Open Access Highly Accessed Research article

Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain

Preethi H Gunaratne123, Ya-Chi Lin4, Ashley L Benham1, Jenny Drnevich5, Cristian Coarfa11, Jayantha B Tennakoon1, Chad J Creighton6, Jong H Kim1, Aleksandar Milosavljevic11, Michael Watson7, Sam Griffiths-Jones8 and David F Clayton1049*

Author Affiliations

1 Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA

2 Departments of Pathology, Baylor College of Medicine, Houston, Texas 77030, USA

3 Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA

4 Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL 61801, USA

5 W.M. Keck Center for Comparative and Functional Genomics, Roy J. Carver Biotechnology Center, University of Illinois, Urbana-Champaign, IL 61801, USA

6 Dan Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA

7 ARK-Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, EH25 9RG, UK

8 Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK

9 Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801, USA

10 Beckman Institute, University of Illinois, Urbana-Champaign, IL 61801, USA

11 Bioinformatics Research Laboratory (BRL), Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA

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BMC Genomics 2011, 12:277  doi:10.1186/1471-2164-12-277

Published: 31 May 2011

Additional files

Additional file 1:

Supplemental tables.xls. This one file contains all four Supplemental Tables, each as a separate worksheet. Table S1 ("1 overview") is a summary of Illumina sequence read alignments for six pools of RNA from zebra finch auditory forebrain responding to song versus silence, and shows the distribution of sequence reads in relation to multiple genomes and multiple annotations in the current genomic databases. Table S2 ("2 novel hairpins") gives detailed alignments of putative pre-miRNAs and read sequences. Table S3 ("3 novel genes") shows annotations of all novel miRNA loci mapped in genome assemblies of zebra finch, chicken or human. Table S4 ("4 all read counts") gives read counts and current annotation in miRBase of all conserved and novel miRNAs, with statistics.

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Additional file 2:

Supplemental figures.doc. This one file contains all three supplemental figures. Figure S1 is a Venn diagram of numbers of miRNAs with significant differential expression in response to novel song in three Illumina experiments. Figure S2 shows a comparative mapping in other avian transcriptomes of tgu-mir-2954. Figure S3 demonstrates the song-specificity of the miRNA response, using TaqMan to compare the levels of specific miRNAs in animals from groups that heard song, matching song-enveloped noise, or silence.

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