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Title: Widespread adenine N6-methylation of active genes in fungi

Abstract

N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes1,2,3,4, but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in early-diverging fungal lineages5. Using single-molecule long-read sequencing of 16 diverse fungal genomes, we observed that up to 2.8% of all adenines were methylated in early-diverging fungi, far exceeding levels observed in other eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT dinucleotides and was concentrated in dense methylated adenine clusters surrounding the transcriptional start sites of expressed genes; its distribution was inversely correlated with that of 5-methylcytosine. Our results show a striking contrast in the genomic distributions of 6mA and 5-methylcytosine and reinforce a distinct role for 6mA as a gene-expression-associated epigenomic mark in eukaryotes.

Authors:
 [1];  [2];  [1];  [1];  [3];  [1];  [1];  [1];  [1];  [4];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [5] more »;  [3];  [6];  [7];  [7];  [8];  [9]; ORCiD logo [10];  [11]; ORCiD logo [12];  [4] « less
+ Show Author Affiliations
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Roche Sequencing Solutions Inc., Pleasanton, CA (United States)
  3. Univ. of Georgia, Athens, GA (United States). Dept. of Genetics
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); The Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
  6. L. F. Lambert Spawn Co., Coatesville, PA (United States)
  7. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  8. Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Ecology and Evolutionary Biology
  9. Univ. of California, Santa Barbara, CA (United States). Dept. of Chemical Engineering
  10. Univ. of California, Riverside, CA (United States). Dept. of Plant Pathology and Microbiology
  11. Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology
  12. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Merced, CA (United States). School of Natural Sciences
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of California, Santa Barbara, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division; National Science Foundation (NSF); Pew Charitable Trusts
OSTI Identifier:
1469129
Alternate Identifier(s):
OSTI ID: 1485164
Grant/Contract Number:  
AC02-05CH11231; DEB-1441715; DEB-1441604; DEB-1354625; SC0010352; W911NF-09- 0001
Resource Type:
Accepted Manuscript
Journal Name:
Nature Genetics
Additional Journal Information:
Journal Volume: 49; Journal Issue: 6; Related Information: © 2017 Nature America, Inc., part of Springer Nature. All rights reserved.; Journal ID: ISSN 1061-4036
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Mondo, Stephen J., Dannebaum, Richard O., Kuo, Rita C., Louie, Katherine B., Bewick, Adam J., LaButti, Kurt, Haridas, Sajeet, Kuo, Alan, Salamov, Asaf, Ahrendt, Steven R., Lau, Rebecca, Bowen, Benjamin P., Lipzen, Anna, Sullivan, William, Andreopoulos, Bill B., Clum, Alicia, Lindquist, Erika, Daum, Christopher, Northen, Trent R., Kunde-Ramamoorthy, Govindarajan, Schmitz, Robert J., Gryganskyi, Andrii, Culley, David, Magnuson, Jon, James, Timothy Y., O'Malley, Michelle A., Stajich, Jason E., Spatafora, Joseph W., Visel, Axel, and Grigoriev, Igor V. Widespread adenine N6-methylation of active genes in fungi. United States: N. p., 2017. Web. doi:10.1038/ng.3859.
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Mondo, Stephen J., Dannebaum, Richard O., Kuo, Rita C., Louie, Katherine B., Bewick, Adam J., LaButti, Kurt, Haridas, Sajeet, Kuo, Alan, Salamov, Asaf, Ahrendt, Steven R., Lau, Rebecca, Bowen, Benjamin P., Lipzen, Anna, Sullivan, William, Andreopoulos, Bill B., Clum, Alicia, Lindquist, Erika, Daum, Christopher, Northen, Trent R., Kunde-Ramamoorthy, Govindarajan, Schmitz, Robert J., Gryganskyi, Andrii, Culley, David, Magnuson, Jon, James, Timothy Y., O'Malley, Michelle A., Stajich, Jason E., Spatafora, Joseph W., Visel, Axel, & Grigoriev, Igor V. Widespread adenine N6-methylation of active genes in fungi. United States. https://doi.org/10.1038/ng.3859
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Mondo, Stephen J., Dannebaum, Richard O., Kuo, Rita C., Louie, Katherine B., Bewick, Adam J., LaButti, Kurt, Haridas, Sajeet, Kuo, Alan, Salamov, Asaf, Ahrendt, Steven R., Lau, Rebecca, Bowen, Benjamin P., Lipzen, Anna, Sullivan, William, Andreopoulos, Bill B., Clum, Alicia, Lindquist, Erika, Daum, Christopher, Northen, Trent R., Kunde-Ramamoorthy, Govindarajan, Schmitz, Robert J., Gryganskyi, Andrii, Culley, David, Magnuson, Jon, James, Timothy Y., O'Malley, Michelle A., Stajich, Jason E., Spatafora, Joseph W., Visel, Axel, and Grigoriev, Igor V. Mon . "Widespread adenine N6-methylation of active genes in fungi". United States. https://doi.org/10.1038/ng.3859. https://www.osti.gov/servlets/purl/1469129.
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@article{osti_1469129,
title = {Widespread adenine N6-methylation of active genes in fungi},
author = {Mondo, Stephen J. and Dannebaum, Richard O. and Kuo, Rita C. and Louie, Katherine B. and Bewick, Adam J. and LaButti, Kurt and Haridas, Sajeet and Kuo, Alan and Salamov, Asaf and Ahrendt, Steven R. and Lau, Rebecca and Bowen, Benjamin P. and Lipzen, Anna and Sullivan, William and Andreopoulos, Bill B. and Clum, Alicia and Lindquist, Erika and Daum, Christopher and Northen, Trent R. and Kunde-Ramamoorthy, Govindarajan and Schmitz, Robert J. and Gryganskyi, Andrii and Culley, David and Magnuson, Jon and James, Timothy Y. and O'Malley, Michelle A. and Stajich, Jason E. and Spatafora, Joseph W. and Visel, Axel and Grigoriev, Igor V.},
abstractNote = {N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes1,2,3,4, but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in early-diverging fungal lineages5. Using single-molecule long-read sequencing of 16 diverse fungal genomes, we observed that up to 2.8% of all adenines were methylated in early-diverging fungi, far exceeding levels observed in other eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT dinucleotides and was concentrated in dense methylated adenine clusters surrounding the transcriptional start sites of expressed genes; its distribution was inversely correlated with that of 5-methylcytosine. Our results show a striking contrast in the genomic distributions of 6mA and 5-methylcytosine and reinforce a distinct role for 6mA as a gene-expression-associated epigenomic mark in eukaryotes.},
doi = {10.1038/ng.3859},
journal = {Nature Genetics},
number = 6,
volume = 49,
place = {United States},
year = {Mon May 08 00:00:00 EDT 2017},
month = {Mon May 08 00:00:00 EDT 2017}
}
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https://doi.org/10.1038/ng.3859
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Cited by: 205 works
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Figures / Tables:

