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Open Access Research article

Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle

Quan Gu12, Shivashankar H Nagaraj1, Nicholas J Hudson1, Brian P Dalrymple1 and Antonio Reverter1*

Author Affiliations

1 Computational and Systems Biology, CSIRO Food Futures Flagship and CSIRO Livestock Industries, 306 Carmody Rd. St. Lucia, Brisbane, Queensland 4067, Australia

2 College of Information Sciences and Technology, Donghua University, Shanghai 201620, PR China

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BMC Genomics 2011, 12:23  doi:10.1186/1471-2164-12-23

Published: 12 January 2011

Abstract

Background

Gene regulation by transcription factors (TF) is species, tissue and time specific. To better understand how the genetic code controls gene expression in bovine muscle we associated gene expression data from developing Longissimus thoracis et lumborum skeletal muscle with bovine promoter sequence information.

Results

We created a highly conserved genome-wide promoter landscape comprising 87,408 interactions relating 333 TFs with their 9,242 predicted target genes (TGs). We discovered that the complete set of predicted TGs share an average of 2.75 predicted TF binding sites (TFBSs) and that the average co-expression between a TF and its predicted TGs is higher than the average co-expression between the same TF and all genes. Conversely, pairs of TFs sharing predicted TGs showed a co-expression correlation higher that pairs of TFs not sharing TGs. Finally, we exploited the co-occurrence of predicted TFBS in the context of muscle-derived functionally-coherent modules including cell cycle, mitochondria, immune system, fat metabolism, muscle/glycolysis, and ribosome. Our findings enabled us to reverse engineer a regulatory network of core processes, and correctly identified the involvement of E2F1, GATA2 and NFKB1 in the regulation of cell cycle, fat, and muscle/glycolysis, respectively.

Conclusion

The pivotal implication of our research is two-fold: (1) there exists a robust genome-wide expression signal between TFs and their predicted TGs in cattle muscle consistent with the extent of promoter sharing; and (2) this signal can be exploited to recover the cellular mechanisms underpinning transcription regulation of muscle structure and development in bovine. Our study represents the first genome-wide report linking tissue specific co-expression to co-regulation in a non-model vertebrate.