Cross-species Alignment Research Articles

LRRfinder2.0: A webserver for the prediction of leucine-rich repeats

Leucine-rich repeats (LRRs) are versatile motifs present in more than 6000 proteins throughout the phylogenetic kingdom. Tandem LRRs generate a characteristic horseshoe with a diverse range of functions. Fulfilling a key role in the innate immune system, LRRs form the TLR and NOD-like receptor (NLR) pathogen-recognition domain. Host-pathogen interactions mediated by LRRs drive those involved in ligand recognition to become distinct from their consensus motif. Most LRRs range between 21 and 30 residues; however, large insertions in certain TLRs can generate repeats of over 60 amino acids. LRR variability makes them ideal for species-specific mediation of host-pathogen interactions. Teleost TLRs show large insertions, making cross-species alignments difficult without prior demarcation of their LRR motifs. We present LRRfinder2.0, a webserver for LRR prediction. LRRfinder2.0 utilizes scoring matrices comprising more than 60,000 LRR motifs from more than 200 species. The underlying TLR database tLRRdb contains more than 3500 manually annotated sequences, augmenting identification of irregular LRR motifs.

Identification of novel mutations in GATA6 gene associated with tetralogy of Fallot

To identify the novel mutations in the GATA6 gene associated with tetralogy of Fallot (TOF). The clinical data and blood samples from 120 unrelated Han Chinese TOF patients and 200 unrelated ethnically matched healthy controls were collected. The coding exons and flanking splice junctions of GATA6 gene were amplified by polymerase chain reaction and sequenced by the technique of di-deoxynucleotide chain termination. The acquired sequences were aligned with those derived from GenBank by the aid of program BLAST to identify the sequence variations. The software ClustalW was applied for the conservation analysis of altered amino acids. The pathogenic probability for each sequence variation was predicted automatically by software MutationTaster. Three novel heterozygous missense GATA6 mutations were identified in 3 TOF patients. Specifically, the triplet substitutions of CTC for CCC at codon 73, CGC for AGC at codon 364 and GGC for GCC at codon 591, predicting the transitions of proline into leucine at amino acid residue 73 (p.P73L), serine into arginine at amino acid residue 364 (p.S364R) and alanine into glycine at amino acid residue 591 (p.A591G), were detected. None of three mutations was observed in 200 healthy controls. A cross-species alignment of GATA6 encoded protein sequences showed that the mutated amino acids were highly conserved evolutionarily and all 3 mutations were predicted to be pathogenic. Novel mutations are identified in the GATA6 gene associated with TOF. Such a finding may contribute to an early prophylaxis and therapy of TOF.

Novel GATA5 loss-of-function mutations underlie familial atrial fibrillation

OBJECTIVE:This study aimed to identify novel GATA5 mutations that underlie familial atrial fibrillation.METHODS:A total of 110 unrelated patients with familial atrial fibrillation and 200 unrelated, ethnically matched healthy controls were recruited. The entire coding region of the GATA5 gene was sequenced in 110 atrial fibrillation probands. The available relatives of the mutation carriers and 200 controls were subsequently genotyped for the identified mutations. The functional effect of the mutated GATA5 was characterized using a luciferase reporter assay system.RESULTS:Two novel heterozygous GATA5 mutations (p.Y138F and p.C210G) were identified in two of the 110 unrelated atrial fibrillation families. These missense mutations cosegregated with AF in the families and were absent in the 400 control chromosomes. A cross-species alignment of GATA5 protein sequence showed that the altered amino acids were completely conserved evolutionarily. A functional analysis revealed that the mutant GATA5 proteins were associated with significantly decreased transcriptional activation when compared with their wild-type counterpart.CONCLUSION:The findings expand the spectrum of GATA5 mutations linked to AF and provide novel insights into the molecular mechanism involved in the pathogenesis of atrial fibrillation, suggesting potential implications for the early prophylaxis and personalized treatment of this common arrhythmia.

Translation Initiator EIF4G1 Mutations in Familial Parkinson Disease

Genome-wide analysis of a multi-incident family with autosomal-dominant parkinsonism has implicated a locus on chromosomal region 3q26-q28. Linkage and disease segregation is explained by a missense mutation c.3614G>A (p.Arg1205His) in eukaryotic translation initiation factor 4-gamma (EIF4G1). Subsequent sequence and genotype analysis identified EIF4G1 c.1505C>T (p.Ala502Val), c.2056G>T (p.Gly686Cys), c.3490A>C (p.Ser1164Arg), c.3589C>T (p.Arg1197Trp) and c.3614G>A (p.Arg1205His) substitutions in affected subjects with familial parkinsonism and idiopathic Lewy body disease but not in control subjects. Despite different countries of origin, persons with EIF4G1 c.1505C>T (p.Ala502Val) or c.3614G>A (p.Arg1205His) mutations appear to share haplotypes consistent with ancestral founders. eIF4G1 p.Ala502Val and p.Arg1205His disrupt eIF4E or eIF3e binding, although the wild-type protein does not, and render mutant cells more vulnerable to reactive oxidative species. EIF4G1 mutations implicate mRNA translation initiation in familial parkinsonism and highlight a convergent pathway for monogenic, toxin and perhaps virally-induced Parkinson disease.

