An integrated expression atlas of miRNAs and their promoters in human and mouse

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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; Severin, Jessica; Shin, Jay W.; Swoboda, Rolf K.; Tarui, Hiroshi; Toyoda, Hiroo; Vitting-Seerup, Kristoffer; Winteringham, Louise; Yamaguchi, Yoko; Yasuzawa, Kayoko; Yoneda, Misako; Yumoto, Noriko; Zabierowski, Susan; Zhang, Peter G.; Wells, Christine A.; Summers, Kim M.; Kawaji, Hideya; Sandelin, Albin; Rehli, Michael; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R.R.; De Hoon, Michiel J.L.

In: Nature Biotechnology, Vol. 35, No. 9, 01.09.2017, p. 872-878.

Research output: Contribution to journalArticle

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, CH, 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, Severin, J, Shin, JW, Swoboda, RK, Tarui, H, Toyoda, H, Vitting-Seerup, K, Winteringham, L, Yamaguchi, Y, Yasuzawa, K, Yoneda, M, Yumoto, N, Zabierowski, S, Zhang, PG, Wells, CA, Summers, KM, Kawaji, H, Sandelin, A, Rehli, M, Hayashizaki, Y, Carninci, P, Forrest, ARR & De Hoon, MJL 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.3947

APA

De Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner, P., Ashoor, H., ... De Hoon, M. J. L. (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.3947

CBE

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 CH, 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, Severin J, Shin JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K, Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M, Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers KM, Kawaji H, Sandelin A, Rehli M, Hayashizaki Y, Carninci P, Forrest ARR, De Hoon MJL. 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.3947

MLA

Vancouver

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 Sep 1;35(9):872-878. https://doi.org/10.1038/nbt.3947

Author

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 ; Severin, Jessica ; Shin, Jay W. ; Swoboda, Rolf K. ; Tarui, Hiroshi ; Toyoda, Hiroo ; Vitting-Seerup, Kristoffer ; Winteringham, Louise ; Yamaguchi, Yoko ; Yasuzawa, Kayoko ; Yoneda, Misako ; Yumoto, Noriko ; Zabierowski, Susan ; Zhang, Peter G. ; Wells, Christine A. ; Summers, Kim M. ; Kawaji, Hideya ; Sandelin, Albin ; Rehli, Michael ; Hayashizaki, Yoshihide ; Carninci, Piero ; Forrest, Alistair R.R. ; De Hoon, Michiel J.L. / An integrated expression atlas of miRNAs and their promoters in human and mouse. In: Nature Biotechnology. 2017 ; Vol. 35, No. 9. pp. 872-878.

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 - Severin, Jessica

AU - Shin, Jay W.

AU - Swoboda, Rolf K.

AU - Tarui, Hiroshi

AU - Toyoda, Hiroo

AU - Vitting-Seerup, Kristoffer

AU - Winteringham, Louise

AU - Yamaguchi, Yoko

AU - Yasuzawa, Kayoko

AU - Yoneda, Misako

AU - Yumoto, Noriko

AU - Zabierowski, Susan

AU - Zhang, Peter G.

AU - Wells, Christine A.

AU - Summers, Kim M.

AU - Kawaji, Hideya

AU - Sandelin, Albin

AU - Rehli, Michael

AU - Hayashizaki, Yoshihide

AU - Carninci, Piero

AU - Forrest, Alistair R.R.

AU - De Hoon, Michiel J.L.

PY - 2017/9/1

Y1 - 2017/9/1

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.

U2 - 10.1038/nbt.3947

DO - 10.1038/nbt.3947

M3 - Article

VL - 35

SP - 872

EP - 878

JO - Nature Biotechnology

T2 - Nature Biotechnology

JF - Nature Biotechnology

SN - 1546-1696

IS - 9

ER -