Figure 1 Figure 1: Phylogenetic diversity of genomes sequenced in this study and associated 6mA features. (a) RAxML (ref. 20) maximum-likelihood phylogeny constructed including 285 single-copy genes from all lineages sequenced in this study and four references in which 6mA has been analyzed previously. Node ages indicate date of divergence, from ref.more » 5. Clades are colored at phylum, class and subphylum levels; bootstrap support for all nodes is 100 unless otherwise noted (shown in black at branches). Mya, million years ago; Bya, billion years ago. (b) Percent of total adenines methylated across all surveyed fungi plus outgroups. For additional data on cytosine methylation, see Supplementary Figure 8. ID abbreviations were generated for each lineage based on the first letter of the genus and first one or two letters of the species. (c) Methylation marks in early-diverging fungi are symmetric at ApT sites. The x axis shows the frequency of ApT methylation compared to any other adenine-containing dinucleotide (AV) combination. Although impacted by GC content, the frequency of ApT methylation by chance is expected to be around 25%. Colors and names of lineage groups as in b. (d) Percent of total 6mA marks found within MACs. No MACs were found in R. globosum or L. creatinivora.« less
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Works referenced in this record:

Modernizing Reference Genome Assemblies
journal, July 2011

Model-based Analysis of ChIP-Seq (MACS)
journal, January 2008

Cutadapt removes adapter sequences from high-throughput sequencing reads
journal, May 2011

