RNA-Rocket: an RNA-Seq analysis resource for infectious disease research

Transcriptional Regulation Analysis of Alzheimer's Disease Based on FastNCA Algorithm

Background:

Understanding the relationship between genetic variation and gene expression is a central issue in genetics. Although many studies have identified genetic variations associated with gene expression, it is unclear how they perturb the underlying regulatory network of gene expression.

Objective:

To explore how genetic variations perturb potential transcriptional regulation networks of Alzheimer’s disease (AD) to paint a more complete picture of the complex landscape of transcription regulation.

Methods:

Fast network component analysis (FastNCA), which can capture the genetic variations in the form of single nucleotide polymorphisms (SNPs), is applied to analyse the expression activities of TFs and their regulatory strengths on TGs using microarray and RNA-seq data of AD. Then, multi-data fusion analysis was used to analyze the different TGs regulated by the same TFs in the different data by constructing the transcriptional regulatory networks of differentially expressed genes.

Results:

the common TF regulating TGs are not necessarily identical in different data, they may be involved in the same pathways that are closely related to the pathogenesis of AD, such as immune response, signal transduction and cytokine-cytokine receptor interaction pathways. Even if they are involved in different pathways, these pathways are also confirmed to have a potential link with AD.

Conclusion:

The study shows that the pathways of different TGs regulated by the same TFs in different data are all closely related to AD. Multi-data fusion analysis can form a certain complement to some extent and get more comprehensive results in the process of exploring the pathogenesis of AD.

A Transcriptomic Approach to Identify Novel Drug Efflux Pumps in Bacteria

The core genomes of most bacterial species include a large number of genes encoding putative efflux pumps. The functional roles of most of these pumps are unknown, however, they are often under tight regulatory control and expressed in response to their substrates. Therefore, one way to identify pumps that function in antimicrobial resistance is to examine the transcriptional responses of efflux pump genes to antimicrobial shock. By conducting complete transcriptomic experiments following antimicrobial shock treatments, it may be possible to identify novel drug efflux pumps encoded in bacterial genomes. In this chapter we describe a complete workflow for conducting transcriptomic analyses by RNA sequencing, to determine transcriptional changes in bacteria responding to antimicrobials.

Dynamic Changes in the Splenic Transcriptome of Chickens during the Early Infection and Progress of Marek's Disease

Gallid alphaherpesvirus 2 (GaHV2) is an oncogenic avian herpesvirus inducing Marek’s disease (MD) and rapid-onset T-cell lymphomas. To reveal molecular events in MD pathogenesis and tumorigenesis, the dynamic splenic transcriptome of GaHV2-infected chickens during early infection and pathogenic phases has been determined utilizing RNA-seq. Based on the significant differentially expressed genes (DEGs), analysis of gene ontology, KEGG pathway and protein-protein interaction network has demonstrated that the molecular events happening during GaHV2 infection are highly relevant to the disease course. In the ‘Cornell Model’ description of MD, innate immune responses and inflammatory responses were established at early cytolytic phase but persisted until lymphoma formation. Humoral immunity in contrast began to play a role firstly in the intestinal system and started at late cytolytic phase. Neurological damage caused by GaHV2 is first seen in early cytolytic phase and is then sustained throughout the following phases over a long time period. During the proliferative phase many pathways associated with transcription and/or translation were significantly enriched, reflecting the cell transformation and lymphoma formation. Our work provides an overall view of host responses to GaHV2 infection and offers a meaningful basis for further studies of MD biology.

PerC Manipulates Metabolism and Surface Antigens in Enteropathogenic Escherichia coli

Enteropathogenic Escherichia coli is an important cause of profuse, watery diarrhea in infants living in developing regions of the world. Typical strains of EPEC (tEPEC) possess a virulence plasmid, while related clinical isolates that lack the pEAF plasmid are termed atypical EPEC (aEPEC). tEPEC and aEPEC tend to cause acute vs. more chronic type infections, respectively. The pEAF plasmid encodes an attachment factor as well as a regulatory operon, perABC. PerC, a poorly understood regulator, was previously shown to regulate expression of the type III secretion system through Ler. Here we elucidate the regulon of PerC using RNA sequencing analysis to better our understanding of the role of the pEAF in tEPEC infection. We demonstrate that PerC controls anaerobic metabolism by increasing expression of genes necessary for nitrate reduction. A tEPEC strain overexpressing PerC exhibited a growth advantage compared to a strain lacking this regulator, when grown anaerobically in the presence of nitrate, conditions mimicking the human intestine. We show that PerC strongly down-regulates type I fimbriae expression by manipulating fim phase variation. The quantities of a number of non-coding RNA molecules were altered by PerC. In sum, this protein controls niche adaptation, and could help to explain the function of the PerC homologs (Pch), many of which are encoded within prophages in related, Gram-negative pathogens.

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by ‘virtual integration’ to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.

