Konno
authors.forename: K
authors.initials: K
authors.lastname: Nakano
authors.forename: N
authors.initials: N
authors.lastname: Ninomiya
authors.forename: T
authors.initials: T
authors.lastname: Nishio
authors.forename: M
authors.initials: M
authors.lastname: Okada
authors.forename: C
authors.initials: C
authors.lastname: Plessy
authors.forename: K
authors.initials: K
authors.lastname: Shibata
authors.forename: T
authors.initials: T
authors.lastname: Shiraki
authors.forename: S
authors.initials: S
authors.lastname: Suzuki
authors.forename: M
authors.initials: M
authors.lastname: Tagami
authors.forename: K
authors.initials: K
authors.lastname: Waki
authors.forename: A
authors.initials: A
authors.lastname: Watahiki
authors.forename: Y
authors.initials: Y
authors.lastname: Okamura-Oho
authors.forename: H
authors.initials: H
authors.lastname: Suzuki
authors.forename: J
authors.initials: J
authors.lastname: Kawai
authors.forename: Y
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D018076:DNA, Complementary / Q000737:chemistry; D016678:Genome; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D051379:Mice / Q000235:genetics*; D011401:Promoter Regions, Genetic; D011506:Proteins / Q000235:genetics; D012313:RNA / Q000737:chemistry / Q000145:classification; D012326:RNA Splicing; D022661:RNA, Untranslated / Q000737:chemistry; D038621:Regulatory Sequences, Ribonucleic Acid; D013728:Terminator Regions, Genetic; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D020413:3' Untranslated Regions; D018076:DNA, Complementary; D011506:Proteins; D022661:RNA, Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid; D012313:RNA