Landscape of transcription in human cells

Sarah Djebali; Carrie A. Davis; Angelika Merkel; Alex Dobin; Timo Lassmann; Ali Mortazavi; Andrea Tanzer; Julien Lagarde; Wei Lin; Felix Schlesinger; Chenghai Xue; Georgi K. Marinov; Jainab Khatun; Brian A. Williams; Chris Zaleski; Joel Rozowsky; Maik Röder; Felix Kokocinski; Rehab F. Abdelhamid; Tyler Alioto; Igor Antoshechkin; Michael T. Baer; Nadav S. Bar; Philippe Batut; Kimberly Bell; Ian Bell; Sudipto Chakrabortty; Xian Chen; Jacqueline Chrast; Joao Curado; Thomas Derrien; Jorg Drenkow; Erica Dumais; Jacqueline Dumais; Radha Duttagupta; Emilie Falconnet; Meagan Fastuca; Kata Fejes-Toth; Pedro Ferreira; Sylvain Foissac; Melissa J. Fullwood; Hui Gao; David Gonzalez; Assaf Gordon; Harsha Gunawardena; Cedric Howald; Sonali Jha; Rory Johnson; Philipp Kapranov; Brandon King; Colin Kingswood; Oscar J. Luo; Eddie Park; Kimberly Persaud; Jonathan B. Preall; Paolo Ribeca; Brian Risk; Daniel Robyr; Michael Sammeth; Lorian Schaffer; Lei Hoon See; Atif Shahab; Jorgen Skancke; Ana Maria Suzuki; Hazuki Takahashi; Hagen Tilgner; Diane Trout; Nathalie Walters; Huaien Wang; John Wrobel; Yanbao Yu; Xiaoan Ruan; Yoshihide Hayashizaki; Jennifer Harrow; Mark Gerstein; Tim Hubbard; Alexandre Reymond; Stylianos E. Antonarakis; Gregory Hannon; Morgan C. Giddings; Yijun Ruan; Barbara Wold; Piero Carninci; Roderic Guig; Thomas R. Gingeras

doi:10.1038/nature11233

Landscape of transcription in human cells

Sarah Djebali, Carrie A. Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger, Chenghai Xue, Georgi K. Marinov, Jainab Khatun, Brian A. Williams, Chris Zaleski, Joel Rozowsky, Maik Röder, Felix Kokocinski, Rehab F. Abdelhamid, Tyler AliotoIgor Antoshechkin, Michael T. Baer, Nadav S. Bar, Philippe Batut, Kimberly Bell, Ian Bell, Sudipto Chakrabortty, Xian Chen, Jacqueline Chrast, Joao Curado, Thomas Derrien, Jorg Drenkow, Erica Dumais, Jacqueline Dumais, Radha Duttagupta, Emilie Falconnet, Meagan Fastuca, Kata Fejes-Toth, Pedro Ferreira, Sylvain Foissac, Melissa J. Fullwood, Hui Gao, David Gonzalez, Assaf Gordon, Harsha Gunawardena, Cedric Howald, Sonali Jha, Rory Johnson, Philipp Kapranov, Brandon King, Colin Kingswood, Oscar J. Luo, Eddie Park, Kimberly Persaud, Jonathan B. Preall, Paolo Ribeca, Brian Risk, Daniel Robyr, Michael Sammeth, Lorian Schaffer, Lei Hoon See, Atif Shahab, Jorgen Skancke, Ana Maria Suzuki, Hazuki Takahashi, Hagen Tilgner, Diane Trout, Nathalie Walters, Huaien Wang, John Wrobel, Yanbao Yu, Xiaoan Ruan, Yoshihide Hayashizaki, Jennifer Harrow, Mark Gerstein, Tim Hubbard, Alexandre Reymond, Stylianos E. Antonarakis, Gregory Hannon, Morgan C. Giddings, Yijun Ruan, Barbara Wold, Piero Carninci, Roderic Guig, Thomas R. Gingeras

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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 cellĝ€™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.

