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References from Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures. Local targets link to admitted publications; unresolved targets remain external evidence.
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea
10.1371/journal.pgen.1002230 · 2011 · External reference
Genetic Control and Host Range of Avirulence Toward <i>Brassica napus</i> Cultivars Quinta and Jet Neuf in <i>Leptosphaeria maculans</i>
10.1094/phyto.2001.91.1.70 · 2001 · External reference
The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo
10.3390/ijms22158233 · 2021 · External reference
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes
10.3390/jof4010039 · 2018 · External reference
Trimmomatic: a flexible trimmer for Illumina sequence data
10.1093/bioinformatics/btu170 · 2014 · External reference
Ferulic acid, an efficient inhibitor of type B trichothecene biosynthesis and Tri gene expression in Fusarium liquid cultures
10.1016/j.mycres.2009.02.010 · 2009 · External reference
DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum
10.1186/1471-2164-15-347 · 2014 · External reference
DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing
10.1101/gr.142067.112 · 2012 · External reference
Heavy transcription of yeast genes correlates with differential loss of histone H2B relative to H4 and queued RNA polymerases
10.1093/nar/gku1013 · 2014 · External reference
Nonproteinaceous effectors: the <i>terra incognita</i> of plant–fungal interactions
10.1111/nph.15785 · 2019 · External reference
Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete?
10.1093/femsre/fuz018 · 2019 · External reference
A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen
10.7554/elife.62208 · 2020 · External reference
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
10.1126/science.1162228 · 2008 · External reference
The <i>Fusarium graminearum</i> Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization
10.1126/science.1143708 · 2007 · External reference
Transcriptome analysis reveals infection strategies employed by Fusarium graminearum as a root pathogen
10.1016/j.micres.2021.126951 · 2022 · External reference
STAR: ultrafast universal RNA-seq aligner
10.1093/bioinformatics/bts635 · 2012 · External reference
Boty, a long-terminal-repeat retroelement in the phytopathogenic fungus Botrytis cinerea
10.1128/aem.61.1.103-108.1995 · 1995 · External reference
De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing
10.1038/sdata.2018.235 · 2018 · External reference
Emerging fungal threats to animal, plant and ecosystem health
10.1038/nature10947 · 2012 · External reference
nucleR: a package for non-parametric nucleosome positioning
10.1093/bioinformatics/btr345 · 2011 · External reference
Heterochromatin-Like Regions as Ecological Niches for Avirulence Genes in the <i>Leptosphaeria maculans</i> Genome: Map-Based Cloning of <i>AvrLm6</i>
10.1094/mpmi-20-4-0459 · 2007 · External reference
Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant
10.1186/s12915-021-00989-3 · 2021 · External reference
Reb1, Cbf1, and Pho4 Bias Histone Sliding and Deposition Away from Their Binding Sites
10.1128/mcb.00472-21 · 2022 · External reference
Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens
10.1186/1471-2164-15-891 · 2014 · External reference
Gene expression shifts during perithecium development in Gibberella zeae (anamorph Fusarium graminearum), with particular emphasis on ion transport proteins
10.1016/j.fgb.2007.04.007 · 2007 · External reference
Fungal Diversity Revisited: 2.2 to 3.8 Million Species
10.1128/microbiolspec.funk-0052-2016 · 2017 · External reference
Nucleosome Organization Affects the Sensitivity of Gene Expression to Promoter Mutations
10.1016/j.molcel.2012.02.019 · 2012 · External reference
CAM: A quality control pipeline for MNase-seq data
10.1371/journal.pone.0182771 · 2017 · External reference
Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing <i>in Vivo</i>
10.1534/g3.115.020271 · 2015 · External reference
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
10.1186/gb-2009-10-10-r109 · 2009 · External reference
A unified computational framework for modeling genome-wide nucleosome landscape
10.1088/1478-3975/aadad2 · 2018 · External reference
The DNA-encoded nucleosome organization of a eukaryotic genome
10.1038/nature07667 · 2008 · External reference
Analysis of the Molecular Dialogue Between Gray Mold (<i>Botrytis cinerea</i>) and Grapevine (<i>Vitis vinifera</i>) Reveals a Clear Shift in Defense Mechanisms During Berry Ripening
10.1094/mpmi-02-15-0039-r · 2015 · External reference
The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum
10.1186/s12864-015-1756-1 · 2015 · External reference
Annotation of Fusarium graminearum (PH-1) Version 5.0
10.1128/genomea.01479-16 · 2017 · External reference
Genomic Nucleosome Organization Reconstituted with Pure Proteins
10.1016/j.cell.2016.09.045 · 2016 · External reference
Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
10.1126/science.1229386 · 2013 · External reference
Fast gapped-read alignment with Bowtie 2
10.1038/nmeth.1923 · 2012 · External reference
Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae
10.1038/nsmb.1741 · 2010 · External reference
Landscape of genomic diversity and host adaptation in Fusarium graminearum
10.1186/s12864-017-3524-x · 2017 · External reference
RNA-Seq gene expression estimation with read mapping uncertainty
10.1093/bioinformatics/btp692 · 2009 · External reference
Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density
10.1128/mcb.01070-14 · 2015 · External reference
Fungal Effectors and Plant Susceptibility
10.1146/annurev-arplant-043014-114623 · 2015 · External reference
Global remodeling of nucleosome positions in C. elegans
10.1186/1471-2164-14-284 · 2013 · External reference
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells
10.1101/gad.2005511 · 2011 · External reference
Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus
10.1093/bioinformatics/btp413 · 2009 · External reference
Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete <i>Mixia osmundae</i> revealed by mono- and dinucleosome mapping
10.1098/rsob.120043 · 2012 · External reference
Genome information processing by the INO80 chromatin remodeler positions nucleosomes
10.1038/s41467-021-23016-z · 2021 · External reference
Ruler elements in chromatin remodelers set nucleosome array spacing and phasing
10.1038/s41467-021-23015-0 · 2021 · External reference
The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing <i>in vivo</i>
10.1093/nar/gkw068 · 2016 · External reference
Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination
10.1101/gr.242032.118 · 2019 · External reference
Collaborative Annotation Redefines Gene Sets for Crucial Phytopathogens
10.3389/fmicb.2019.02477 · 2019 · External reference
Nucleosome landscape and control of transcription in the human malaria parasite
10.1101/gr.101063.109 · 2010 · External reference
The botrydial biosynthetic gene cluster of Botrytis cinerea displays a bipartite genomic structure and is positively regulated by the putative Zn(II)2Cys6 transcription factor BcBot6
10.1016/j.fgb.2016.10.003 · 2016 · External reference
Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea
10.1186/s13059-021-02446-4 · 2021 · External reference
Nucleosome positioning: How is it established, and why does it matter?