Novel connexin40 missense mutations in patients with familial atrial fibrillation

This research was aimed at screening connexin40, a cardiac gap junction protein alpha 5, for genetic defects in patients with familial atrial fibrillation (AF). The subjects included 218 unrelated families with lone AF and 200 ethnically matched unrelated healthy individuals as controls. The entire coding region of the connexin40 gene was sequenced initially in 218 unrelated probands with familial AF. The relatives of mutation carriers and 200 controls were subsequently genotyped for the presence of mutations identified in probands. Three novel connexin40 mutations, p.V85I, p.L221I, and p.L229M, were identified in 3 of 218 unrelated AF families, respectively. These heterozygous missense mutations co-segregated with AF in the families and were absent in the 200 unrelated control subjects. A cross-species alignment of connexin40 protein sequences revealed that the altered amino acids were completely conserved evolutionarily. The findings expand the spectrum of mutations in connexin40 linked to AF and provide new insight into the molecular aetiology involved in the pathogenesis of AF.

Novel GATA4 mutations identified in patients with congenital heart disease

To identify the novel genetic determinants in patients with congenital heart disease (CHD). The clinical data and peripheral venous blood samples from 120 unrelated individuals with idiopathic CHD were collected and evaluated compared to 100 unrelated healthy controls. The complete coding exons and the partial flanking introns of GATA4 gene were amplified by polymerase chain reaction and sequenced by di-deoxynucleotide chain termination. The generated sequences were aligned with those retrieved from GenBank with the aid of programme BLAST to identify the sequence variations. The software Clustal W was utilized to analyze the conservation of altered amino acids. Three novel heterozygous missense GATA4 mutations were identified in 3 of 120 CHD cases. Namely, the triplet substitutions of AGA for AGC at codon 90, GAG for GAC at codon 95, and AAT for AAG at codon 329, predicting the conversions of serine into arginine at amino acid residue 90 (S90R), aspartic acid into glutamic acid at amino acid residue 95 (D95E) and lysine into asparagine at amino acid residue 329 (K329N), were detected. None of these three mutations were probed in 100 controls. A cross-species alignment of GATA4 encoded protein sequences displayed that the lysine at amino acid residue 329 was completely conserved evolutionarily. Additionally, a single nucleotide polymorphism c. 99G>T was observed. However, the polymorphic frequency distribution in CHD patients was not statistically different from that in controls (for genotypes, chi(2) = 0.2640, P = 0.6074; for alleles, chi(2) = 0.2514, P = 0.6161). The idiopathic CHD has a marked heterogeneity and the mutated GATA4 gene may be responsible for CHD in a subset of patients.

Novel NKX2-5 mutations identified in patients with congenital ventricular septal defects

To identify the novel genetic defects in patients with congenital ventricular septal defect (VSD). The clinical data and blood samples from 160 unrelated subjects with congenital VSD were collected and evaluated in comparison with 200 healthy individuals. The coding exons and flanking introns of NKX2-5 gene were amplified by polymerase chain reaction and sequenced using the di-deoxynucleotide chain termination approach. The acquired sequences were aligned with those publicized in GenBank by the aid of program BLAST to identify the sequence variations. The software Clustal W was applied to analyzing the conservation of altered amino acids. Two novel heterozygous missense NKX2-5 mutations were identified in 3 of 160 VSD patients. The same triplet substitution of TTC for TCC at codon 179, predicting the conversion of serine into phenylalanine at amino acid residue 179 (Ser179Phe), was detected in two cases. Another transition of CGC into AGC at codon 36, leading to the change of arginine into serine at amino acid residue 36 (Arg36Ser), was detected in a third case. These two mutations were not observed in 200 healthy controls. A cross-species alignment of NKX2-5 encoded protein sequences displayed that the mutated amino acids were highly conserved evolutionarily. Additionally, two single nucleotide polymorphisms including a common c. 63A > G and a rare c. 606G > C were observed. However, the polymorphic frequency distributions in VSD cases were not statistically different from those in healthy controls (c. 63A > G: chi(2) = 3.403, P = 0.0651; c. 606G > C: chi(2) = 3.278, P = 0.0702). Novel NKX2-5 mutations are identified in patients with ASD. They may provide new insight into the molecular etiology responsible for VSD.

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner

The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

Analysis of Complex Disease Association and Linkage Studies Using the University of California Santa Cruz Genome Browser

