A database of microRNA expression patterns in Xenopus laevis

Ayisha Ahmed; Nicole J. Ward; Simon Moxon; Sara Lopez-Gomollon; Camille Viaut; Matthew L. Tomlinson; Ilya Patrushev; Michael J. Gilchrist; Tamas Dalmay; Dario Dotlic; Andrea E. Munsterberg; Grant N. Wheeler

doi:10.1371/journal.pone.0138313

A database of microRNA expression patterns in Xenopus laevis

Ayisha Ahmed, Nicole J. Ward, Simon Moxon, Sara Lopez-Gomollon, Camille Viaut, Matthew L. Tomlinson, Ilya Patrushev, Michael J. Gilchrist, Tamas Dalmay, Dario Dotlic, Andrea E. Munsterberg, Grant N. Wheeler (Lead Author)

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

18 Citations (Scopus)

15 Downloads (Pure)

Abstract

MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAs
we have looked at show expression in the heart. Our results have been made freely
available as a resource in both XenMARK and Xenbase.

Original language	English
Article number	e0138313
Journal	PLoS One
Volume	10
Issue number	10
DOIs	https://doi.org/10.1371/journal.pone.0138313
Publication status	Published - 27 Oct 2015

Access to Document

10.1371/journal.pone.0138313Licence: CC BY

15-PloSONE-microRNA_Xenmir
© 2015 Ahmed et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Final published version, 9.27 MBLicence: CC BY

Tamas Dalmay
- T.Dalmayuea.acuk
- School of Biological Sciences - Professor of RNA Biology
- Plant Sciences - Member
Person: Research Group Member, Academic, Teaching & Research
Simon Moxon
- S.Moxonuea.acuk
- School of Biological Sciences - Associate Professor in Bioinformatics
Person: Academic, Teaching & Research
Andrea Münsterberg
- A.Munsterberguea.acuk
- School of Biological Sciences - Professor of Developmental Biology
- Cells and Tissues - Member
Person: Research Group Member, Academic, Teaching & Research

XenmiR - A resource of Xenopus microRNA expression patterns
Wheeler, G.
Biotechnology and Biological Sciences Research Council
16/11/09 → 15/05/12
Project: Research

Cite this

@article{9203e23807dd43d38990b329bd399701,

title = "A database of microRNA expression patterns in Xenopus laevis",

abstract = "MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAswe have looked at show expression in the heart. Our results have been made freelyavailable as a resource in both XenMARK and Xenbase.",

author = "Ayisha Ahmed and Ward, {Nicole J.} and Simon Moxon and Sara Lopez-Gomollon and Camille Viaut and Tomlinson, {Matthew L.} and Ilya Patrushev and Gilchrist, {Michael J.} and Tamas Dalmay and Dario Dotlic and Munsterberg, {Andrea E.} and Wheeler, {Grant N.}",

note = "{\textcopyright} 2015 Ahmed et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",

year = "2015",

month = oct,

day = "27",

doi = "10.1371/journal.pone.0138313",

language = "English",

volume = "10",

journal = "PLoS One",

issn = "1932-6203",

publisher = "Public Library of Science",

number = "10",

}

A database of microRNA expression patterns in Xenopus laevis. / Ahmed, Ayisha; Ward, Nicole J.; Moxon, Simon; Lopez-Gomollon, Sara; Viaut, Camille; Tomlinson, Matthew L.; Patrushev, Ilya; Gilchrist, Michael J.; Dalmay, Tamas; Dotlic, Dario; Munsterberg, Andrea E.; Wheeler, Grant N. (Lead Author).

In: PLoS One, Vol. 10, No. 10, e0138313, 27.10.2015.

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

TY - JOUR

T1 - A database of microRNA expression patterns in Xenopus laevis

AU - Ahmed, Ayisha

AU - Ward, Nicole J.

AU - Moxon, Simon

AU - Lopez-Gomollon, Sara

AU - Viaut, Camille

AU - Tomlinson, Matthew L.

AU - Patrushev, Ilya

AU - Gilchrist, Michael J.

AU - Dalmay, Tamas

AU - Dotlic, Dario

AU - Munsterberg, Andrea E.

AU - Wheeler, Grant N.

N1 - © 2015 Ahmed et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2015/10/27

Y1 - 2015/10/27

N2 - MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAswe have looked at show expression in the heart. Our results have been made freelyavailable as a resource in both XenMARK and Xenbase.

AB - MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAswe have looked at show expression in the heart. Our results have been made freelyavailable as a resource in both XenMARK and Xenbase.

U2 - 10.1371/journal.pone.0138313

DO - 10.1371/journal.pone.0138313

M3 - Article

VL - 10

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 10

M1 - e0138313

ER -

A database of microRNA expression patterns in Xenopus laevis

Abstract

Access to Document

Profiles

Tamas Dalmay

Simon Moxon

Andrea Münsterberg

Projects

XenmiR - A resource of Xenopus microRNA expression patterns

Cite this