Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae
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Title
Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae
Authors
Keywords
Structural genomics, Gene expression, Fungal genomics, Sequence assembly tools, Sequence motif analysis, Chromatin, Genomic libraries, Repeated sequences
Journal
PLoS Genetics
Volume 14, Issue 10, Pages e1007467
Publisher
Public Library of Science (PLoS)
Online
2018-10-25
DOI
10.1371/journal.pgen.1007467
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Note: Only part of the references are listed.- Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen
- (2018) Lamprinos Frantzeskakis et al. BMC GENOMICS
- The fine balance between mutualism and antagonism in the Epichloë festucae –grass symbiotic interaction
- (2018) Barry Scott et al. CURRENT OPINION IN PLANT BIOLOGY
- Evolutionarily Conserved Principles Predict 3D Chromatin Organization
- (2017) M. Jordan Rowley et al. MOLECULAR CELL
- Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo
- (2017) Lars L. P. Hanssen et al. NATURE CELL BIOLOGY
- Widespread adenine N6-methylation of active genes in fungi
- (2017) Stephen J Mondo et al. NATURE GENETICS
- Form and function of topologically associating genomic domains in budding yeast
- (2017) Umut Eser et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Epichloë festucae antifungal protein has activity against the plant pathogen Sclerotinia homoeocarpa, the causal agent of dollar spot disease
- (2017) Zipeng Tian et al. Scientific Reports
- OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes
- (2016) Alison C. Testa et al. Genome Biology and Evolution
- A gapless genome sequence of the fungusBotrytis cinerea
- (2016) Jan A. L. Van Kan et al. MOLECULAR PLANT PATHOLOGY
- Regulatory activities of transposable elements: from conflicts to benefits
- (2016) Edward B. Chuong et al. NATURE REVIEWS GENETICS
- Organization and function of the 3D genome
- (2016) Boyan Bonev et al. NATURE REVIEWS GENETICS
- Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture
- (2016) Caelin Cubeñas-Potts et al. NUCLEIC ACIDS RESEARCH
- Normal chromosome conformation depends on subtelomeric facultative heterochromatin inNeurospora crassa
- (2016) Andrew D. Klocko et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- On TADs and LADs: Spatial Control Over Gene Expression
- (2016) Adriana Gonzalez-Sandoval et al. TRENDS IN GENETICS
- BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
- (2015) Felipe A. Simão et al. BIOINFORMATICS
- HiCdat: a fast and easy-to-use Hi-C data analysis tool
- (2015) Marc W. Schmid et al. BMC BIOINFORMATICS
- CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
- (2015) Zhonghui Tang et al. CELL
- The two-speed genomes of filamentous pathogens: waltz with plants
- (2015) Suomeng Dong et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
- A Core Gene Set Describes the Molecular Basis of Mutualism and Antagonism inEpichloëspp.
- (2015) Carla J. Eaton et al. MOLECULAR PLANT-MICROBE INTERACTIONS
- Accurate identification of centromere locations in yeast genomes using Hi-C
- (2015) N. Varoquaux et al. NUCLEIC ACIDS RESEARCH
- TopDom: an efficient and deterministic method for identifying topological domains in genomes
- (2015) Hanjun Shin et al. NUCLEIC ACIDS RESEARCH
- The 3D folding of metazoan genomes correlates with the association of similar repetitive elements
- (2015) Axel Cournac et al. NUCLEIC ACIDS RESEARCH
- Endophytic Epichloë species and their grass hosts: from evolution to applications
- (2015) Kari Saikkonen et al. PLANT MOLECULAR BIOLOGY
- Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome
- (2015) Luigi Faino et al. mBio
- MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis
- (2015) Kieu Thi Minh Pham et al. PLoS Genetics
- Models of chromosome structure
- (2014) Mario Nicodemi et al. CURRENT OPINION IN CELL BIOLOGY
- Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation
- (2014) François Le Dily et al. GENES & DEVELOPMENT
- Histone H3K9 and H3K27 methylation regulates fungal alkaloid biosynthesis in a fungal endophyte-plant symbiosis
- (2014) Tetsuya Chujo et al. MOLECULAR MICROBIOLOGY
- Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe
- (2014) Takeshi Mizuguchi et al. NATURE
- Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure
- (2014) Ralph S. Grand et al. NUCLEIC ACIDS RESEARCH
- Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
- (2014) Bruce J. Walker et al. PLoS One
- Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps
- (2014) Joshua N. Burton et al. G3-Genes Genomes Genetics
- Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans
- (2014) Jessica L. Soyer et al. PLoS Genetics
- Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms
- (2014) Martial Marbouty et al. eLife
- MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum
- (2013) Sarah M Schmidt et al. BMC GENOMICS
- A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs
- (2013) G. Andrey et al. SCIENCE
- The Fusarium graminearum Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters
- (2013) Lanelle R. Connolly et al. PLoS Genetics
- Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci
- (2013) Christopher L. Schardl et al. PLoS Genetics
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations
- (2012) Yu Zhang et al. CELL
- Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
- (2012) Guoliang Li et al. CELL
- Transcription factories: genetic programming in three dimensions
- (2012) Lucas Brandon Edelman et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
- Fungal endophytes of grasses
- (2012) Aiko Tanaka et al. CURRENT OPINION IN PLANT BIOLOGY
- New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species
- (2012) Lijuan Wei et al. Molecular Plant
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- Spatial partitioning of the regulatory landscape of the X-inactivation centre
- (2012) Elphège P. Nora et al. NATURE
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
- (2012) Cole Trapnell et al. Nature Protocols
- Identification of novel transcripts in annotated genomes using RNA-Seq
- (2011) A. Roberts et al. BIOINFORMATICS
- Abundant Degenerate Miniature Inverted-Repeat Transposable Elements in Genomes of Epichloid Fungal Endophytes of Grasses
- (2011) Damien J. Fleetwood et al. Genome Biology and Evolution
- SignalP 4.0: discriminating signal peptides from transmembrane regions
- (2011) Thomas Nordahl Petersen et al. NATURE METHODS
- Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis
- (2011) Stephen B. Goodwin et al. PLoS Genetics
- Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens
- (2011) Steven J. Klosterman et al. PLoS Pathogens
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
- (2010) Sven Heinz et al. MOLECULAR CELL
- A three-dimensional model of the yeast genome
- (2010) Zhijun Duan et al. NATURE
- Disruption of Signaling in a Fungal-Grass Symbiosis Leads to Pathogenesis
- (2010) C. J. Eaton et al. PLANT PHYSIOLOGY
- What triggers grass endophytes to switch from mutualism to pathogenism?
- (2010) Carla J. Eaton et al. PLANT SCIENCE
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- Target site selection by the mariner-like element, Mos1
- (2009) Gwénaelle Crénès et al. GENETICA
- Effects of endophytic fungi on some drought tolerance mechanisms of tall fescue in a hydroponics culture
- (2009) F. Bayat et al. RUSSIAN JOURNAL OF PLANT PHYSIOLOGY
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
- (2009) E. Lieberman-Aiden et al. SCIENCE
- Repeat induced point mutation in two asexual fungi, Aspergillus niger and Penicillium chrysogenum
- (2008) Ilka Braumann et al. CURRENT GENETICS
- CTCF-dependent enhancer-blocking by alternative chromatin loop formation
- (2008) C. Hou et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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