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Epigenomic and functional characterization of a core DNA methyltransferase in the human pathogen Clostridium difficile

https://doi.org/10.1101/398891
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-1-4939-6361-4_10openalex-snapshot
Inducing and Quantifying Clostridium difficile Spore Formation
inferredcites →https://doi.org/10.1007/978-1-62703-646-7_8openalex-snapshot
MAFFT: Iterative Refinement and Additional Methods
inferredcites →https://doi.org/10.1016/j.anaerobe.2016.04.010openalex-snapshot
Sporulation properties and antimicrobial susceptibility in endemic and rare Clostridium difficile PCR ribotypes
inferredcites →https://doi.org/10.1016/j.cell.2007.11.009openalex-snapshot
The ATPase SpoIIIE Transports DNA across Fused Septal Membranes during Sporulation in Bacillus subtilis
inferredcites →https://doi.org/10.1016/j.mib.2013.01.011openalex-snapshot
Entering the era of bacterial epigenomics with single molecule real time DNA sequencing
inferredcites →https://doi.org/10.1016/j.mib.2015.03.004openalex-snapshot
DNA methylation in bacteria: from the methyl group to the methylome
inferredcites →https://doi.org/10.1016/j.tim.2014.04.003openalex-snapshot
Clostridium difficile spore biology: sporulation, germination, and spore structural proteins
inferredcites →https://doi.org/10.1016/s0378-1097(03)00795-xopenalex-snapshot
Gene transfer intoClostridium difficileCD630 and characterisation of its methylase genes
inferredcites →https://doi.org/10.1038/nature25178openalex-snapshot
Dietary trehalose enhances virulence of epidemic Clostridium difficile
inferredcites →https://doi.org/10.1038/nbt.2432openalex-snapshot
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
inferredcites →https://doi.org/10.1038/ncomms6055openalex-snapshot
A random six-phase switch regulates pneumococcal virulence via global epigenetic changes
inferredcites →https://doi.org/10.1038/ncomms8828openalex-snapshot
A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae
inferredcites →https://doi.org/10.1038/ng.2478openalex-snapshot
Emergence and global spread of epidemic healthcare-associated Clostridium difficile
inferredcites →https://doi.org/10.1038/ng.3530openalex-snapshot
A role for the bacterial GATC methylome in antibiotic stress survival
inferredcites →https://doi.org/10.1038/ng1830openalex-snapshot
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome
inferredcites →https://doi.org/10.1038/ng1956openalex-snapshot
A multistep epigenetic switch enables the stable inheritance of DNA methylation states
inferredcites →https://doi.org/10.1038/nmeth.1459openalex-snapshot
Direct detection of DNA methylation during single-molecule, real-time sequencing
inferredcites →https://doi.org/10.1038/nmeth.2924openalex-snapshot
Multiscale representation of genomic signals
inferredcites →https://doi.org/10.1038/nrdp.2016.20openalex-snapshot
Clostridium difficile infection
inferredcites →https://doi.org/10.1038/nrmicro.2016.108openalex-snapshot
Clostridium difficile colitis: pathogenesis and host defence
inferredcites →https://doi.org/10.1038/nrmicro1350openalex-snapshot
N6-methyl-adenine: an epigenetic signal for DNA–protein interactions
inferredcites →https://doi.org/10.1038/s41576-018-0081-3openalex-snapshot
Deciphering bacterial epigenomes using modern sequencing technologies
inferredcites →https://doi.org/10.1038/srep16923openalex-snapshot
Efficient Test and Visualization of Multi-Set Intersections
inferredcites →https://doi.org/10.1046/j.1365-2958.1999.01255.xopenalex-snapshot
A vital stain for studying membrane dynamics in bacteria: a novel mechanism controlling septation during Bacillus subtilis sporulation
inferredcites →https://doi.org/10.1053/j.gastro.2008.09.002openalex-snapshot
A Mouse Model of Clostridium difficile–Associated Disease
inferredcites →https://doi.org/10.1056/nejmoa1408913openalex-snapshot
Burden of Clostridium difficile Infection in the United States
inferredcites →https://doi.org/10.1073/pnas.1603257113openalex-snapshot
Regulation of genetic flux between bacteria by restriction–modification systems
inferredcites →https://doi.org/10.1093/bioinformatics/14.1.48openalex-snapshot
Combining evidence using p-values: application to sequence homology searches.