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
journal, April 2000

Transcriptome analysis by strand-specific sequencing of complementary DNA
journal, July 2009

  • Parkhomchuk, Dmitri; Borodina, Tatiana; Amstislavskiy, Vyacheslav
  • Nucleic Acids Research, Vol. 37, Issue 18
  • DOI: 10.1093/nar/gkp596

Genetic damage following introduction of DNA in Phycomyces
journal, February 2004

  • Obraztsova, Irina N.; Prados, Nicolás; Holzmann, Klaus
  • Fungal Genetics and Biology, Vol. 41, Issue 2
  • DOI: 10.1016/j.fgb.2003.09.007

FlyBase: establishing a Gene Group resource for Drosophila melanogaster
journal, October 2015

  • Attrill, Helen; Falls, Kathleen; Goodman, Joshua L.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1046

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
journal, January 2009

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
journal, May 2013

  • Chin, Chen-Shan; Alexander, David H.; Marks, Patrick
  • Nature Methods, Vol. 10, Issue 6
  • DOI: 10.1038/nmeth.2474

TopHat: discovering splice junctions with RNA-Seq
journal, March 2009

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements
journal, January 2015

Basic Local Alignment Search Tool
journal, October 1990

DNA Methylation on N6-Adenine in C. elegans
journal, May 2015

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation
journal, April 2010

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
journal, March 2012

Core promoter T-blocks correlate with gene expression levels in C. elegans
journal, March 2011

  • Grishkevich, V.; Hashimshony, T.; Yanai, I.
  • Genome Research, Vol. 21, Issue 5
  • DOI: 10.1101/gr.113381.110

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
journal, April 2012

  • Dominissini, Dan; Moshitch-Moshkovitz, Sharon; Schwartz, Schraga
  • Nature, Vol. 485, Issue 7397
  • DOI: 10.1038/nature11112

Full-length transcriptome assembly from RNA-Seq data without a reference genome
journal, May 2011

  • Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran
  • Nature Biotechnology, Vol. 29, Issue 7
  • DOI: 10.1038/nbt.1883

Human body epigenome maps reveal noncanonical DNA methylation variation
journal, June 2015

  • Schultz, Matthew D.; He, Yupeng; Whitaker, John W.
  • Nature, Vol. 523, Issue 7559
  • DOI: 10.1038/nature14465

Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
journal, January 2013

  • Katoh, K.; Standley, D. M.
  • Molecular Biology and Evolution, Vol. 30, Issue 4
  • DOI: 10.1093/molbev/mst010

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014

The Epigenomic Landscape of Prokaryotes
journal, February 2016

N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas
journal, May 2015

Rfam 12.0: updates to the RNA families database
journal, November 2014

  • Nawrocki, Eric P.; Burge, Sarah W.; Bateman, Alex
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1063

The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
journal, October 2007

  • Merchant, S. S.; Prochnik, S. E.; Vallon, O.
  • Science, Vol. 318, Issue 5848, p. 245-250
  • DOI: 10.1126/science.1143609

Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing
journal, January 2013

  • Dominissini, Dan; Moshitch-Moshkovitz, Sharon; Salmon-Divon, Mali
  • Nature Protocols, Vol. 8, Issue 1
  • DOI: 10.1038/nprot.2012.148

Gene expression regulation mediated through reversible m6A RNA methylation
journal, March 2014

  • Fu, Ye; Dominissini, Dan; Rechavi, Gideon
  • Nature Reviews Genetics, Vol. 15, Issue 5
  • DOI: 10.1038/nrg3724

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing
journal, February 2015

  • Urich, Mark A.; Nery, Joseph R.; Lister, Ryan
  • Nature Protocols, Vol. 10, Issue 3
  • DOI: 10.1038/nprot.2014.114

The Pfam protein families database: towards a more sustainable future
journal, December 2015

  • Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1344

Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes
journal, February 2016

  • Solomon, Kevin V.; Haitjema, Charles H.; Henske, John K.
  • Science, Vol. 351, Issue 6278
  • DOI: 10.1126/science.aad1431

