Skip Navigation



Bioinformatics Advance Access published online on November 24, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm572
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
24/2/165    most recent
btm572v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Wang, X.
Right arrow Articles by Li, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wang, X.
Right arrow Articles by Li, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila

Xiaowo Wang 1, Jin Gu 1, Michael Q. Zhang 2,1 and Yanda Li 1,*

1MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China and
2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11274, USA

*To whom correspondence should be addressed. Xiaowo Wang, E-mail: daulyd{at}tsinghua.edu.cn


  Abstract

Motivation: MicroRNAs are a class of endogenous small RNAs that play regulatory roles. Intergenic miRNAs are believed to be transcribed independently, but the transcriptional control of these crucial regulators is still poorly understood.

Results: In this work, phylogenetic footprinting is used to identify conserved cis-regulatory elements (CCEs) surrounding intergenic miRNAs in Drosophila. With a two-step strategy that takes the advantage of both alignment-based and motif-based methods, we identified cis-regulatory elements that are conserved across the twelve fly species. When compared with TRANSFAC database, these CCEs are significantly enriched in known transcription factor binding sites (TFBSs). Moreover, several TFs that play essential role in Drosophila development (e.g. Adf-1, Abd-B, Sd, Prd, Ubx, Zen and En) are found to be preferentially regulating the miRNA genes. Further analysis revealed many over-represented cis-regulatory modules (CRMs) composed of multiple known TFBSs, motif pairs with significant distance constraints and a number of de novo motifs, many of which preferentially occur near the transcription start site of protein-coding genes. Additionally, a number of putative miRNA-TF regulatory feedback loops were also detected.

Availability: Supplementary information and the Perl scripts performing two-step phylogenetic footprinting are available at http://bioinfo.au.tsinghua.edu.cn/member/xwwang/mircisreg

Contact: daulyd{at}tsinghua.edu.cn

Associate Editor: Dr. Limsoon Wong

Received on May 14, 2007; revised on July 18, 2007; accepted on November 9, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Genome ResHome page
X. Wang, Z. Xuan, X. Zhao, Y. Li, and M. Q. Zhang
High-resolution human core-promoter prediction with CoreBoost_HM
Genome Res., February 1, 2009; 19(2): 266 - 275.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
E. Wingender
The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
Brief Bioinform, July 1, 2008; 9(4): 326 - 332.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.