COTRASIF: conservation-aided transcription-factor-binding site finder

A new insight into mechanisms of interferon alpha neurotoxicity: Expression of GRIN3A subunit of NMDA receptors and NMDA-evoked exocytosis

Neurological and psychiatric side effects accompany the high-dose interferon-alpha (IFNA) therapy. The primary genes responsible for these complications are mostly unknown. Our genome-wide search in mouse and rat genomes for the conservative genes containing IFN-stimulated response elements (ISRE) in their promoters revealed a new potential target gene of IFNA, Grin3α, which encodes the 3A subunit of NMDA receptor. This study aimed to explore the impact of IFNA on the expression of Grin3α and Ifnα genes and neurotransmitters endo/exocytosis in the mouse brain. We administered recombinant human IFN-alpha 2b (rhIFN-α2b) intracranially, and 24 h later, we isolated six brain regions and used the samples for RT-qPCR and western blot analysis. Synaptosomes were isolated from the cortex to analyze endo/exocytosis with acridine orange and L-[14C]glutamate. IFNA induced an increase in Grin3α mRNA and GRIN3A protein, but a decrease in Ifnα mRNA and protein. IFNA did not affect the accumulation and distribution of L-[14C]glutamate and acridine orange between synaptosomes and the extra-synaptosomal space. It caused the more significant acridine orange release activated by NMDA or glutamate than from control mice's synaptosomes. In response to IFNA, the newly discovered association between elevated Grin3α expression and NMDA- and glutamate-evoked neurotransmitters release from synaptosomes implies a new molecular mechanism of IFNA neurotoxicity.

Hepatocytes response to interferon alpha levels recorded after liver resection

Extensive damage of liver parenchyma stimulates hepatic cells to transit from quiescence to proliferation with eventual restoration of liver mass and function. Our recent studies have revealed upregulated expression of interferon (IFN)-α and its antiviral activity during the early hours after partial hepatectomy. In this study, we analyzed the response of primary hepatocytes from intact liver to IFN-α mimicking its levels (250 U/mL) during the transition period of liver restoration. The gene expression profile was analyzed with rat genome array 230 2.0 (Affymetrix). After 3- and 6-h treatment we identified respectively 28 and 124 differentially expressed genes responsible for autonomous changes in hepatocytes and those involving non-parenchymal cells in a concerted response to IFN-α. The response has an energy sparing character and affects all levels of gene expression. The factors activating T cells and apoptosis are opposed by those restricting the signal propagation, inhibiting T cells activation, and promoting survival. The partial resemblance between the specific in vitro response to IFN-α and the processes in regenerating liver is discussed. Our study opens the way to a more focused investigation of the liver cell response to quasiphysiological dose of IFN-α.

LASAGNA-Search: an integrated web tool for transcription factor binding site search and visualization

The release of ChIP-seq data from the ENCyclopedia Of DNA Elements (ENCODE) and Model Organism ENCyclopedia Of DNA Elements (modENCODE) projects has significantly increased the amount of transcription factor (TF) binding affinity information available to researchers. However, scientists still routinely use TF binding site (TFBS) search tools to scan unannotated sequences for TFBSs, particularly when searching for lesser-known TFs or TFs in organisms for which ChIP-seq data are unavailable. The sequence analysis often involves multiple steps such as TF model collection, promoter sequence retrieval, and visualization; thus, several different tools are required. We have developed a novel integrated web tool named LASAGNA-Search that allows users to perform TFBS searches without leaving the web site. LASAGNA-Search uses the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm for TFBS alignment. Important features of LASAGNA-Search include (i) acceptance of unaligned variable-length TFBSs, (ii) a collection of 1726 TF models, (iii) automatic promoter sequence retrieval, (iv) visualization in the UCSC Genome Browser, and (v) gene regulatory network inference and visualization based on binding specificities. LASAGNA-Search is freely available at http://biogrid.engr.uconn.edu/lasagna_search/.

CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

Background

Information about the composition of regulatory regions is of great value for designing experiments to functionally characterize gene expression. The multiplicity of available applications to predict transcription factor binding sites in a particular locus contrasts with the substantial computational expertise that is demanded to manipulate them, which may constitute a potential barrier for the experimental community.

Results

CBS (Conserved regulatory Binding Sites, http://compfly.bio.ub.es/CBS) is a public platform of evolutionarily conserved binding sites and enhancers predicted in multiple Drosophila genomes that is furnished with published chromatin signatures associated to transcriptionally active regions and other experimental sources of information. The rapid access to this novel body of knowledge through a user-friendly web interface enables non-expert users to identify the binding sequences available for any particular gene, transcription factor, or genome region.

Conclusions

The CBS platform is a powerful resource that provides tools for data mining individual sequences and groups of co-expressed genes with epigenomics information to conduct regulatory screenings in Drosophila.

ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites

Motivation: The prediction and annotation of the genomic regions involved in gene expression has been largely explored. Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding sites (TFBSs) largely unexplored and with important quantitative and qualitative methodological gaps.

Results: We have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith–Waterman algorithm that allows local searches of conserved TFBS clusters and the detection of regulatory regions proximal to genes and enhancer regions. ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively.

Availability: The source code of ReLA's is freely available and can be remotely used through our web server under http://www.bsc.es/cg/rela.

Contact:david.torrents@bsc.es

Supplementary information:Supplementary data are available at Bioinformatics online.

