Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

Pavesi, Giulio; Mereghetti, Paolo; Mauri, Giancarlo; Pesole, Graziano

doi:10.1093/nar/gkh465

Cited by 441 publications

(434 citation statements)

References 14 publications

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“…To assess whether co-regulated genes possess a common r-regulatory signature, we searched for putative TF binding sites (TFBS) by de novo motif discovery 38 in the promoters of 63 stipe/rhizomorph and 28 cap/rhizomorph co-expressed genes as well as of those that showed constant high expression in all complex multicellular structures. The predicted motifs and their UPGMA trees is shown on Fig.…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

“…We used 1 kb sequences of co-expressed genes (which are most likely to contain their promoter), located upstream of the start codon, including 5' UTR, to predict putative TFBS. We performed de novo motif discovery in our co-expressed gene sets using Weeder 2.0 38,96 . We created frequency files from promoter regions of all genes of A. ostoyae using the Weeder2.0 frequencymaker.…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

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Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

et al. 2017

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T he genus Armillaria causes root rot disease in both gymnoand angiosperms, in forests, parks, and even vineyards in more than 500 host plant species 1 across the world. Most Armillaria species are facultative necrotrophs, which, after colonizing and killing the root cambium, transition to a saprobic phase, decomposing dead woody tissues of the host. As saprotrophs, Armillaria spp. are white rot (WR) fungi, which can efficiently decompose all components of plant cell walls, including lignin, (hemi-)cellulose and pectin 2 . They produce fleshy fruiting bodies (honey mushrooms) that appear in large clumps around infected plants and produce sexual spores. The vegetative phase of Armillaria is predominantly diploid rather than dikaryotic like most basidiomycetes.Individuals of Armillaria can reach immense sizes and include the 'humongous fungus' , one of the largest terrestrial organisms on Earth 3 , measuring up to 965 hectares and 600 tons 4 , and can display a mutation rate ≅ 3 orders of magnitude lower than most filamentous fungi 5 . Individuals reach this immense size via growing rhizomorphs, dark mycelial strings 1-4 mm wide that allow the fungus to bridge gaps between food sources or host plants 1,6 (hence the name shoestring root rot). Rhizomorphs develop through the aggregation and coordinated parallel growth of hyphae, similar to some fruiting body tissues 7,8 . As migratory and exploratory organs, rhizomorphs can grow approximately 1 m yr −1 and cross several metres underground in search for new hosts, although roles in uptake and longrange translocation of nutrients have also been proposed 1,9,10 . Root contact by rhizomorphs is the main mode of infection by the fungus, which makes the prevention of recurrent infection in Armillariacontaminated areas particularly difficult 1 . Despite their huge impact on forestry, horticulture and agriculture, the genetics of the pathogenicity of Armillaria species is poorly understood. The only -omics data published so far have highlighted a substantial repertoire of plant cell wall degrading enzymes (PCWDE) and secreted proteins, among others, in A. mellea and A. solidipes 11,12 , while analyses of the genomes of other pathogenic basidiomycetes (such as Moniliophthora 13,14 , Heterobasidion 15 and Rhizoctonia 16 ) identified genes coding for PCWDEs, secreted and effector proteins or secondary metabolism (SM) as putative pathogenicity factors. However, the lifecycle and unique dispersal strategy of Armillaria prefigure other evolutionary routes to pathogenicity, which, along with other potential genomic factors (such as transposable elements 17 ) are not yet known.Here, we investigate genome evolution and the origin of pathogenicity in Armillaria using comparative genomics, transcriptomics

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Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

et al. 2017

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“…Given the abundant appearance of silencers and EBs in our assay, we searched for the presence of novel DNA motifs using the programs MEME (Multiple Em for Motif Elicitation) (Bailey et al 2006) and Weeder (Pavesi et al 2004). MEME uses a gapless, local, multiple sequence alignment to search for statistically significant motifs in the input set compared to a random background set.…”

Section: Motif Analyses Of Silencer Elementsmentioning

confidence: 99%

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus

Petrykowska¹,

Vockley²,

Elnitski³

2008

Genome Res.

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Silencers and enhancer-blockers (EBs) are cis-acting, negative regulatory elements (NREs) that control interactions between promoters and enhancers. Although relatively uncharacterized in terms of biological mechanisms, these elements are likely to be abundant in the genome. We developed an experimental strategy to identify silencers and EBs using transient transfection assays. A known insulator and EB from the chicken beta-globin locus, cHS4, served as a control element for these assays. We examined 47 sequences from a 1.8-Mb region of human chromosome 7 for silencer and EB activities. The majority of functional elements displayed directional and promoter-specific activities. A limited number of sequences acted in a dual manner, as both silencers and EBs. We examined genomic data, epigenetic modifications, and sequence motifs within these regions. Strong silencer elements contained a novel CT-rich motif, often in multiple copies. Deletion of the motif from three regions caused a measurable loss of silencing ability in these sequences. Moreover, five duplicate occurrences of this motif were identified in the cHS4 insulator. These motifs provided an explanation for an uncharacterized silencing activity we measured in the insulator element. Overall, we identified 15 novel NREs, which contribute new insights into the prevalence and composition of sequences that negatively regulate gene expression.

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“…In this work, we target Weeder [9], a de novo motif-finding software package. It is one of the widely-used tools for de novo motif discovery [7], [12].…”

Section: Introductionmentioning

confidence: 99%

Accelerating Weeder: A DNA Motif Search Tool Using the Micron Automata Processor and FPGA

Wang

El-Hadedy

Skadron

et al. 2017

IEICE Trans. Inf. & Syst.

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SUMMARYMotif searching, i.e., identifying meaningful patterns from biological data, has been studied extensively due to its importance in the biomedical sciences. In this work, we seek to improve the performance of Weeder, a widely-used tool for automatic de novo motif searching. Weeder consists of several functions, among which we find that the function oligo scan, which handles the pattern matching, is the bottleneck, especially when dealing with large datasets. Motivated by this observation, we adopt the Micron Automata Processor (AP) to accelerate the pattern-matching stage of Weeder. The AP is a massively-parallel, nonvon-Neumann semiconductor architecture that is purpose-built for symbolic pattern matching. Relying on the fact that AP is capable of performing matching for thousands of patterns in parallel, we develop an APaccelerated Weeder implementation in this work. In particular, we describe how to map Weeder's pattern matching to the AP chip and use the high-end FPGA on the AP board to postprocess the output from AP. Our experiment shows that the AP-accelerated Weeder achieves 751x speedup on pattern matching, compared to a single-threaded CPU implementation.

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Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

Cited by 441 publications

References 14 publications

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus

Accelerating Weeder: A DNA Motif Search Tool Using the Micron Automata Processor and FPGA

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