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
journal, March 2007

FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads
journal, June 2015

De novo identification of repeat families in large genomes
journal, June 2005

‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes
journal, December 2012

  • Schultz, Matthew D.; Schmitz, Robert J.; Ecker, Joseph R.
  • Trends in Genetics, Vol. 28, Issue 12
  • DOI: 10.1016/j.tig.2012.10.012

DNA methylation on N6-adenine in mammalian embryonic stem cells
journal, March 2016

  • Wu, Tao P.; Wang, Tao; Seetin, Matthew G.
  • Nature, Vol. 532, Issue 7599
  • DOI: 10.1038/nature17640

An efficient algorithm for large-scale detection of protein families
journal, April 2002

GMAP: a genomic mapping and alignment program for mRNA and EST sequences
journal, February 2005

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data
journal, September 2016

  • Spatafora, Joseph W.; Chang, Ying; Benny, Gerald L.
  • Mycologia, Vol. 108, Issue 5
  • DOI: 10.3852/16-042

Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond
journal, July 2015

Dating divergences in the Fungal Tree of Life: review and new analyses
journal, November 2006

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
journal, January 2010

Fungi evolved right on track
journal, November 2009

  • Lücking, Robert; Huhndorf, Sabine; Pfister, Donald H.
  • Mycologia, Vol. 101, Issue 6
  • DOI: 10.3852/09-016

MycoCosm portal: gearing up for 1000 fungal genomes
journal, December 2013

  • Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1183

Software for Computing and Annotating Genomic Ranges
journal, August 2013

N6-Methyladenine DNA Modification in Drosophila
journal, May 2015

Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology
journal, December 1998

Ascorbic Acid Enhances Tet-Mediated 5-Methylcytosine Oxidation and Promotes DNA Demethylation in Mammals
journal, May 2013

  • Yin, Ruichuan; Mao, Shi-Qing; Zhao, Bailin
  • Journal of the American Chemical Society, Vol. 135, Issue 28
  • DOI: 10.1021/ja4028346

Direct detection of DNA methylation during single-molecule, real-time sequencing
journal, May 2010

  • Flusberg, Benjamin A.; Webster, Dale R.; Lee, Jessica H.
  • Nature Methods, Vol. 7, Issue 6
  • DOI: 10.1038/nmeth.1459

Dating divergences in the Fungal Tree of Life: review and new analyses
journal, November 2006

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins
journal, March 2021

Production of viable chicken by allogeneic transplantation of primordial germ cells induced from somatic cells
journal, May 2021

SPOCD1 is an essential executor of piRNA-directed de novo DNA methylation
journal, July 2020

HNRNPA2B1 promotes multiple myeloma progression by increasing AKT3 expression via m6A-dependent stabilization of ILF3 mRNA
journal, April 2021

seqQscorer: automated quality control of next-generation sequencing data using machine learning
journal, March 2021

  • Albrecht, Steffen; Sprang, Maximilian; Andrade-Navarro, Miguel A.
  • Genome Biology, Vol. 22, Issue 1
  • DOI: 10.1186/s13059-021-02294-2

DNA methylation on N6-adenine in mammalian embryonic stem cells
text, January 2016

  • Yongquan, Lai,; Kaixuan, Lin,; P., Wu, Tao
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/982a-3f06

Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha
text, January 2021

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    Works referencing / citing this record:

    Enzymes of early-diverging, zoosporic fungi
    journal, July 2019

    • Lange, Lene; Barrett, Kristian; Pilgaard, Bo
    • Applied Microbiology and Biotechnology, Vol. 103, Issue 17
    • DOI: 10.1007/s00253-019-09983-w

    MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae
    journal, June 2019

    Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons
    journal, April 2018

    • de Mendoza, Alex; Bonnet, Amandine; Vargas-Landin, Dulce B.
    • Nature Communications, Vol. 9, Issue 1
    • DOI: 10.1038/s41467-018-03724-9

    Single-molecule sequencing detection of N6-methyladenine in microbial reference materials
    journal, February 2019

    • McIntyre, Alexa B. R.; Alexander, Noah; Grigorev, Kirill
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-019-08289-9

    Identification and analysis of adenine N6-methylation sites in the rice genome
    journal, July 2018

    Diversity of cytosine methylation across the fungal tree of life
    journal, February 2019

