TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Background

A strong focus of the post-genomic era is mining of the non-coding regulatory genome in order to unravel the function of regulatory elements that coordinate gene expression (Nat 489:57–74, 2012; Nat 507:462–70, 2014; Nat 507:455–61, 2014; Nat 518:317–30, 2015). Whole-genome approaches based on next-generation sequencing (NGS) have provided insight into the genomic location of regulatory elements throughout different cell types, organs and organisms. These technologies are now widespread and commonly used in laboratories from various fields of research. This highlights the need for fast and user-friendly software tools dedicated to extracting cis-regulatory information contained in these regulatory regions; for instance transcription factor binding site (TFBS) composition. Ideally, such tools should not require prior programming knowledge to ensure they are accessible for all users.

Results

We present TrawlerWeb, a web-based version of the Trawler_standalone tool (Nat Methods 4:563–5, 2007; Nat Protoc 5:323–34, 2010), to allow for the identification of enriched motifs in DNA sequences obtained from next-generation sequencing experiments in order to predict their TFBS composition. TrawlerWeb is designed for online queries with standard options common to web-based motif discovery tools. In addition, TrawlerWeb provides three unique new features: 1) TrawlerWeb allows the input of BED files directly generated from NGS experiments, 2) it automatically generates an input-matched biologically relevant background, and 3) it displays resulting conservation scores for each instance of the motif found in the input sequences, which assists the researcher in prioritising the motifs to validate experimentally. Finally, to date, this web-based version of Trawler_standalone remains the fastest online de novo motif discovery tool compared to other popular web-based software, while generating predictions with high accuracy.

Conclusions

TrawlerWeb provides users with a fast, simple and easy-to-use web interface for de novo motif discovery. This will assist in rapidly analysing NGS datasets that are now being routinely generated. TrawlerWeb is freely available and accessible at: http://trawler.erc.monash.edu.au.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4630-0) contains supplementary material, which is available to authorized users.

Gill structural change in response to turbidity has no effect on the oxygen uptake of a juvenile sparid fish

Turbidity as a result of increased suspended sediments in coastal waters is an environmental stress of worldwide concern. Recent research on fish suggests that detrimental changes to gill structure can occur in turbid waters, with speculation that these alterations diminish fitness variables, such as growth and development, by negatively impacting the O₂ uptake capacity (respiration) of fish. Specifically to address this unknown, the impact of turbid water on the gill structure, somatic growth rate and O₂ uptake rates of a juvenile sparid species (Pagrus auratus) was addressed following exposure to five different turbidity treatments (<10, 20, 40, 60 or 80 nephelometric turbidity units) for 30 days. Significant gill structural change was apparent with a progressive increase in turbidity and was quantified as a reduction in lamellar density, as well as an increase in basal hyperplasia, epithelial lifting and increased oxygen diffusion distance across the lamellae. The weight of control fish did not change throughout the experiment, but all fish exposed to turbid waters lost weight, and weight loss increased with nephelometric turbidity units, confirming that long-term turbidity exposure is detrimental to growth productivity. The growth of fish could be impacted in a variety of ways, but the specific hypothesis that structural alteration of the gills impairs O₂ uptake across the gills and limits growth fitness was not supported because there was no measurable difference in the standard metabolic rate, maximal metabolic rate, aerobic metabolic scope or critical oxygen saturation limit of fish measured in clear water after 30 days of exposure. Although impaired O₂ uptake as a result of structurally adjusted gills is unlikely to be the cause of poor fish growth, the exact mechanism by which growth productivity is affected in turbid conditions remains unclear and warrants further investigation.

Interferon-ε protects the female reproductive tract from viral and bacterial infection

The innate immune system senses pathogens through pattern-recognition receptors (PRRs) that signal to induce effector cytokines, such as type I interferons (IFNs). We characterized IFN-ε as a type I IFN because it signaled via the Ifnar1 and Ifnar2 receptors to induce IFN-regulated genes. In contrast to other type I IFNs, IFN-ε was not induced by known PRR pathways; instead, IFN-ε was constitutively expressed by epithelial cells of the female reproductive tract (FRT) and was hormonally regulated. Ifn-ε-deficient mice had increased susceptibility to infection of the FRT by the common sexually transmitted infections (STIs) herpes simplex virus 2 and Chlamydia muridarum. Thus, IFN-ε is a potent antipathogen and immunoregulatory cytokine that may be important in combating STIs that represent a major global health and socioeconomic burden.

Interferome v2.0: an updated database of annotated interferon-regulated genes

Interferome v2.0 (http://interferome.its.monash.edu.au/interferome/) is an update of an earlier version of the Interferome DB published in the 2009 NAR database edition. Vastly improved computational infrastructure now enables more complex and faster queries, and supports more data sets from types I, II and III interferon (IFN)-treated cells, mice or humans. Quantitative, MIAME compliant data are collected, subjected to thorough, standardized, quantitative and statistical analyses and then significant changes in gene expression are uploaded. Comprehensive manual collection of metadata in v2.0 allows flexible, detailed search capacity including the parameters: range of -fold change, IFN type, concentration and time, and cell/tissue type. There is no limit to the number of genes that can be used to search the database in a single query. Secondary analysis such as gene ontology, regulatory factors, chromosomal location or tissue expression plots of IFN-regulated genes (IRGs) can be performed in Interferome v2.0, or data can be downloaded in convenient text formats compatible with common secondary analysis programs. Given the importance of IFN to innate immune responses in infectious, inflammatory diseases and cancer, this upgrade of the Interferome to version 2.0 will facilitate the identification of gene signatures of importance in the pathogenesis of these diseases.

