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An integrated expression atlas of miRNAs and their promoters in human and mouse. / de Rie, Derek; Abugessaisa, Imad; Alam, Tanvir; Arner, Erik; Arner, Peter; Ashoor, Haitham; Åström, Gaby; Babina, Magda; Bertin, Nicolas; Burroughs, A. Maxwell; Carlisle, Ailsa J.; Daub, Carsten O.; Detmar, Michael; Deviatiiarov, Ruslan; Fort, Alexandre; Gebhard, Claudia; Goldowitz, Daniel; Guhl, Sven; Ha, Thomas J.; Harshbarger, Jayson; Hasegawa, Akira; Hashimoto, Kosuke; Herlyn, Meenhard; Heutink, Peter; Hitchens, Kelly J.; Hon, Chung Chau; Huang, Edward; Ishizu, Yuri; Kai, Chieko; Kasukawa, Takeya; Klinken, Peter; Lassmann, Timo; Lecellier, Charles-Henri; Lee, Weonju; Lizio, Marina; Makeev, Vsevolod; Mathelier, Anthony; Medvedeva, Yulia A.; Mejhert, Niklas; Mungall, Christopher J.; Noma, Shohei; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Persson, Helena; Rizzu, Patrizia; Roudnicky, Filip; Sætrom, Pål; Sato, Hiroki; Vitting-Seerup, Kristoffer; Sandelin, Albin Gustav; FANTOM Consortium.
In:
Nature Biotechnology, Vol. 35, No. 9, 21.08.2017, p. 872-878.
Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
de Rie, D, Abugessaisa, I, Alam, T, Arner, E, Arner, P, Ashoor, H, Åström, G, Babina, M, Bertin, N, Burroughs, AM, Carlisle, AJ, Daub, CO, Detmar, M, Deviatiiarov, R, Fort, A, Gebhard, C, Goldowitz, D, Guhl, S, Ha, TJ, Harshbarger, J, Hasegawa, A, Hashimoto, K, Herlyn, M, Heutink, P, Hitchens, KJ, Hon, CC, Huang, E, Ishizu, Y, Kai, C, Kasukawa, T, Klinken, P, Lassmann, T, Lecellier, C-H, Lee, W, Lizio, M, Makeev, V, Mathelier, A, Medvedeva, YA, Mejhert, N, Mungall, CJ, Noma, S, Ohshima, M, Okada-Hatakeyama, M, Persson, H, Rizzu, P, Roudnicky, F, Sætrom, P, Sato, H, Vitting-Seerup, K
, Sandelin, AG & FANTOM Consortium 2017, '
An integrated expression atlas of miRNAs and their promoters in human and mouse',
Nature Biotechnology, vol. 35, no. 9, pp. 872-878.
https://doi.org/10.1038/nbt.3947APA
de Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner, P., Ashoor, H., Åström, G., Babina, M., Bertin, N., Burroughs, A. M., Carlisle, A. J., Daub, C. O., Detmar, M., Deviatiiarov, R., Fort, A., Gebhard, C., Goldowitz, D., Guhl, S., Ha, T. J., ... FANTOM Consortium (2017).
An integrated expression atlas of miRNAs and their promoters in human and mouse.
Nature Biotechnology,
35(9), 872-878.
https://doi.org/10.1038/nbt.3947Vancouver
de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H et al.
An integrated expression atlas of miRNAs and their promoters in human and mouse.
Nature Biotechnology. 2017 Aug 21;35(9):872-878.
https://doi.org/10.1038/nbt.3947Author
de Rie, Derek ; Abugessaisa, Imad ; Alam, Tanvir ; Arner, Erik ; Arner, Peter ; Ashoor, Haitham ; Åström, Gaby ; Babina, Magda ; Bertin, Nicolas ; Burroughs, A. Maxwell ; Carlisle, Ailsa J. ; Daub, Carsten O. ; Detmar, Michael ; Deviatiiarov, Ruslan ; Fort, Alexandre ; Gebhard, Claudia ; Goldowitz, Daniel ; Guhl, Sven ; Ha, Thomas J. ; Harshbarger, Jayson ; Hasegawa, Akira ; Hashimoto, Kosuke ; Herlyn, Meenhard ; Heutink, Peter ; Hitchens, Kelly J. ; Hon, Chung Chau ; Huang, Edward ; Ishizu, Yuri ; Kai, Chieko ; Kasukawa, Takeya ; Klinken, Peter ; Lassmann, Timo ; Lecellier, Charles-Henri ; Lee, Weonju ; Lizio, Marina ; Makeev, Vsevolod ; Mathelier, Anthony ; Medvedeva, Yulia A. ; Mejhert, Niklas ; Mungall, Christopher J. ; Noma, Shohei ; Ohshima, Mitsuhiro ; Okada-Hatakeyama, Mariko ; Persson, Helena ; Rizzu, Patrizia ; Roudnicky, Filip ; Sætrom, Pål ; Sato, Hiroki ; Vitting-Seerup, Kristoffer ; Sandelin, Albin Gustav ; FANTOM Consortium. / An integrated expression atlas of miRNAs and their promoters in human and mouse. In: Nature Biotechnology. 2017 ; Vol. 35, No. 9. pp. 872-878.