inferredcites →https://doi.org/10.1093/bioinformatics/bti610openalex-snapshot
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp356openalex-snapshot
Reordering contigs of draft genomes using the Mauve Aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/bts611openalex-snapshot
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btu042openalex-snapshot
Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/femspd/ftw061openalex-snapshot
Type IV pili promote early biofilm formation byClostridium difficile
inferredcites →https://doi.org/10.1093/molbev/msp259openalex-snapshot
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building
inferredcites →https://doi.org/10.1093/nar/30.7.1575openalex-snapshot
An efficient algorithm for large-scale detection of protein families
inferredcites →https://doi.org/10.1093/nar/gkg006openalex-snapshot
Rfam: an RNA family database
inferredcites →https://doi.org/10.1093/nar/gkg274openalex-snapshot
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
inferredcites →https://doi.org/10.1093/nar/gkm415openalex-snapshot
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
inferredcites →https://doi.org/10.1093/nar/gkr367openalex-snapshot
HMMER web server: interactive sequence similarity searching
inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
inferredcites →https://doi.org/10.1093/nar/gks891openalex-snapshot
The methylomes of six bacteria
inferredcites →https://doi.org/10.1093/nar/gku1046openalex-snapshot
REBASE—a database for DNA restriction and modification: enzymes, genes and genomes
inferredcites →https://doi.org/10.1093/nar/gku734openalex-snapshot
The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts
inferredcites →https://doi.org/10.1093/nar/gkv1483openalex-snapshot
OxyR-dependent formation of DNA methylation patterns in OpvABOFFand OpvABONcell lineages ofSalmonella enterica
inferredcites →https://doi.org/10.1093/nar/gky1038openalex-snapshot
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools
inferredcites →https://doi.org/10.1111/1469-0691.12619openalex-snapshot
The Clostridium difficile PCR ribotype 027 lineage: a pathogen on the move
inferredcites →https://doi.org/10.1111/1574-6968.12540openalex-snapshot
The regulatory network controlling spore formation in Clostridium difficile
inferredcites →https://doi.org/10.1111/mmi.12856openalex-snapshot
SpoIIID ‐mediated regulation of σ K function during C lostridium difficile sporulation
inferredcites →https://doi.org/10.1111/mmi.14090openalex-snapshot
Differential requirements for conserved peptidoglycan remodeling enzymes during Clostridioides difficile spore formation
inferredcites →https://doi.org/10.1128/iai.00147-12openalex-snapshot
The Clostridium difficile spo0A Gene Is a Persistence and Transmission Factor
inferredcites →https://doi.org/10.1128/iai.00943-17openalex-snapshot
Type IV Pili Promote Clostridium difficile Adherence and Persistence in a Mouse Model of Infection
inferredcites →https://doi.org/10.1128/iai.69.12.7197-7204.2001openalex-snapshot
Roles of DNA Adenine Methylation in Regulating Bacterial Gene Expression and Virulence
inferredcites →https://doi.org/10.1128/jb.00986-15openalex-snapshot
Characterization of Clostridium difficile Spores Lacking Either SpoVAC or Dipicolinic Acid Synthetase
inferredcites →https://doi.org/10.1128/jcm.16.6.1096-1101.1982openalex-snapshot
Investigation of an outbreak of antibiotic-associated colitis by various typing methods
inferredcites →https://doi.org/10.1128/mbio.02383-14openalex-snapshot
High-Throughput Analysis of Gene Essentiality and Sporulation in Clostridium difficile
inferredcites →https://doi.org/10.1128/mmbr.00016-06openalex-snapshot
Epigenetic Gene Regulation in the Bacterial World
