5′ isomiR variation is of functional and evolutionary importance

Geok Chin Tan; Elcie Chan; Attila Molnar; Rupa Sarkar; Diana Alexieva; Ihsan Mad Isa; Sophie Robinson; Shuchen Zhang; Peter Ellis; Cordelia F. Langford; Pascale V. Guillot; Anil Chandrashekran; Nick M. Fisk; Leandro Castellano; Gunter Meister; Robert M. Winston; Wei Cui; David Baulcombe; Nick J. Dibb

doi:10.1093/nar/gku656

5′ isomiR variation is of functional and evolutionary importance

Geok Chin Tan, Elcie Chan, Attila Molnar, Rupa Sarkar, Diana Alexieva, Ihsan Mad Isa, Sophie Robinson, Shuchen Zhang, Peter Ellis, Cordelia F. Langford, Pascale V. Guillot, Anil Chandrashekran, Nick M. Fisk, Leandro Castellano, Gunter Meister, Robert M. Winston, Wei Cui, David Baulcombe, Nick J. Dibb^*

^*Corresponding author for this work

School of Biological Sciences

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

Abstract / Description of output

We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3′ and/or 5′ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5′ differences and in support of this we report that a 5′ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis ofmiRBase shows that 5′ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes.

Original language	English
Pages (from-to)	9424-9435
Number of pages	12
Journal	Nucleic Acids Research
Volume	42
Issue number	14
DOIs	https://doi.org/10.1093/nar/gku656
Publication status	Published - 23 Jul 2014

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10.1093/nar/gku656Licence: Creative Commons: Attribution (CC-BY)

5′ isomiR variation is of functional and evolutionary importance
The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Downloaded from http://nar.oxfordjournals.org/ at Edinburgh University on November 3, 2015
Final published version, 2.3 MBLicence: Creative Commons: Attribution (CC-BY)

Attila Molnar
- School of Biological Sciences - Senior Lecturer
- Centre for Engineering Biology
Person: Academic: Research Active

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Tan, G. C., Chan, E., Molnar, A., Sarkar, R., Alexieva, D., Isa, I. M., Robinson, S., Zhang, S., Ellis, P., Langford, C. F., Guillot, P. V., Chandrashekran, A., Fisk, N. M., Castellano, L., Meister, G., Winston, R. M., Cui, W., Baulcombe, D., & Dibb, N. J. (2014). 5′ isomiR variation is of functional and evolutionary importance. Nucleic Acids Research, 42(14), 9424-9435. https://doi.org/10.1093/nar/gku656

@article{a90c32209d1c4059a2a1e5c725011618,

title = "5′ isomiR variation is of functional and evolutionary importance",

abstract = "We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3′ and/or 5′ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5′ differences and in support of this we report that a 5′ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis ofmiRBase shows that 5′ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes.",

author = "Tan, {Geok Chin} and Elcie Chan and Attila Molnar and Rupa Sarkar and Diana Alexieva and Isa, {Ihsan Mad} and Sophie Robinson and Shuchen Zhang and Peter Ellis and Langford, {Cordelia F.} and Guillot, {Pascale V.} and Anil Chandrashekran and Fisk, {Nick M.} and Leandro Castellano and Gunter Meister and Winston, {Robert M.} and Wei Cui and David Baulcombe and Dibb, {Nick J.}",

note = "Date of Acceptance: 08/07/2014",

year = "2014",

month = jul,

day = "23",

doi = "10.1093/nar/gku656",

language = "English",

volume = "42",

pages = "9424--9435",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

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Tan, GC, Chan, E, Molnar, A, Sarkar, R, Alexieva, D, Isa, IM, Robinson, S, Zhang, S, Ellis, P, Langford, CF, Guillot, PV, Chandrashekran, A, Fisk, NM, Castellano, L, Meister, G, Winston, RM, Cui, W, Baulcombe, D & Dibb, NJ 2014, '5′ isomiR variation is of functional and evolutionary importance', Nucleic Acids Research, vol. 42, no. 14, pp. 9424-9435. https://doi.org/10.1093/nar/gku656

TY - JOUR

T1 - 5′ isomiR variation is of functional and evolutionary importance

AU - Tan, Geok Chin

AU - Chan, Elcie

AU - Molnar, Attila

AU - Sarkar, Rupa

AU - Alexieva, Diana

AU - Isa, Ihsan Mad

AU - Robinson, Sophie

AU - Zhang, Shuchen

AU - Ellis, Peter

AU - Langford, Cordelia F.

AU - Guillot, Pascale V.

AU - Chandrashekran, Anil

AU - Fisk, Nick M.

AU - Castellano, Leandro

AU - Meister, Gunter

AU - Winston, Robert M.

AU - Cui, Wei

AU - Baulcombe, David

AU - Dibb, Nick J.

N1 - Date of Acceptance: 08/07/2014

PY - 2014/7/23

Y1 - 2014/7/23

N2 - We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3′ and/or 5′ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5′ differences and in support of this we report that a 5′ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis ofmiRBase shows that 5′ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes.

AB - We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3′ and/or 5′ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5′ differences and in support of this we report that a 5′ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis ofmiRBase shows that 5′ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes.

U2 - 10.1093/nar/gku656

DO - 10.1093/nar/gku656

M3 - Article

C2 - 25056318

AN - SCOPUS:84906283860

SN - 0305-1048

VL - 42

SP - 9424

EP - 9435

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 14

ER -

5′ isomiR variation is of functional and evolutionary importance

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