title: Landscape of transcription in human cells.
abstract: Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.
authors.affiliation: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.
authors.forename: Sarah
authors.initials: S
authors.lastname: Djebali
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Davis
authors.forename: Angelika
authors.initials: A
authors.lastname: Merkel
authors.forename: Alex
authors.initials: A
authors.lastname: Dobin
authors.forename: Timo
authors.initials: T
authors.lastname: Lassmann
authors.forename: Ali
authors.initials: A
authors.lastname: Mortazavi
authors.forename: Andrea
authors.initials: A
authors.lastname: Tanzer
authors.forename: Julien
authors.initials: J
authors.lastname: Lagarde
authors.forename: Wei
authors.initials: W
authors.lastname: Lin
authors.forename: Felix
authors.initials: F
authors.lastname: Schlesinger
authors.forename: Chenghai
authors.initials: C
authors.lastname: Xue
authors.forename: Georgi K
authors.initials: GK
authors.lastname: Marinov
authors.forename: Jainab
authors.initials: J
authors.lastname: Khatun
authors.forename: Brian A
authors.initials: BA
authors.lastname: Williams
authors.forename: Chris
authors.initials: C
authors.lastname: Zaleski
authors.forename: Joel
authors.initials: J
authors.lastname: Rozowsky
authors.forename: Maik
authors.initials: M
authors.lastname: Röder
authors.forename: Felix
authors.initials: F
authors.lastname: Kokocinski
authors.forename: Rehab F
authors.initials: RF
authors.lastname: Abdelhamid
authors.forename: Tyler
authors.initials: T
authors.lastname: Alioto
authors.forename: Igor
authors.initials: I
authors.lastname: Antoshechkin
authors.forename: Michael T
authors.initials: MT
authors.lastname: Baer
authors.forename: Nadav S
authors.initials: NS
authors.lastname: Bar
authors.forename: Philippe
authors.initials: P
authors.lastname: Batut
authors.forename: Kimberly
authors.initials: K
authors.lastname: Bell
authors.forename: Ian
authors.initials: I
authors.lastname: Bell
authors.forename: Sudipto
authors.initials: S
authors.lastname: Chakrabortty
authors.forename: Xian
authors.initials: X
authors.lastname: Chen
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Chrast
authors.forename: Joao
authors.initials: J
authors.lastname: Curado
authors.forename: Thomas
authors.initials: T
authors.lastname: Derrien
authors.forename: Jorg
authors.initials: J
authors.lastname: Drenkow
authors.forename: Erica
authors.initials: E
authors.lastname: Dumais
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Dumais
authors.forename: Radha
authors.initials: R
authors.lastname: Duttagupta
authors.forename: Emilie
authors.initials: E
authors.lastname: Falconnet
authors.forename: Meagan
authors.initials: M
authors.lastname: Fastuca
authors.forename: Kata
authors.initials: K
authors.lastname: Fejes-Toth
authors.forename: Pedro
authors.initials: P
authors.lastname: Ferreira
authors.forename: Sylvain
authors.initials: S
authors.lastname: Foissac
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Fullwood
authors.forename: Hui
authors.initials: H
authors.lastname: Gao
authors.forename: David
authors.initials: D
authors.lastname: Gonzalez
authors.forename: Assaf
authors.initials: A
authors.lastname: Gordon
authors.forename: Harsha
authors.initials: H
authors.lastname: Gunawardena
authors.forename: Cedric
authors.initials: C
authors.lastname: Howald
authors.forename: Sonali
authors.initials: S
authors.lastname: Jha
authors.forename: Rory
authors.initials: R
authors.lastname: Johnson
authors.forename: Philipp
authors.initials: P
authors.lastname: Kapranov
authors.forename: Brandon
authors.initials: B
authors.lastname: King
authors.forename: Colin
authors.initials: C
authors.lastname: Kingswood
authors.forename: Oscar J
authors.initials: OJ
authors.lastname: Luo
authors.forename: Eddie
authors.initials: E
authors.lastname: Park
authors.forename: Kimberly
authors.initials: K
authors.lastname: Persaud
authors.forename: Jonathan B
authors.initials: JB
authors.lastname: Preall
authors.forename: Paolo
authors.initials: P
authors.lastname: Ribeca
authors.forename: Brian
authors.initials: B
authors.lastname: Risk
authors.forename: Daniel
authors.initials: D
authors.lastname: Robyr
authors.forename: Michael
authors.initials: M
authors.lastname: Sammeth
authors.forename: Lorian
authors.initials: L
authors.lastname: Schaffer
authors.forename: Lei-Hoon
authors.initials: LH
authors.lastname: See
authors.forename: Atif
authors.initials: A
authors.lastname: Shahab
authors.forename: Jorgen
authors.initials: J
authors.lastname: Skancke
authors.forename: Ana Maria
authors.initials: AM
authors.lastname: Suzuki
authors.forename: Hazuki
authors.initials: H
authors.lastname: Takahashi
authors.forename: Hagen
authors.initials: H
authors.lastname: Tilgner
authors.forename: Diane
authors.initials: D
authors.lastname: Trout
authors.forename: Nathalie
authors.initials: N
authors.lastname: Walters
authors.forename: Huaien
authors.initials: H
authors.lastname: Wang
authors.forename: John
authors.initials: J
authors.lastname: Wrobel
authors.forename: Yanbao
authors.initials: Y
authors.lastname: Yu
authors.forename: Xiaoan
authors.initials: X
authors.lastname: Ruan
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Jennifer
authors.initials: J
authors.lastname: Harrow
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
authors.forename: Tim
authors.initials: T
authors.lastname: Hubbard
authors.forename: Alexandre
authors.initials: A
authors.lastname: Reymond
authors.forename: Stylianos E
authors.initials: SE
authors.lastname: Antonarakis
authors.forename: Gregory
authors.initials: G
authors.lastname: Hannon
authors.forename: Morgan C
authors.initials: MC
authors.lastname: Giddings
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.forename: Barbara
authors.initials: B
authors.lastname: Wold
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
mesh_terms: D000483:Alleles; D002460:Cell Line; D004247:DNA / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics; D004690:Encyclopedias as Topic; D004742:Enhancer Elements, Genetic; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D005796:Genes / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics; D006801:Humans; D058977:Molecular Sequence Annotation; D026723:Polyadenylation / Q000235:genetics; D020033:Protein Isoforms / Q000235:genetics; D012313:RNA / Q000096:biosynthesis / Q000235:genetics; D017393:RNA Editing / Q000235:genetics; D012326:RNA Splicing / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic; D020033:Protein Isoforms; D012313:RNA; D004247:DNA