Original language	English
Pages (from-to)	101-108
Number of pages	8
Journal	Nature
Volume	489
Issue number	7414
DOIs	https://doi.org/10.1038/nature11233
Publication status	Published - 6 Sept 2012
Externally published	Yes

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Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G. K., Khatun, J., Williams, B. A., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R. F., ... Gingeras, T. R. (2012). Landscape of transcription in human cells. Nature, 489(7414), 101-108. https://doi.org/10.1038/nature11233

@article{3cb1b6ef3d7543d9ac03b293bf7cece2,

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 cellĝ€{\texttrademark}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.",

author = "Sarah Djebali and Davis, {Carrie A.} and Angelika Merkel and Alex Dobin and Timo Lassmann and Ali Mortazavi and Andrea Tanzer and Julien Lagarde and Wei Lin and Felix Schlesinger and Chenghai Xue and Marinov, {Georgi K.} and Jainab Khatun and Williams, {Brian A.} and Chris Zaleski and Joel Rozowsky and Maik R{\"o}der and Felix Kokocinski and Abdelhamid, {Rehab F.} and Tyler Alioto and Igor Antoshechkin and Baer, {Michael T.} and Bar, {Nadav S.} and Philippe Batut and Kimberly Bell and Ian Bell and Sudipto Chakrabortty and Xian Chen and Jacqueline Chrast and Joao Curado and Thomas Derrien and Jorg Drenkow and Erica Dumais and Jacqueline Dumais and Radha Duttagupta and Emilie Falconnet and Meagan Fastuca and Kata Fejes-Toth and Pedro Ferreira and Sylvain Foissac and Fullwood, {Melissa J.} and Hui Gao and David Gonzalez and Assaf Gordon and Harsha Gunawardena and Cedric Howald and Sonali Jha and Rory Johnson and Philipp Kapranov and Brandon King and Colin Kingswood and Luo, {Oscar J.} and Eddie Park and Kimberly Persaud and Preall, {Jonathan B.} and Paolo Ribeca and Brian Risk and Daniel Robyr and Michael Sammeth and Lorian Schaffer and See, {Lei Hoon} and Atif Shahab and Jorgen Skancke and Suzuki, {Ana Maria} and Hazuki Takahashi and Hagen Tilgner and Diane Trout and Nathalie Walters and Huaien Wang and John Wrobel and Yanbao Yu and Xiaoan Ruan and Yoshihide Hayashizaki and Jennifer Harrow and Mark Gerstein and Tim Hubbard and Alexandre Reymond and Antonarakis, {Stylianos E.} and Gregory Hannon and Giddings, {Morgan C.} and Yijun Ruan and Barbara Wold and Piero Carninci and Roderic Guig and Gingeras, {Thomas R.}",

note = "Funding Information: Acknowledgements This work was supported by the National Human Genome Research Institute (NHGRI) production grants U54HG004557, U54HG004555, U54HG004576 and U54HG004558, and by the NHGRI pilot grant R01HG003700. It was also supported by the NHGRI ARRA stimulus grant 1RC2HG005591, the National Science Foundation (SNF) grant 127375, the European Research Council (ERC) grant 249968, a research grant for the RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology, and grants BIO2011-26205, CSD2007-00050 and INB GNV-1 from the Spanish Ministry of Science. We would also like to thank C. Gunter and W. Spitzer for editorial assistance with the manuscript.",

year = "2012",

month = sep,

day = "6",

doi = "10.1038/nature11233",

language = "English",

volume = "489",

pages = "101--108",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group - Macmillan Publishers",

number = "7414",

}

Djebali, S, Davis, CA, Merkel, A, Dobin, A, Lassmann, T, Mortazavi, A, Tanzer, A, Lagarde, J, Lin, W, Schlesinger, F, Xue, C, Marinov, GK, Khatun, J, Williams, BA, Zaleski, C, Rozowsky, J, Röder, M, Kokocinski, F, Abdelhamid, RF, Alioto, T, Antoshechkin, I, Baer, MT, Bar, NS, Batut, P, Bell, K, Bell, I, Chakrabortty, S, Chen, X, Chrast, J, Curado, J, Derrien, T, Drenkow, J, Dumais, E, Dumais, J, Duttagupta, R, Falconnet, E, Fastuca, M, Fejes-Toth, K, Ferreira, P, Foissac, S, Fullwood, MJ, Gao, H, Gonzalez, D, Gordon, A, Gunawardena, H, Howald, C, Jha, S, Johnson, R, Kapranov, P, King, B, Kingswood, C, Luo, OJ, Park, E, Persaud, K, Preall, JB, Ribeca, P, Risk, B, Robyr, D, Sammeth, M, Schaffer, L, See, LH, Shahab, A, Skancke, J, Suzuki, AM, Takahashi, H, Tilgner, H, Trout, D, Walters, N, Wang, H, Wrobel, J, Yu, Y, Ruan, X, Hayashizaki, Y, Harrow, J, Gerstein, M, Hubbard, T, Reymond, A, Antonarakis, SE, Hannon, G, Giddings, MC, Ruan, Y, Wold, B, Carninci, P, Guig, R & Gingeras, TR 2012, 'Landscape of transcription in human cells', Nature, vol. 489, no. 7414, pp. 101-108. https://doi.org/10.1038/nature11233

TY - JOUR

T1 - Landscape of transcription in human cells

AU - Djebali, Sarah

AU - Davis, Carrie A.