    • Bewick, Adam J.; Hofmeister, Brigitte T.; Powers, Rob A.
    • Nature Ecology & Evolution, Vol. 3, Issue 3
    • DOI: 10.1038/s41559-019-0810-9

    Deciphering bacterial epigenomes using modern sequencing technologies
    journal, December 2018

    Regulation of transposable elements by DNA modifications
    journal, March 2019

    Fungi in aquatic ecosystems
    journal, March 2019

    • Grossart, Hans-Peter; Van den Wyngaert, Silke; Kagami, Maiko
    • Nature Reviews Microbiology, Vol. 17, Issue 6
    • DOI: 10.1038/s41579-019-0175-8

    N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells
    journal, December 2019

    N6-Methyladenine DNA modification in Xanthomonas oryzae pv. oryzicola genome
    journal, November 2018

    Study of the whole genome, methylome and transcriptome of Cordyceps militaris
    journal, January 2019

    Characteristics and homogeneity of N6-methylation in human genomes
    journal, March 2019

    csDMA: an improved bioinformatics tool for identifying DNA 6 mA modifications via Chou’s 5-step rule
    journal, September 2019

    Methylation content sensitive enzyme ddRAD (MCSeEd): a reference-free, whole genome profiling system to address cytosine/adenine methylation changes
    journal, October 2019

    Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species
    journal, January 2018

    • Kjærbølling, Inge; Vesth, Tammi C.; Frisvad, Jens C.
    • Proceedings of the National Academy of Sciences, Vol. 115, Issue 4
    • DOI: 10.1073/pnas.1715954115

    N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena
    journal, October 2017

    • Wang, Yuanyuan; Chen, Xiao; Sheng, Yalan
    • Nucleic Acids Research, Vol. 45, Issue 20
    • DOI: 10.1093/nar/gkx883

    Single-nucleotide-resolution sequencing of human N 6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome
    journal, November 2018

    • Koh, Casslynn W. Q.; Goh, Yeek Teck; Toh, Joel D. W.
    • Nucleic Acids Research, Vol. 46, Issue 22
    • DOI: 10.1093/nar/gky1104

    Structural insights into target DNA recognition by R2R3-MYB transcription factors
    journal, November 2019

    Chromatin features define adaptive genomic regions in a fungal plant pathogen
    posted_content, January 2020

    Adenine DNA methylation, 3D genome organization and gene expression in the parasite Trichomonas vaginalis
    posted_content, October 2019

    • Lizarraga, Ayelen; O’Brown, Zach Klapholz; Boulias, Konstantinos
    • DOI: 10.1101/603894

    Chytrid rhizoid morphogenesis is adaptive and resembles hyphal development in ‘higher’ fungi
    posted_content, August 2019

    Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing
    journal, May 2018

    • Zhu, Shijia; Beaulaurier, John; Deikus, Gintaras
    • Genome Research, Vol. 28, Issue 7
    • DOI: 10.1101/gr.231068.117

    Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme ) and its bacterial endosymbionts
    journal, October 2018

    • Sun, Xuepeng; Chen, Wenbo; Ivanov, Sergey
    • New Phytologist, Vol. 221, Issue 3
    • DOI: 10.1111/nph.15472

    N6-Methyladenosine in RNA and DNA: An Epitranscriptomic and Epigenetic Player Implicated in Determination of Stem Cell Fate
    journal, October 2018

    Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA
    journal, June 2019

    DNA N6-Methyladenosine modification role in transmitted variations from genomic DNA to RNA in Herrania umbratica
    journal, June 2019

    Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network
    journal, November 2019

    Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions
    journal, October 2018

    N6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA
    journal, November 2018

    Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery
    journal, September 2019

    • Mondo, Stephen J.; Jiménez, Diego Javier; Hector, Ronald E.
    • Biotechnology for Biofuels, Vol. 12, Issue 1
    • DOI: 10.1186/s13068-019-1569-6

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    journal, October 2019

    Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes
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    journal, September 2019

    SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis
    journal, July 2017

    PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities
    journal, September 2017

    • Edwards, Joan E.; Forster, Robert J.; Callaghan, Tony M.
    • Frontiers in Microbiology, Vol. 8
    • DOI: 10.3389/fmicb.2017.01657

