A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing

Pablo Landgraf, Mirabela Rusu, Robert Sheridan, Alain Sewer, Nicola Iovino, Alexei Aravin, Sébastien Pfeffer, Amanda Rice, Alice O. Kamphorst, Markus Landthaler, Carolina Lin, Nicholas D. Socci, Leandro Hermida, Valerio Fulci, Sabina Chiaretti, Robin Foà, Julia Schliwka, Uta Fuchs, Astrid Novosel, Roman Ulrich MüllerBernhard Schermer, Ute Bissels, Jason Inman, Quang Phan, Minchen Chien, David B. Weir, Ruchi Choksi, Gabriella De Vita, Daniela Frezzetti, Hans Ingo Trompeter, Veit Hornung, Grace Teng, Gunther Hartmann, M. Palkóvits, Roberto Di Lauro, Peter Wernet, Giuseppe Macino, Charles E. Rogler, James W. Nagle, Jingyue Ju, F. Nina Papavasiliou, Thomas Benzing, Peter Lichter, Wayne Tam, Michael J. Brownstein, Andreas Bosio, Arndt Borkhardt, James J. Russo, Chris Sander, Mihaela Zavolan, Thomas Tuschl

Research output: Contribution to journalArticle

2499 Citations (Scopus)

Abstract

MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequence-complementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units, and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses.

Original languageEnglish
Pages (from-to)1401-1414
Number of pages14
JournalCell
Volume129
Issue number7
DOIs
Publication statusPublished - Jun 29 2007

Fingerprint

RNA Sequence Analysis
Atlases
MicroRNAs
Libraries
RNA
Tissue
Small Untranslated RNA
RNA Stability
Cell Lineage
Rodentia
Conservation
Clone Cells
Genes
Genome
Messenger RNA

Keywords

  • MOLENEURO
  • MOLIMMUNO
  • RNA

ASJC Scopus subject areas

  • Cell Biology
  • Molecular Biology

Cite this

Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A., ... Tuschl, T. (2007). A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing. Cell, 129(7), 1401-1414. https://doi.org/10.1016/j.cell.2007.04.040

A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing. / Landgraf, Pablo; Rusu, Mirabela; Sheridan, Robert; Sewer, Alain; Iovino, Nicola; Aravin, Alexei; Pfeffer, Sébastien; Rice, Amanda; Kamphorst, Alice O.; Landthaler, Markus; Lin, Carolina; Socci, Nicholas D.; Hermida, Leandro; Fulci, Valerio; Chiaretti, Sabina; Foà, Robin; Schliwka, Julia; Fuchs, Uta; Novosel, Astrid; Müller, Roman Ulrich; Schermer, Bernhard; Bissels, Ute; Inman, Jason; Phan, Quang; Chien, Minchen; Weir, David B.; Choksi, Ruchi; De Vita, Gabriella; Frezzetti, Daniela; Trompeter, Hans Ingo; Hornung, Veit; Teng, Grace; Hartmann, Gunther; Palkóvits, M.; Di Lauro, Roberto; Wernet, Peter; Macino, Giuseppe; Rogler, Charles E.; Nagle, James W.; Ju, Jingyue; Papavasiliou, F. Nina; Benzing, Thomas; Lichter, Peter; Tam, Wayne; Brownstein, Michael J.; Bosio, Andreas; Borkhardt, Arndt; Russo, James J.; Sander, Chris; Zavolan, Mihaela; Tuschl, Thomas.

In: Cell, Vol. 129, No. 7, 29.06.2007, p. 1401-1414.

Research output: Contribution to journalArticle

Landgraf, P, Rusu, M, Sheridan, R, Sewer, A, Iovino, N, Aravin, A, Pfeffer, S, Rice, A, Kamphorst, AO, Landthaler, M, Lin, C, Socci, ND, Hermida, L, Fulci, V, Chiaretti, S, Foà, R, Schliwka, J, Fuchs, U, Novosel, A, Müller, RU, Schermer, B, Bissels, U, Inman, J, Phan, Q, Chien, M, Weir, DB, Choksi, R, De Vita, G, Frezzetti, D, Trompeter, HI, Hornung, V, Teng, G, Hartmann, G, Palkóvits, M, Di Lauro, R, Wernet, P, Macino, G, Rogler, CE, Nagle, JW, Ju, J, Papavasiliou, FN, Benzing, T, Lichter, P, Tam, W, Brownstein, MJ, Bosio, A, Borkhardt, A, Russo, JJ, Sander, C, Zavolan, M & Tuschl, T 2007, 'A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing', Cell, vol. 129, no. 7, pp. 1401-1414. https://doi.org/10.1016/j.cell.2007.04.040
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A et al. A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing. Cell. 2007 Jun 29;129(7):1401-1414. https://doi.org/10.1016/j.cell.2007.04.040
Landgraf, Pablo ; Rusu, Mirabela ; Sheridan, Robert ; Sewer, Alain ; Iovino, Nicola ; Aravin, Alexei ; Pfeffer, Sébastien ; Rice, Amanda ; Kamphorst, Alice O. ; Landthaler, Markus ; Lin, Carolina ; Socci, Nicholas D. ; Hermida, Leandro ; Fulci, Valerio ; Chiaretti, Sabina ; Foà, Robin ; Schliwka, Julia ; Fuchs, Uta ; Novosel, Astrid ; Müller, Roman Ulrich ; Schermer, Bernhard ; Bissels, Ute ; Inman, Jason ; Phan, Quang ; Chien, Minchen ; Weir, David B. ; Choksi, Ruchi ; De Vita, Gabriella ; Frezzetti, Daniela ; Trompeter, Hans Ingo ; Hornung, Veit ; Teng, Grace ; Hartmann, Gunther ; Palkóvits, M. ; Di Lauro, Roberto ; Wernet, Peter ; Macino, Giuseppe ; Rogler, Charles E. ; Nagle, James W. ; Ju, Jingyue ; Papavasiliou, F. Nina ; Benzing, Thomas ; Lichter, Peter ; Tam, Wayne ; Brownstein, Michael J. ; Bosio, Andreas ; Borkhardt, Arndt ; Russo, James J. ; Sander, Chris ; Zavolan, Mihaela ; Tuschl, Thomas. / A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing. In: Cell. 2007 ; Vol. 129, No. 7. pp. 1401-1414.
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abstract = "MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequence-complementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units, and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses.",
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AU - Aravin, Alexei

AU - Pfeffer, Sébastien

AU - Rice, Amanda

AU - Kamphorst, Alice O.

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AU - Chiaretti, Sabina

AU - Foà, Robin

AU - Schliwka, Julia

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AU - Novosel, Astrid

AU - Müller, Roman Ulrich

AU - Schermer, Bernhard

AU - Bissels, Ute

AU - Inman, Jason

AU - Phan, Quang

AU - Chien, Minchen

AU - Weir, David B.

AU - Choksi, Ruchi

AU - De Vita, Gabriella

AU - Frezzetti, Daniela

AU - Trompeter, Hans Ingo

AU - Hornung, Veit

AU - Teng, Grace

AU - Hartmann, Gunther

AU - Palkóvits, M.

AU - Di Lauro, Roberto

AU - Wernet, Peter

AU - Macino, Giuseppe

AU - Rogler, Charles E.

AU - Nagle, James W.

AU - Ju, Jingyue

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AU - Lichter, Peter

AU - Tam, Wayne

AU - Brownstein, Michael J.

AU - Bosio, Andreas

AU - Borkhardt, Arndt

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AU - Zavolan, Mihaela

AU - Tuschl, Thomas

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