inferredcites →https://doi.org/10.1128/msphere.00089-18openalex-snapshot
Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model
inferredcites →https://doi.org/10.1128/msystems.00063-17openalex-snapshot
Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes
inferredcites →https://doi.org/10.1142/9789814327732_0002openalex-snapshot
R'MES: A Tool to Find Motifs with a Significantly Unexpected Frequency in Biological Sequences
inferredcites →https://doi.org/10.1146/annurev-micro-090816-093549openalex-snapshot
Microbiota-Based Therapies for Clostridium difficile and Antibiotic-Resistant Enteric Infections
inferredcites →https://doi.org/10.1146/annurev.genet.40.110405.090442openalex-snapshot
Bacterial Contingency Loci: The Role of Simple Sequence DNA Repeats in Bacterial Adaptation
inferredcites →https://doi.org/10.1172/jci72336openalex-snapshot
Clostridium difficile and the microbiota
inferredcites →https://doi.org/10.1186/1471-2164-14-745openalex-snapshot
RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria
inferredcites →https://doi.org/10.1186/s12864-015-1252-7openalex-snapshot
Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1371/journal.pgen.1002039openalex-snapshot
c-di-GMP Turn-Over in Clostridium difficile Is Controlled by a Plethora of Diguanylate Cyclases and Phosphodiesterases
inferredcites →https://doi.org/10.1371/journal.pgen.1003660openalex-snapshot
Global Analysis of the Sporulation Pathway of Clostridium difficile
inferredcites →https://doi.org/10.1371/journal.pgen.1003756openalex-snapshot
Genome-Wide Analysis of Cell Type-Specific Gene Transcription during Spore Formation in Clostridium difficile
inferredcites →https://doi.org/10.1371/journal.pgen.1003782openalex-snapshot
The Spore Differentiation Pathway in the Enteric Pathogen Clostridium difficile
inferredcites →https://doi.org/10.1371/journal.pgen.1005562openalex-snapshot
Regulation of Clostridium difficile Spore Formation by the SpoIIQ and SpoIIIA Proteins
inferredcites →https://doi.org/10.1371/journal.pgen.1006312openalex-snapshot
A Recombination Directionality Factor Controls the Cell Type-Specific Activation of σK and the Fidelity of Spore Development in Clostridium difficile
inferredcites →https://doi.org/10.1371/journal.pgen.1006499openalex-snapshot
Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria
inferredcites →https://doi.org/10.1371/journal.pone.0011147openalex-snapshot
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
inferredcites →https://doi.org/10.1371/journal.pone.0048608openalex-snapshot
C. difficile 630Δerm Spo0A Regulates Sporulation, but Does Not Contribute to Toxin Production, by Direct High-Affinity Binding to Target DNA
inferredcites →https://doi.org/10.1371/journal.pone.0056051openalex-snapshot
Expanding the Repertoire of Gene Tools for Precise Manipulation of the Clostridium difficile Genome: Allelic Exchange Using pyrE Alleles
inferredcites →https://doi.org/10.1371/journal.pone.0144612openalex-snapshot
DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates
inferredcites →https://doi.org/10.1371/journal.ppat.1001061openalex-snapshot
Variations in TcdB Activity and the Hypervirulence of Emerging Strains of Clostridium difficile
inferredcites →https://doi.org/10.2217/fmb.14.2openalex-snapshot
Clostridium difficile Spores: A Major Threat to the Hospital Environment
inferredcites →https://doi.org/10.4161/gmic.19142openalex-snapshot
Cefoperazone-treated mice as an experimental platform to assess differential virulence ofClostridium difficilestrains
inferredcites →https://doi.org/10.4161/viru.26297openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.tim.2020.04.008openalex-snapshot
Epigenetics: A New Frontier in Probiotic Research
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