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    journal, June 2019

    • Akapo, Olufunmilayo Olukemi; Padayachee, Tiara; Chen, Wanping
    • International Journal of Molecular Sciences, Vol. 20, Issue 12
    • DOI: 10.3390/ijms20122889

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    • Li, Zhiqing; Zhao, Ping; Xia, Qingyou
    • International Journal of Molecular Sciences, Vol. 20, Issue 12
    • DOI: 10.3390/ijms20122931

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    journal, October 2018

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    journal, August 2018

    • Arnesen, Jonathan A.; Małagocka, Joanna; Gryganskyi, Andrii
    • G3: Genes|Genomes|Genetics, Vol. 8, Issue 10
    • DOI: 10.1534/g3.118.200656

    Characteristics and homogeneity of N6-methylation in human genomes.
    text, January 2019

    • Pacini, Clare E.; Bradshaw, Charles; Garrett, Nigel
    • Apollo - University of Cambridge Repository
    • DOI: 10.17863/cam.37741

    Adenine DNA methylation, 3D genome organization, and gene expression in the parasite Trichomonas vaginalis
    journal, May 2020

    • Lizarraga, Ayelen; O’Brown, Zach Klapholz; Boulias, Konstantinos
    • Proceedings of the National Academy of Sciences, Vol. 117, Issue 23
    • DOI: 10.1073/pnas.1917286117

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    • Lange, Lene; Barrett, Kristian; Pilgaard, Bo
    • Applied Microbiology and Biotechnology, Vol. 103, Issue 17
    • DOI: 10.1007/s00253-019-09983-w

    Structural insight into human N6amt1–Trm112 complex functioning as a protein methyltransferase
    journal, September 2019

    Author Correction: Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons
    journal, May 2018

    • de Mendoza, Alex; Bonnet, Amandine; Vargas-Landin, Dulce B.
    • Nature Communications, Vol. 9, Issue 1
    • DOI: 10.1038/s41467-018-04260-2

    Diversity of cytosine methylation across the fungal tree of life
    journal, February 2019

    • Bewick, Adam J.; Hofmeister, Brigitte T.; Powers, Rob A.
    • Nature Ecology & Evolution, Vol. 3, Issue 3
    • DOI: 10.1038/s41559-019-0810-9

    Study of the whole genome, methylome and transcriptome of Cordyceps militaris
    journal, January 2019

    Methylation content sensitive enzyme ddRAD (MCSeEd): a reference-free, whole genome profiling system to address cytosine/adenine methylation changes
    journal, October 2019

    N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena
    journal, October 2017

    • Wang, Yuanyuan; Chen, Xiao; Sheng, Yalan
    • Nucleic Acids Research, Vol. 45, Issue 20
    • DOI: 10.1093/nar/gkx883

    N6-Methyladenosine in RNA and DNA: An Epitranscriptomic and Epigenetic Player Implicated in Determination of Stem Cell Fate
    journal, October 2018

    Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA
    journal, June 2019

    DNA N6-Methyladenosine modification role in transmitted variations from genomic DNA to RNA in Herrania umbratica
    journal, June 2019

    Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network
    journal, November 2019

    Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions
    journal, October 2018

    Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery
    journal, September 2019

    • Mondo, Stephen J.; Jiménez, Diego Javier; Hector, Ronald E.
    • Biotechnology for Biofuels, Vol. 12, Issue 1
    • DOI: 10.1186/s13068-019-1569-6

    Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes
    journal, July 2019

    Early Diverging Insect-Pathogenic Fungi of the Order Entomophthorales Possess Diverse and Unique Subtilisin-Like Serine Proteases
    journal, August 2018

    • Arnesen, Jonathan A.; Małagocka, Joanna; Gryganskyi, Andrii
    • G3: Genes|Genomes|Genetics, Vol. 8, Issue 10
    • DOI: 10.1534/g3.118.200656

    SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis
    journal, July 2017

    Distribution and Diversity of Cytochrome P450 Monooxygenases in the Fungal Class Tremellomycetes
    journal, June 2019

    • Akapo, Olufunmilayo Olukemi; Padayachee, Tiara; Chen, Wanping
    • International Journal of Molecular Sciences, Vol. 20, Issue 12
    • DOI: 10.3390/ijms20122889
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