TSSFinder—fast and accurate<i>ab initio</i>prediction of the core promoter in eukaryotic genomes

Oliveira, Mona N.; Bonadio, Ígor; Melo, Alicia Lie de; Souza, Gláucia Mendes; Durham, Alan Mitchell

doi:10.1093/bib/bbab198

Cited by 13 publications

(9 citation statements)

References 58 publications

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“…A new algorithm and software package for TSS search, TSSFinder, has recently been developed based on the linear chain conditional random fields (LCCRFs) method [ 24 ]. Compared with the other algorithms, TSSFinder shows high accuracy in detecting TSSs of coding genes, whereas for the genes with a dispersed TSS signal, it determines the TSS closest to the start codon.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, a problem that cannot be solved by the currently developed mathematical methods is the generation of a large number of false positives. Thus, even the best promoter search programs produce one false positive result per 20,000 bp [ 19 , 20 , 21 , 22 , 23 , 24 , 25 ], which, if extrapolated to a whole genome of about 3 × 10 9 bp, yields more than 300,000 false positives. Given that such a genome contains over 10 4 genes, it means that the number of false positives exceeds that of gene promoters by several times.…”

Section: Introductionmentioning

confidence: 99%

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Database of Potential Promoter Sequences in the Capsicum annuum Genome

Rudenko

Korotkov

2022

Biology

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In this study, we used a mathematical method for the multiple alignment of highly divergent sequences (MAHDS) to create a database of potential promoter sequences (PPSs) in the Capsicum annuum genome. To search for PPSs, 20 statistically significant classes of sequences located in the range from −499 to +100 nucleotides near the annotated genes were calculated. For each class, a position–weight matrix (PWM) was computed and then used to identify PPSs in the C. annuum genome. In total, 825,136 PPSs were detected, with a false positive rate of 0.13%. The PPSs obtained with the MAHDS method were tested using TSSFinder, which detects transcription start sites. The databank of the found PPSs provides their coordinates in chromosomes, the alignment of each PPS with the PWM, and the level of statistical significance as a normal distribution argument, and can be used in genetic engineering and biotechnology.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Database of Potential Promoter Sequences in the Capsicum annuum Genome

Rudenko

Korotkov

2022

Biology

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“…Potato peroxidases were identified with protein sequence BLAST against the RedoxiBase database 56 and the secretory signal peptides were predicted with SignalP 5.0 57 (Supplementary Table 5). Predictions of transcription factor binding motifs in promoter sequences were performed with TRANSFAC 58 and predictions of transcription start sites with TSSFinder 59 .…”

Section: Methodsmentioning

confidence: 99%

A mini-TGA protein, lacking a functional DNA-binding domain, modulates gene expression through heterogeneous association with transcription factors

Tomaž

Petek

Lukan

et al. 2022

Preprint

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TGA transcription factors, which bind their target DNA through a conserved basic region leucine zipper (bZIP) domain, are vital regulators of gene expression in salicylic acid (SA)-mediated plant immunity. Here, we investigate the role of StTGA2.1, a potato TGA lacking the full bZIP, which we name a mini-TGA. Such truncated proteins have been widely assigned as loss-of-function mutants. We, however, confirm that StTGA2.1 overexpression compensates for SA-deficiency. To understand the underlying mechanisms, we show that StTGA2.1 can physically interact with StTGA2.2 and StTGA2.3, while its interaction with DNA was not detected. We investigate the changes in transcriptional regulation due to StTGA2.1 overexpression, identifying direct and indirect target genes. Using in planta transactivation assays, we confirm that StTGA2.1 interacts with StTGA2.3 to activate StPRX07, a member of class III peroxidases, which are known to play role in immune response. Finally, via structural modelling and molecular dynamics simulations, we hypothesise that the compact molecular architecture of StTGA2.1 distorts DNA conformation upon heterodimer binding to enable transcriptional activation. This study demonstrates how protein truncation can lead to novel functions and that such events should be studied carefully in other protein families.

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“…Several computational approaches have been developed to provide fast and accurate ways to predict the location of TSSs and regulatory motifs on the whole-genome scale. These include Bayesian classification based on positional densities of oligonucleotides for detecting TSS in human genomic sequences [19], neural networks for predicting TSS in plant promoters [20,21], and conditional random fields for identifying TSS in eukaryotic promoters [22]. Strategies for genome-wide discovery of novel cis-regulatory motifs using position weight matrices (PWMs) and expression data were successfully implemented for rice and Arabidopsis [6,23], hop [24], and grapevine [25].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Prediction of Transcription Start Sites in Conifers

Bondar

Troukhan²,

Krutovsky

et al. 2022

IJMS

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The identification of promoters is an essential step in the genome annotation process, providing a framework for gene regulatory networks and their role in transcription regulation. Despite considerable advances in the high-throughput determination of transcription start sites (TSSs) and transcription factor binding sites (TFBSs), experimental methods are still time-consuming and expensive. Instead, several computational approaches have been developed to provide fast and reliable means for predicting the location of TSSs and regulatory motifs on a genome-wide scale. Numerous studies have been carried out on the regulatory elements of mammalian genomes, but plant promoters, especially in gymnosperms, have been left out of the limelight and, therefore, have been poorly investigated. The aim of this study was to enhance and expand the existing genome annotations using computational approaches for genome-wide prediction of TSSs in the four conifer species: loblolly pine, white spruce, Norway spruce, and Siberian larch. Our pipeline will be useful for TSS predictions in other genomes, especially for draft assemblies, where reliable TSS predictions are not usually available. We also explored some of the features of the nucleotide composition of the predicted promoters and compared the GC properties of conifer genes with model monocot and dicot plants. Here, we demonstrate that even incomplete genome assemblies and partial annotations can be a reliable starting point for TSS annotation. The results of the TSS prediction in four conifer species have been deposited in the Persephone genome browser, which allows smooth visualization and is optimized for large data sets. This work provides the initial basis for future experimental validation and the study of the regulatory regions to understand gene regulation in gymnosperms.

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TSSFinder—fast and accurateab initioprediction of the core promoter in eukaryotic genomes

Cited by 13 publications

References 58 publications

Database of Potential Promoter Sequences in the Capsicum annuum Genome

Database of Potential Promoter Sequences in the Capsicum annuum Genome

A mini-TGA protein, lacking a functional DNA-binding domain, modulates gene expression through heterogeneous association with transcription factors

Genome-Wide Prediction of Transcription Start Sites in Conifers

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