High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries

Gavriel Mullokandov; Alessia Baccarini; Albert Ruzo; Anitha D. Jayaprakash; Navpreet Tung; Benjamin Israelow; Matthew J. Evans; Ravi Sachidanandam; Brian D. Brown

doi:10.1038/nmeth.2078

High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries

Gavriel Mullokandov, Alessia Baccarini, Albert Ruzo, Anitha D. Jayaprakash, Navpreet Tung, Benjamin Israelow, Matthew J. Evans, Ravi Sachidanandam, Brian D. Brown

Research output: Contribution to journal › Article › peer-review

321 Scopus citations

Abstract

We introduce two large-scale resources for functional analysis of microRNA (miRNA): a decoy library for inhibiting miRNA function and a sensor library for monitoring microRNA activity. To take advantage of the sensor library, we developed a high-throughput assay called Sensor-seq to simultaneously quantify the activity of hundreds of miRNAs. Using this approach, we show that only the most abundant miRNAs in a cell mediate target suppression. Over 60% of detected miRNAs had no discernible activity, which indicated that the functional 'miRNome' of a cell is considerably smaller than currently inferred from profiling studies. Moreover, some highly expressed miRNAs exhibited relatively weak activity, which in some cases correlated with a high target-to-miRNA ratio or increased nuclear localization of the miRNA. Finally, we show that the miRNA decoy library can be used for pooled loss-of-function studies. These tools are valuable resources for studying miRNA biology and for miRNA-based therapeutics.

Original language	English
Pages (from-to)	840-846
Number of pages	7
Journal	Nature Methods
Volume	9
Issue number	8
DOIs	https://doi.org/10.1038/nmeth.2078
State	Published - Aug 2012

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title = "High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries",

abstract = "We introduce two large-scale resources for functional analysis of microRNA (miRNA): a decoy library for inhibiting miRNA function and a sensor library for monitoring microRNA activity. To take advantage of the sensor library, we developed a high-throughput assay called Sensor-seq to simultaneously quantify the activity of hundreds of miRNAs. Using this approach, we show that only the most abundant miRNAs in a cell mediate target suppression. Over 60% of detected miRNAs had no discernible activity, which indicated that the functional 'miRNome' of a cell is considerably smaller than currently inferred from profiling studies. Moreover, some highly expressed miRNAs exhibited relatively weak activity, which in some cases correlated with a high target-to-miRNA ratio or increased nuclear localization of the miRNA. Finally, we show that the miRNA decoy library can be used for pooled loss-of-function studies. These tools are valuable resources for studying miRNA biology and for miRNA-based therapeutics.",

author = "Gavriel Mullokandov and Alessia Baccarini and Albert Ruzo and Jayaprakash, {Anitha D.} and Navpreet Tung and Benjamin Israelow and Evans, {Matthew J.} and Ravi Sachidanandam and Brown, {Brian D.}",

note = "Funding Information: We thank L. Naldini, B. Gentner, E. Bernstein, E.C. Lai, A. Ventura and A. Chess for helpful discussions, and H. Iba (University of Tokyo) for pmU6-TuD-shuttle. We also thank the Mount Sinai Genomics Core Facility for deep sequencing. Oligo libraries were accessed through a collaborative technology program from Agilent Technologies. B.D.B. is supported by a US National Institute of Health Pathfinder Award (DP2DK083052-01) and funding from the Juvenile Diabetes Research Foundation (JDRF-17-2010-770). M.J.E. is supported by the Pew Charitable Funds and US National Institute of Health (R56AI091792). G.M. is supported by a Helmsley Trust Award.",

year = "2012",

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AU - Mullokandov, Gavriel

AU - Baccarini, Alessia

AU - Ruzo, Albert

AU - Jayaprakash, Anitha D.

AU - Tung, Navpreet

AU - Israelow, Benjamin

AU - Evans, Matthew J.

AU - Sachidanandam, Ravi

AU - Brown, Brian D.

N1 - Funding Information: We thank L. Naldini, B. Gentner, E. Bernstein, E.C. Lai, A. Ventura and A. Chess for helpful discussions, and H. Iba (University of Tokyo) for pmU6-TuD-shuttle. We also thank the Mount Sinai Genomics Core Facility for deep sequencing. Oligo libraries were accessed through a collaborative technology program from Agilent Technologies. B.D.B. is supported by a US National Institute of Health Pathfinder Award (DP2DK083052-01) and funding from the Juvenile Diabetes Research Foundation (JDRF-17-2010-770). M.J.E. is supported by the Pew Charitable Funds and US National Institute of Health (R56AI091792). G.M. is supported by a Helmsley Trust Award.

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N2 - We introduce two large-scale resources for functional analysis of microRNA (miRNA): a decoy library for inhibiting miRNA function and a sensor library for monitoring microRNA activity. To take advantage of the sensor library, we developed a high-throughput assay called Sensor-seq to simultaneously quantify the activity of hundreds of miRNAs. Using this approach, we show that only the most abundant miRNAs in a cell mediate target suppression. Over 60% of detected miRNAs had no discernible activity, which indicated that the functional 'miRNome' of a cell is considerably smaller than currently inferred from profiling studies. Moreover, some highly expressed miRNAs exhibited relatively weak activity, which in some cases correlated with a high target-to-miRNA ratio or increased nuclear localization of the miRNA. Finally, we show that the miRNA decoy library can be used for pooled loss-of-function studies. These tools are valuable resources for studying miRNA biology and for miRNA-based therapeutics.

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High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries

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