CardioSignal: a database of transcriptional regulation in cardiac development and hypertrophy

CardioTF, a database of deconstructing transcriptional circuits in the heart system

Background: Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method.

Methods: The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results.

Results: Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype.

Discussion: The CardioTF database can be used as a portal to construct transcriptional network of cardiac development.

Availability and Implementation: Database URL: http://www.cardiosignal.org/database/cardiotf.html.

Angiotensin II signalling and calcineurin in cardiac fibroblasts: differential effects of calcineurin inhibitors FK506 and cyclosporine A

INTRODUCTION

Cardiac remodelling is controlled by complex systems, including activation of the renin-angiotensin system (RAS) and signalling through MAP kinases and Ca2+-activated calcineurin. Whether Ang II, which increases [Ca2+]i and stimulates MAP kinases, mediates myocardial effects through calcineurin-dependent pathways remain unclear. We investigated effects of two calcineurin inhibitors, cyclosporine A (CsA) and tacrolimus (FK506) (10-10-10-6 mol/L, 20 mins) on activation of MAP kinases and on growth, pro-fibrotic and pro-inflammatory responses in Ang II-stimulated rat cardiac fibroblasts.

METHODS AND RESULTS

Ang II increased phosphorylation of ERK1/2 and p38MAPK (1.5-1.8-fold, p<0.05) without effect on JNK. FK506, but not CsA, attenuated Ang II-stimulated MAP kinase activation. Molecular indices of cell growth (proliferating cell nuclear antigen (PCNA)), fibrosis (fibronectin, pro-collagen) and inflammation (iNOS), were upregulated by Ang II (12 hrs). FK506 and CsA inhibited PCNA effects. Ang II-induced pro-fibrotic and pro-inflammatory responses were inhibited by CsA. Ang II receptors, AT1R and AT2R, were not influenced by calcineurin inhibitors. Our data indicate differential calcineurin inhibitor sensitivity of MAP kinases and cellular responses in Ang II-stimulated fibroblasts. p38MAP kinase and ERK1/2 are regulated in a FK506-sensitive manner, whereas fibrosis and inflammation are CsA-sensitive. Cell proliferation is inhibited by both FKC506 and CsA. These are post-receptor phenomena, since AT1R and AT2R status was unaltered by treatment.

CONCLUSIONS

Our findings identify an important role for calcineurin in MAP kinase/growth/pro-fibrotic/pro-inflammatory signalling by Ang II in cardiac fibroblasts. Although both FK506 and CsA inhibit calcineurin, they exert differential effects on molecular and cellular responses. Such differences may contribute to variable clinical responses of these agents.

Mef2c is an essential regulatory element required for unique expression of the cardiac-specific CARK gene

The cardiac ankyrin repeat kinase (CARK) gene, also named TNNI3K for its interaction with cardiac troponin I, is both a unique expression and heart-enriched gene. To understand the mechanisms of CARK gene expression and regulation, we first cloned the full-length mRNA sequence and mapped the transcription start site of the mouse CARK gene and characterized its promoter regions. Two transcriptional isoforms of the CARK gene were identified in mouse heart tissue. Truncation analysis of the CARK promoter identified a minimal 151 bp region that has strong basal transcription activity. Mutational analysis revealed five conserved cis-acting elements in this 151-bp long minimal promoter. Mutational and loss-of-functional analysis and co-transfection studies indicated that MEF2 binding region is the most critical cis-acting element in the CARK promoter, and CARK transcription level can be down-regulated by MEF2C antisense. Binding to the MEF2 sites by Mef2c protein was confirmed by electrophoretic mobility shift assay and competition and supershift electrophoretic mobility shift assays.

Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors

BACKGROUND

Evolutionary conservation has been used successfully to help identify cis-acting DNA regions that are important in regulating tissue-specific gene expression. Motivated by increasing evidence that some DNA regulatory regions are not evolutionary conserved, we have developed an approach for cis-regulatory region identification that does not rely upon evolutionary sequence conservation.

RESULTS

The conservation-independent approach is based on an empirical potential energy between interacting transcription factors (TFs). In this analysis, the potential energy is defined as a function of the number of TF interactions in a genomic region and the strength of the interactions. By identifying sets of interacting TFs, the analysis locates regions enriched with the binding sites of these interacting TFs. We applied this approach to 30 human tissues and identified 6232 putative cis-regulatory modules (CRMs) regulating 2130 tissue-specific genes. Interestingly, some genes appear to be regulated by different CRMs in different tissues. Known regulatory regions are highly enriched in our predicted CRMs. In addition, DNase I hypersensitive sites, which tend to be associated with active regulatory regions, significantly overlap with the predicted CRMs, but not with more conserved regions. We also find that conserved and non-conserved CRMs regulate distinct gene groups. Conserved CRMs control more essential genes and genes involved in fundamental cellular activities such as transcription. In contrast, non-conserved CRMs, in general, regulate more non-essential genes, such as genes related to neural activity.

CONCLUSION

These results demonstrate that identifying relevant sets of binding motifs can help in the mapping of DNA regulatory regions, and suggest that non-conserved CRMs play an important role in gene regulation.