AU - Merkel, Angelika

AU - Dobin, Alex

AU - Lassmann, Timo

AU - Mortazavi, Ali

AU - Tanzer, Andrea

AU - Lagarde, Julien

AU - Lin, Wei

AU - Schlesinger, Felix

AU - Xue, Chenghai

AU - Marinov, Georgi K.

AU - Khatun, Jainab

AU - Williams, Brian A.

AU - Zaleski, Chris

AU - Rozowsky, Joel

AU - Röder, Maik

AU - Kokocinski, Felix

AU - Abdelhamid, Rehab F.

AU - Alioto, Tyler

AU - Antoshechkin, Igor

AU - Baer, Michael T.

AU - Bar, Nadav S.

AU - Batut, Philippe

AU - Bell, Kimberly

AU - Bell, Ian

AU - Chakrabortty, Sudipto

AU - Chen, Xian

AU - Chrast, Jacqueline

AU - Curado, Joao

AU - Derrien, Thomas

AU - Drenkow, Jorg

AU - Dumais, Erica

AU - Dumais, Jacqueline

AU - Duttagupta, Radha

AU - Falconnet, Emilie

AU - Fastuca, Meagan

AU - Fejes-Toth, Kata

AU - Ferreira, Pedro

AU - Foissac, Sylvain

AU - Fullwood, Melissa J.

AU - Gao, Hui

AU - Gonzalez, David

AU - Gordon, Assaf

AU - Gunawardena, Harsha

AU - Howald, Cedric

AU - Jha, Sonali

AU - Johnson, Rory

AU - Kapranov, Philipp

AU - King, Brandon

AU - Kingswood, Colin

AU - Luo, Oscar J.

AU - Park, Eddie

AU - Persaud, Kimberly

AU - Preall, Jonathan B.

AU - Ribeca, Paolo

AU - Risk, Brian

AU - Robyr, Daniel

AU - Sammeth, Michael

AU - Schaffer, Lorian

AU - See, Lei Hoon

AU - Shahab, Atif

AU - Skancke, Jorgen

AU - Suzuki, Ana Maria

AU - Takahashi, Hazuki

AU - Tilgner, Hagen

AU - Trout, Diane

AU - Walters, Nathalie

AU - Wang, Huaien

AU - Wrobel, John

AU - Yu, Yanbao

AU - Ruan, Xiaoan

AU - Hayashizaki, Yoshihide

AU - Harrow, Jennifer

AU - Gerstein, Mark

AU - Hubbard, Tim

AU - Reymond, Alexandre

AU - Antonarakis, Stylianos E.

AU - Hannon, Gregory

AU - Giddings, Morgan C.

AU - Ruan, Yijun

AU - Wold, Barbara

AU - Carninci, Piero

AU - Guig, Roderic

AU - Gingeras, Thomas R.

N1 - Funding Information: Acknowledgements This work was supported by the National Human Genome Research Institute (NHGRI) production grants U54HG004557, U54HG004555, U54HG004576 and U54HG004558, and by the NHGRI pilot grant R01HG003700. It was also supported by the NHGRI ARRA stimulus grant 1RC2HG005591, the National Science Foundation (SNF) grant 127375, the European Research Council (ERC) grant 249968, a research grant for the RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology, and grants BIO2011-26205, CSD2007-00050 and INB GNV-1 from the Spanish Ministry of Science. We would also like to thank C. Gunter and W. Spitzer for editorial assistance with the manuscript.

PY - 2012/9/6

Y1 - 2012/9/6

N2 - 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 cellĝ€™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.

AB - 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 cellĝ€™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.

UR - http://www.scopus.com/inward/record.url?scp=84865757142&partnerID=8YFLogxK

U2 - 10.1038/nature11233

DO - 10.1038/nature11233

M3 - Article

C2 - 22955620

AN - SCOPUS:84865757142

SN - 0028-0836

VL - 489

SP - 101

EP - 108

JO - Nature

JF - Nature

IS - 7414

ER -

Landscape of transcription in human cells

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