Repression of human gamma-globin gene expression by a short isoform of the NF-E4 protein is associated with loss of NF-E2 and RNA polymerase II recruitment to the promoter

Binding of the stage selector protein (SSP) to the stage selector element (SSE) in the human gamma-globin promoter contributes to the preferential expression of the gamma-gene in fetal erythroid cells. The SSP contains the transcription factor CP2 and an erythroid-specific partner, NF-E4. The NF-E4 gene encodes a 22-kDa polypeptide employing a non-AUG initiation codon. Antisera specific to NF-E4 detects this species and an additional 14 kDa protein, which initiates from an internal methionine. Enforced expression of p14 NF-E4 in the K562 fetal/erythroid cell line, and in primary erythroid cord blood progenitors, results in repression of gamma-gene expression. Biochemical studies reveal that p14 NF-E4 interacts with CP2, resulting in diminished association of CP2 with the SSE in chromatin immunoprecipitation assays. p45 NF-E2 recruitment to the gamma-promoter is also lost, resulting in a reduction in RNA polymerase II and TBP binding and a fall in promoter transcriptional activity. This effect is specific, as enforced expression of a mutant form of p14 NF-E4, which fails to interact with CP2, also fails to repress gamma-gene expression in K562 cells. These findings provide one potential mechanism that could contribute to the autonomous silencing of the human gamma-genes in adult erythroid cells.

Site-specific acetylation of the fetal globin activator NF-E4 prevents its ubiquitination and regulates its interaction with the histone deacetylase, HDAC1

Acetylation provides one mechanism by which the functional diversity of individual transcription factors can be expanded. This is valuable in the setting of complex multigene loci that are regulated by a limited number of proteins, such as the human beta-globin locus. We have studied the role of acetylation in the regulation of the transcription factor NF-E4, a component of a protein complex that facilitates the preferential expression of the human gamma-globin genes in fetal erythroid cells. We have shown that NF-E4 interacts directly with, and serves as a substrate for, the acetyltransferase co-activator PCAF. Acetylation of NF-E4 is restricted to a single residue (Lys(43)) in the amino-terminal domain of the protein and results in two important functional consequences. Acetylation of NF-E4 prolongs the protein half-life by preventing ubiquitin-mediated degradation. This stabilization is PCAF-dependent, since enforced expression in fetal/erythroid cells of a mutant form of PCAF lacking the histone acetyltransferase domain (PCAFDeltaHAT) decreases NF-E4 stability. Acetylation of Lys(43) also reduces the interaction between NF-E4 and HDAC1, potentially maximizing the activating ability of the factor at the gamma-promoter. These results provide further demonstration that co-activators, such as PCAF, can influence individual transcription factor properties at multiple levels to alter their effects on gene expression.

The Role of p22 NF-E4 in Human Globin Gene Switching

The human stage selector protein, a complex containing the ubiquitous transcription factor CP2 and the erythroid-specific factor p22 NF-E4, facilitates the interaction of the gamma-globin genes with the locus control region in fetal erythroid cells. Enforced expression of p22 NF-E4 in K562 cells and human cord blood progenitors increases fetal globin gene expression, and in progenitors, reduces beta-globin expression. To examine the role of NF-E4 in an in vivo model of hemoglobin switching, we enforced the expression of p22 NF-E4 in transgenic mice carrying the human beta-globin locus yeast artificial chromosome. Although murine erythropoiesis and globin gene expression is unaffected in these mice, the expression profile of the human globin genes is altered. All three transgenic lines displayed an increased gamma:beta-globin ratio in E12.5-14.5 fetal liver, resulting in a delay in the fetal/adult switch. At E12.5, this is primarily due to a reduction of beta-gene expression, whereas at E14.5, the increased gamma:beta ratio is due to enhanced gamma-gene expression. Despite this, the switch in globin subtype is fully completed in the adult bone marrow. These findings indicate that p22 NF-E4 is capable of influencing human globin gene expression in vivo but is incapable of overriding the intrinsic mechanisms governing gamma-gene silencing in this context.

Enterovirus-specific IgM in the diagnosis of meningitis

Samples of serum from 557 patients with a clinical diagnosis of meningitis or encephalitis and referred to the Epsom Public Health Laboratory during a period of 3 years were tested for enterovirus-specific IgM in a mu capture enzyme-linked immunosorbent assay (ELISA). Enterovirus-specific IgM was detected in 45% samples from all age groups. In the 3-5-year age group, 67% specimens were positive. A notable male predominance (73%) was seen in the age group 0-15 years. As predicted, a seasonal increase in incidence was found in the summer and autumn months. Data from a questionnaire sent to the referring laboratories showed only a 5% enterovirus isolation rate from cerebrospinal fluids when isolation of a virus was attempted. The enterovirus IgM ELISA is a sensitive economical and rapid method for use in the diagnosis of viral meningitis.

Coxsackie viruses and diabetes mellitus

Serum specimens from 162 patients with insulin-dependent diabetes of recent onset and 319 controls were tested for neutralizing antibodies to Coxsackie viruses types B1 to B5. Antibody to type B4 virus was more often found in diabetics than in controls, particularly in the 10-19 year age group. Though controls were not matched for geographical area it was thought that this was unlikely to explain the difference found. The month of onset of diabetes in the patients studied showed a pronounced seasonal incidence, which resembled that found in earlier studies.