De novo assembly and characterization of the Trichuris trichiura adult worm transcriptome using Ion Torrent sequencing

Infection with helminthic parasites, including the soil-transmitted helminth Trichuris trichiura (human whipworm), has been shown to modulate host immune responses and, consequently, to have an impact on the development and manifestation of chronic human inflammatory diseases. De novo derivation of helminth proteomes from sequencing of transcriptomes will provide valuable data to aid identification of parasite proteins that could be evaluated as potential immunotherapeutic molecules in near future. Herein, we characterized the transcriptome of the adult stage of the human whipworm T. trichiura, using next-generation sequencing technology and a de novo assembly strategy. Nearly 17.6 million high-quality clean reads were assembled into 6414 contiguous sequences, with an N50 of 1606bp. In total, 5673 protein-encoding sequences were confidentially identified in the T. trichiura adult worm transcriptome; of these, 1013 sequences represent potential newly discovered proteins for the species, most of which presenting orthologs already annotated in the related species T. suis. A number of transcripts representing probable novel non-coding transcripts for the species T. trichiura were also identified. Among the most abundant transcripts, we found sequences that code for proteins involved in lipid transport, such as vitellogenins, and several chitin-binding proteins. Through a cross-species expression analysis of gene orthologs shared by T. trichiura and the closely related parasites T. suis and T. muris it was possible to find twenty-six protein-encoding genes that are consistently highly expressed in the adult stages of the three helminth species. Additionally, twenty transcripts could be identified that code for proteins previously detected by mass spectrometry analysis of protein fractions of the whipworm somatic extract that present immunomodulatory activities. Five of these transcripts were amongst the most highly expressed protein-encoding sequences in the T. trichiura adult worm. Besides, orthologs of proteins demonstrated to have potent immunomodulatory properties in related parasitic helminths were also predicted from the T. trichiura de novo assembled transcriptome.

Identification of bacterial sRNA regulatory targets using ribosome profiling

Bacteria express large numbers of non-coding, regulatory RNAs known as ‘small RNAs’ (sRNAs). sRNAs typically regulate expression of multiple target messenger RNAs (mRNAs) through base-pairing interactions. sRNA:mRNA base-pairing often results in altered mRNA stability and/or altered translation initiation. Computational identification of sRNA targets is challenging due to the requirement for only short regions of base-pairing that can accommodate mismatches. Experimental approaches have been applied to identify sRNA targets on a genomic scale, but these focus only on those targets regulated at the level of mRNA stability. Here, we utilize ribosome profiling (Ribo-seq) to experimentally identify regulatory targets of the Escherichia coli sRNA RyhB. We not only validate a majority of known RyhB targets using the Ribo-seq approach, but also discover many novel ones. We further confirm regulation of a selection of known and novel targets using targeted reporter assays. By mutating nucleotides in the mRNA of a newly discovered target, we demonstrate direct regulation of this target by RyhB. Moreover, we show that Ribo-seq distinguishes between mRNAs regulated at the level of RNA stability and those regulated at the level of translation. Thus, Ribo-seq represents a powerful approach for genome-scale identification of sRNA targets.

Cyclic di-GMP modulates gene expression in Lyme disease spirochetes at the tick-mammal interface to promote spirochete survival during the blood meal and tick-to-mammal transmission

Borrelia burgdorferi, the Lyme disease spirochete, couples environmental sensing and gene regulation primarily via the Hk1/Rrp1 two-component system (TCS) and Rrp2/RpoN/RpoS pathways. Beginning with acquisition, we reevaluated the contribution of these pathways to spirochete survival and gene regulation throughout the enzootic cycle. Live imaging of B. burgdorferi caught in the act of being acquired revealed that the absence of RpoS and the consequent derepression of tick-phase genes impart a Stay signal required for midgut colonization. In addition to the behavioral changes brought on by the RpoS-off state, acquisition requires activation of cyclic di-GMP (c-di-GMP) synthesis by the Hk1/Rrp1 TCS; B. burgdorferi lacking either component is destroyed during the blood meal. Prior studies attributed this dramatic phenotype to a metabolic lesion stemming from reduced glycerol uptake and utilization. In a head-to-head comparison, however, the B. burgdorferi Δglp mutant had a markedly greater capacity to survive tick feeding than B. burgdorferi Δhk1 or Δrrp1 mutants, establishing unequivocally that glycerol metabolism is only one component of the protection afforded by c-di-GMP. Data presented herein suggest that the protective response mediated by c-di-GMP is multifactorial, involving chemotactic responses, utilization of alternate substrates for energy generation and intermediary metabolism, and remodeling of the cell envelope as a means of defending spirochetes against threats engendered during the blood meal. Expression profiling of c-di-GMP-regulated genes through the enzootic cycle supports our contention that the Hk1/Rrp1 TCS functions primarily, if not exclusively, in ticks. These data also raise the possibility that c-di-GMP enhances the expression of a subset of RpoS-dependent genes during nymphal transmission.