The sequencing of the human genome, the identification of common single-nucleotide polymorphisms (SNPs) and haplotype blocks, and advances in microarray technology have enabled the study of complex diseases at a level of detail not previously imaginable. These have aided in the design and analyses of association and linkage studies of many complex diseases including cardiovascular disease. Recent technological advances have enabled the undertaking of large-scale genome-wide association studies (GWAS) that can assay hundreds of thousands of polymorphic sites on hundreds to thousands of individuals to find genomic regions associated with disease. Although results from these experiments enable the identification of smaller regions of association compared with previous studies, as with all linkage and association studies, there is the need for the further investigation of regions of interest for the causal genes or variants. The purpose of this review is to present a detailed demonstration as to how publicly available resources can be used to easily guide more detailed research into genomic regions of interest identified in linkage and association study data. Large-scale projects, such as the Human Genome Sequencing project,1,2 have generated large volumes and varieties of annotated genomic data necessitating the development of Internet-based tools to organize and make practically available these public data. One important tool in human disease research is the web-based graphical genome browsers that use the human genome sequence as the framework on which to organize genomic annotations, providing various ways for researchers to view and extract important information. Currently, there are 3 human genome browsers that have been developed for public use: (1) the National Center for Biotechnology Information (NCBI) Map Viewer3; (2) the University of California Santa Cruz (UCSC) Genome Browser4; and (3) the European Bioinformatics Institute’s Ensembl system.5 Although these genome browsers share common features and …

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

BackgroundThe regulation of gene expression is complex and occurs at many levels, including transcriptional and post-transcriptional, in metazoans. Transcriptional regulation is mainly determined by sequence elements within the promoter regions of genes while sequence elements within the 3' untranslated regions of mRNAs play important roles in post-transcriptional regulation such as mRNA stability and translation efficiency. Identifying cis-regulatory elements, or motifs, in multicellular eukaryotes is more difficult compared to unicellular eukaryotes due to the larger intergenic sequence space and the increased complexity in regulation. Experimental techniques for discovering functional elements are often time consuming and not easily applied on a genome level. Consequently, computational methods are advantageous for genome-wide cis-regulatory motif detection. To decrease the search space in metazoans, many algorithms use cross-species alignment, although studies have demonstrated that a large portion of the binding sites for the same trans-acting factor do not reside in alignable regions. Therefore, a computational algorithm should account for both conserved and nonconserved cis-regulatory elements in metazoans.ResultsWe present CompMoby (Comparative MobyDick), software developed to identify cis-regulatory binding sites at both the transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factors. The CompMoby algorithm was previously shown to identify cis-regulatory binding sites in upstream regions of genes co-regulated in embryonic stem cells. In this paper, we extend the software to identify putative cis-regulatory motifs in 3' UTR sequences and verify our results using experimentally validated data sets in mouse and human. We also detail the implementation of CompMoby into a user-friendly tool that includes a web interface to a streamlined analysis. Our software allows detection of motifs in the following three categories: one, those that are alignable and conserved; two, those that are conserved but not alignable; three, those that are species specific. One of the output files from CompMoby gives the user the option to decide what category of cis-regulatory element to experimentally pursue based on their biological problem. Using experimentally validated biological datasets, we demonstrate that CompMoby is successful in detecting cis-regulatory target sites of known and novel trans-acting factors at the transcriptional and post-transcriptional levels.ConclusionCompMoby is a powerful software tool for systematic de novo discovery of evolutionarily conserved and nonconserved cis-regulatory sequences involved in transcriptional or post-transcriptional regulation in metazoans. This software is freely available to users at .

A cross-species alignment tool (CAT).

BackgroundThe main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more sensitive methods which are usually applied in aligning inter-species sequences.ResultsHere we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web at .ConclusionsExamined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT and sim4, with the sensitivity of the best inter-species tools, like GeneWise.

PEDF and the serpins: Phylogeny, sequence conservation, and functional domains

Pigment epithelium derived factor (PEDF) is non-inhibitory serpin with neurotrophic and antiangiogenic functions. In this study, we have assembled PEDF sequences for 9 additional species by data base mining and performed cross-species alignment for 14 PEDF sequences to identify conserved structural domains. We found evolutionary conservation of a leader sequence, a single C-terminal glycosylation site, collagen-binding residues, and four specific conserved PEDF peptides. The C-terminus, 384–415 and an N-terminal region 78–95, show close homology with many other serpins, and there is strong conservation of 39 of 51 consensus key residues involved in serpin structure and function. Two peptide regions, 40–67 and 277–301, are unique to PEDF but conserved in all species. Conserved residues at the N-terminus, helix d (hD), and helix A (hA) of PEDF form a structure similar to the heparin-binding groove of other serpins. We identified a motif in PEDF that is homologous to the nuclear localization signals of other proteins. A bitopographical localization of PEDF was confirmed by immunocytochemistry and Western blots. Our results suggest that secretion is required for PEDF’s activity, that PEDF can migrate to the nucleus, and that PEDF has structural and functional features more common with inhibitory serpins.

A novel index which precisely derives protein coding regions from cross-species genome alignments.

We introduce here a novel index which precisely derives protein coding regions from cross-species genome alignments. The index is deeply related to frame recovery observed in coding sequence alignments, that is, if insertions or deletions of nucleotides causes frame shifts in coding regions, other in-dels which recover the reading frames will be often observed in the vicinity. In contrast, such frame recoveries are not observed in other conserved regions. We prepared two gene models: a model which finds gene by using sequence similarity and intrinsic gene measures (basic model), and the other model which finds gene by using frame recovery index in addition to sequence similarity and intrinsic gene measures (frame recovery model). We evaluated the prediction accuracies of the two models, and our benchmark test revealed that frame recovery model significantly improved the prediction accuracy in comparison with basic model.