Publications by Year: 2011

2011
Cho-Yi Chen, Shui-Tein Chen, Chiou-Shann Fuh, Hsueh-Fen Juan, and Hsuan-Cheng Huang. 2011. “Coregulation of transcription factors and microRNAs in human transcriptional regulatory network.” BMC Bioinformatics, 12 Suppl 1, Pp. S41.Abstract

BACKGROUND: MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression at the post-transcriptional level. Recent studies have suggested that miRNAs and transcription factors are primary metazoan gene regulators; however, the crosstalk between them still remains unclear.

METHODS: We proposed a novel model utilizing functional annotation information to identify significant coregulation between transcriptional and post-transcriptional layers. Based on this model, function-enriched coregulation relationships were discovered and combined into different kinds of functional coregulation networks. RESULTS: We found that miRNAs may engage in a wider diversity of biological processes by coordinating with transcription factors, and this kind of cross-layer coregulation may have higher specificity than intra-layer coregulation. In addition, the coregulation networks reveal several types of network motifs, including feed-forward loops and massive upstream crosstalk. Finally, the expression patterns of these coregulation pairs in normal and tumour tissues were analyzed. Different coregulation types show unique expression correlation trends. More importantly, the disruption of coregulation may be associated with cancers.

CONCLUSION: Our findings elucidate the combinatorial and cooperative properties of transcription factors and miRNAs regulation, and we proposes that the coordinated regulation may play an important role in many biological processes.

ESI Highly Cited Paper

Chen el al. (2011) used gene functional enrichment analysis (second filter in Figure 3) to explore the co-regulatory relationships.... It was found that some biological processes emerged only in co-regulation and that the disruption of co-regulation might be closely related to cancers, suggesting the importance of the co-regulation of miRNAs and TFs.

Le et alBrief Bioinform (2014)

One of the most notable features is that the same transcription factor can activate or repress gene expression and even change binding specificities according to its dynamic interactions with other transcription factors and coactivators (Chen et al. 2011).

Gennarino et al, Genome Res (2012)

Our results also indicate that miR-145 interferes with transcription factors responsible for the initiation of melanogenesis. Interestingly, it has been proposed that co-regulation of miRNAs and transcription factors is of particular importance in pigment pathways (Chen et al. 2011).

Dynoodt et al, J Invest Dermatol (2012)