10.1016/j.ydbio.2009.06.012 · 2010 · External reference
Structure and Function of Chromatin Remodelers
10.1016/j.jmb.2021.166929 · 2021 · External reference
The structure of DNA in the nucleosome core
10.1038/nature01595 · 2003 · External reference
EM measurements define the dimensions of the “30-nm” chromatin fiber: Evidence for a compact, interdigitated structure
10.1073/pnas.0601212103 · 2006 · External reference
Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
10.1038/ncomms1189 · 2011 · External reference
Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites
10.1186/1471-2164-15-848 · 2014 · External reference
The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens
10.1146/annurev-phyto-080516-035303 · 2018 · External reference
Sequence periodicities in chicken nucleosome core DNA
10.1016/0022-2836(86)90452-3 · 1986 · External reference
A genomic code for nucleosome positioning
10.1038/nature04979 · 2006 · External reference
Poly(dA:dT) tracts: major determinants of nucleosome organization
10.1016/j.sbi.2009.01.004 · 2009 · External reference
What controls nucleosome positions?
10.1016/j.tig.2009.06.002 · 2009 · External reference
The transcription cycle in eukaryotes: From productive initiation to RNA polymerase II recycling
10.1016/j.bbagrm.2012.01.010 · 2012 · External reference
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
10.1093/bioinformatics/btv351 · 2015 · External reference
Screening of a Botrytis cinerea one-hybrid library reveals a Cys2His2 transcription factor involved in the regulation of secondary metabolism gene clusters
10.1016/j.fgb.2013.01.006 · 2013 · External reference
Nucleosome Positioning and Spacing: From Mechanism to Function
10.1016/j.jmb.2021.166847 · 2021 · External reference
Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans
10.1371/journal.pgen.1004227 · 2014 · External reference
Chromatin analyses of Zymoseptoria tritici : Methods for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq)
10.1016/j.fgb.2015.03.006 · 2015 · External reference
To B or not to B: a tale of unorthodox chromosomes
10.1016/j.mib.2018.01.012 · 2018 · External reference
Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization
10.1007/s10577-021-09658-1 · 2021 · External reference
Chromatin-based control of effector gene expression in plant-associated fungi
10.1016/j.pbi.2015.05.025 · 2015 · External reference
Determinants of nucleosome positioning
10.1038/nsmb.2506 · 2013 · External reference
Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structure
10.1139/o10-139 · 2011 · External reference
The importance of fungi in shaping the paleoecosystem
10.1016/0034-6667(95)00086-0 · 1996 · External reference
High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
10.1371/journal.pone.0009129 · 2010 · External reference
Two strategies for gene regulation by promoter nucleosomes
10.1101/gr.076059.108 · 2008 · External reference
Plant-Pathogen Effectors: Cellular Probes Interfering with Plant Defenses in Spatial and Temporal Manners
10.1146/annurev-phyto-080615-100204 · 2016 · External reference
The Role of Nucleosome Positioning in the Evolution of Gene Regulation
10.1371/journal.pbio.1000414 · 2010 · External reference
A high-resolution, nucleosome position map of <i>C. elegans</i> reveals a lack of universal sequence-dictated positioning
10.1101/gr.076463.108 · 2008 · External reference
Determinants of nucleosome organization in primary human cells
10.1038/nature10002 · 2011 · External reference
A gapless genome sequence of the fungus <i>Botrytis cinerea</i>
10.1111/mpp.12384 · 2016 · External reference
A canonical promoter organization of the transcription machinery and its regulators in the <i>Saccharomyces</i> genome
10.1101/gr.084970.108 · 2009 · External reference
Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome
10.1038/s41586-020-2088-0 · 2020 · External reference
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
10.1093/molbev/msx319 · 2017 · External reference
Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways
10.1126/science.1239705 · 2013 · External reference
A conserved role of the RSC chromatin remodeler in the establishment of nucleosome-depleted regions
10.1007/s00294-016-0642-y · 2016 · External reference
Genome-Scale Identification of Nucleosome Positions in <i>S. cerevisiae</i>
10.1126/science.1112178 · 2005 · External reference
Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants
10.1104/pp.15.00125 · 2015 · External reference
Distinct Transcriptomic Reprogramming in the Wheat Stripe Rust Fungus During the Initial Infection of Wheat and Barberry
10.1094/mpmi-08-20-0244-r · 2021 · External reference
Structural insights of nucleosome and the 30-nm chromatin fiber
10.1016/j.sbi.2016.01.013 · 2016 · External reference