Bibtex
@article{6e620c08698c47979965ebf901db3117,
title = "An integrated expression atlas of miRNAs and their promoters in human and mouse",
abstract = "MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.",
keywords = "Journal Article",
author = "{de Rie}, Derek and Imad Abugessaisa and Tanvir Alam and Erik Arner and Peter Arner and Haitham Ashoor and Gaby {\AA}str{\"o}m and Magda Babina and Nicolas Bertin and Burroughs, {A. Maxwell} and Carlisle, {Ailsa J.} and Daub, {Carsten O.} and Michael Detmar and Ruslan Deviatiiarov and Alexandre Fort and Claudia Gebhard and Daniel Goldowitz and Sven Guhl and Ha, {Thomas J.} and Jayson Harshbarger and Akira Hasegawa and Kosuke Hashimoto and Meenhard Herlyn and Peter Heutink and Hitchens, {Kelly J.} and Hon, {Chung Chau} and Edward Huang and Yuri Ishizu and Chieko Kai and Takeya Kasukawa and Peter Klinken and Timo Lassmann and Charles-Henri Lecellier and Weonju Lee and Marina Lizio and Vsevolod Makeev and Anthony Mathelier and Medvedeva, {Yulia A.} and Niklas Mejhert and Mungall, {Christopher J.} and Shohei Noma and Mitsuhiro Ohshima and Mariko Okada-Hatakeyama and Helena Persson and Patrizia Rizzu and Filip Roudnicky and P{\aa}l S{\ae}trom and Hiroki Sato and Kristoffer Vitting-Seerup and Sandelin, {Albin Gustav} and {FANTOM Consortium}",
year = "2017",
month = aug,
day = "21",
doi = "10.1038/nbt.3947",
language = "English",
volume = "35",
pages = "872--878",
journal = "Nature Biotechnology",
issn = "1087-0156",
publisher = "nature publishing group",
number = "9",
}
RIS
TY - JOUR
T1 - An integrated expression atlas of miRNAs and their promoters in human and mouse
AU - de Rie, Derek
AU - Abugessaisa, Imad
AU - Alam, Tanvir
AU - Arner, Erik
AU - Arner, Peter
AU - Ashoor, Haitham
AU - Åström, Gaby
AU - Babina, Magda
AU - Bertin, Nicolas
AU - Burroughs, A. Maxwell
AU - Carlisle, Ailsa J.
AU - Daub, Carsten O.
AU - Detmar, Michael
AU - Deviatiiarov, Ruslan
AU - Fort, Alexandre
AU - Gebhard, Claudia
AU - Goldowitz, Daniel
AU - Guhl, Sven
AU - Ha, Thomas J.
AU - Harshbarger, Jayson
AU - Hasegawa, Akira
AU - Hashimoto, Kosuke
AU - Herlyn, Meenhard
AU - Heutink, Peter
AU - Hitchens, Kelly J.
AU - Hon, Chung Chau
AU - Huang, Edward
AU - Ishizu, Yuri
AU - Kai, Chieko
AU - Kasukawa, Takeya
AU - Klinken, Peter
AU - Lassmann, Timo
AU - Lecellier, Charles-Henri
AU - Lee, Weonju
AU - Lizio, Marina
AU - Makeev, Vsevolod
AU - Mathelier, Anthony
AU - Medvedeva, Yulia A.
AU - Mejhert, Niklas
AU - Mungall, Christopher J.
AU - Noma, Shohei
AU - Ohshima, Mitsuhiro
AU - Okada-Hatakeyama, Mariko
AU - Persson, Helena
AU - Rizzu, Patrizia
AU - Roudnicky, Filip
AU - Sætrom, Pål
AU - Sato, Hiroki
AU - Vitting-Seerup, Kristoffer
AU - Sandelin, Albin Gustav
AU - FANTOM Consortium
PY - 2017/8/21
Y1 - 2017/8/21
N2 - MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.
AB - MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.
KW - Journal Article
U2 - 10.1038/nbt.3947
DO - 10.1038/nbt.3947
M3 - Journal article
C2 - 28829439
VL - 35
SP - 872
EP - 878
JO - Nature Biotechnology
JF - Nature Biotechnology
SN - 1087-0156
IS - 9
ER -