Identifying functional single nucleotide polymorphisms in the human CArGome

Regulatory SNPs (rSNPs) reside primarily within the nonprotein coding genome and are thought to disturb normal patterns of gene expression by altering DNA binding of transcription factors. Nevertheless, despite the explosive rise in SNP association studies, there is little information as to the function of rSNPs in human disease. Serum response factor (SRF) is a widely expressed DNA-binding transcription factor that has variable affinity to at least 1,216 permutations of a 10 bp transcription factor binding site (TFBS) known as the CArG box. We developed a robust in silico bioinformatics screening method to evaluate sequences around RefSeq genes for conserved CArG boxes. Utilizing a predetermined phastCons threshold score, we identified 8,252 strand-specific CArGs within an 8 kb window around the transcription start site of 5,213 genes, including all previously defined SRF target genes. We then interrogated this CArG dataset for the presence of previously annotated common polymorphisms. We found a total of 118 unique CArG boxes harboring a SNP within the 10 bp CArG sequence and 1,130 CArG boxes with SNPs located just outside the CArG element. Gel shift and luciferase reporter assays validated SRF binding and functional activity of several new CArG boxes. Importantly, SNPs within or just outside the CArG box often resulted in altered SRF binding and activity. Collectively, these findings demonstrate a powerful approach to computationally define rSNPs in the human CArGome and provide a foundation for similar analyses of other TFBS. Such information may find utility in genetic association studies of human disease where little insight is known regarding the functionality of rSNPs.

A mutation degree model for the identification of transcriptional regulatory elements

BACKGROUND

Current approaches for identifying transcriptional regulatory elements are mainly via the combination of two properties, the evolutionary conservation and the overrepresentation of functional elements in the promoters of co-regulated genes. Despite the development of many motif detection algorithms, the discovery of conserved motifs in a wide range of phylogenetically related promoters is still a challenge, especially for the short motifs embedded in distantly related gene promoters or very closely related promoters, or in the situation that there are not enough orthologous genes available.

RESULTS

A mutation degree model is proposed and a new word counting method is developed for the identification of transcriptional regulatory elements from a set of co-expressed genes. The new method comprises two parts: 1) identifying overrepresented oligo-nucleotides in promoters of co-expressed genes, 2) estimating the conservation of the oligo-nucleotides in promoters of phylogenetically related genes by the mutation degree model. Compared with the performance of other algorithms, our method shows the advantages of low false positive rate and higher specificity, especially the robustness to noisy data. Applying the method to co-expressed gene sets from Arabidopsis, most of known cis-elements were successfully detected. The tool and example are available at http://mcube.nju.edu.cn/jwang/lab/soft/ocw/OCW.html.

CONCLUSIONS

The mutation degree model proposed in this paper is adapted to phylogenetic data of different qualities, and to a wide range of evolutionary distances. The new word-counting method based on this model has the advantage of better performance in detecting short sequence of cis-elements from co-expressed genes of eukaryotes and is robust to less complete phylogenetic data.

Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs

Background

Bi-directional gene pairs have received considerable attention for their prevalence in vertebrate genomes. However, their biological relevance and exact regulatory mechanism remain less understood. To study the inner properties of this gene organization and the difference between bi- and uni-directional genes, we conducted a genome-wide investigation in terms of their sequence composition, functional association and regulatory motif discovery.

Results

We identified 1210 bi-directional gene pairs based on the GRCh37 assembly data, accounting for 11.6% of all the human genes owning RNAs. CpG islands were detected in 98.42% of bi-directional promoters and 61.07% of unidirectional promoters. Functional enrichment analysis in GO and GeneGO both revealed that bi-directional genes tend to be associated with housekeeping functions in metabolism pathways and nuclear processes, and 46.84% of the pair members are involved in the same biological function. By fold-enrichment analysis, we characterized 73 and 43 putative transcription factor binding sites(TFBS) that preferentially occur in bi-directional promoters from TRANSFAC and JASPAR database respectively. By text mining, some of them were verified by individual experiments and several novel binding motifs were also identified.

Conclusions

Bi-directional promoters feature a significant enrichment of CpG-islands as well as a high GC content. We provided insight into the function constraints of bi-directional genes and found that paired genes are biased toward functional similarities. We hypothesized that the functional association underlies the co-expression of bi-directional genes. Furthermore, we proposed a set of putative regulatory motifs in the bi-directional promoters for further experimental studies to investigate transcriptional regulation of bi-directional genes.

CCRXP: exploring clusters of conserved residues in protein structures

Conserved residues forming tightly packed clusters have been shown to be energy hot spots in both protein–protein and protein–DNA complexes. A number of analyses on these clusters of conserved residues (CCRs) have been reported, all pointing to a crucial role that these clusters play in protein function, especially protein–protein and protein–DNA interactions. However, currently there is no publicly available tool to automatically detect such clusters. Here, we present a web server that takes a coordinate file in PDB format as input and automatically executes all the steps to identify CCRs in protein structures. In addition, it calculates the structural properties of each residue and of the CCRs. We also present statistics to show that CCRs, determined by these procedures, are significantly enriched in ‘hot spots’ in protein–protein and protein–RNA complexes, which supplements our more detailed similar results on protein–DNA complexes. We expect that CCRXP web server will be useful in studies of protein structures and their interactions and selecting mutagenesis targets. The web server can be accessed at http://ccrxp.netasa.org.