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Synthesis of a eukaryotic chromosome reveals a role for N6-methyladenine in nucleosome organization

https://doi.org/10.1101/184929
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists
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DamIP: Using Mutant DNA Adenine Methyltransferase to Study DNA‐Protein Interactions In Vivo
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Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification
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Middle‐down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post‐translational modifications in histones
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New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
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Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method
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Methylated bases in DNA from Paramecium aurelia
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Nucleosomal organization of macronuclear chromatin in oxytricha fallax
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DNA of ciliated protozoa: DNA sequence diminution during macronuclear development of oxytricha
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Chromatin structure of the molecular ends of oxytricha macronuclear DNA: phased nucleosomes and a telomeric complex
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Telomere proteins: Specific recognition and protection of the natural termini of Oxytricha macronuclear DNA
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Cloning and expression of genes for the Oxytricha telomere-binding protein: Specific subunit interactions in the telomeric complex
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High-Resolution Genome-wide Mapping of the Primary Structure of Chromatin
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Genomes on the Edge: Programmed Genome Instability in Ciliates
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The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development
inferredcites →https://doi.org/10.1016/j.cell.2015.04.005openalex-snapshot
DNA Methylation on N6-Adenine in C. elegans
inferredcites →https://doi.org/10.1016/j.cell.2015.04.010openalex-snapshot
N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas
inferredcites →https://doi.org/10.1016/j.cell.2015.04.018openalex-snapshot
N6-Methyladenine DNA Modification in Drosophila
inferredcites →https://doi.org/10.1016/j.ejop.2016.12.003openalex-snapshot
N 6 -methyladenine DNA modification in the unicellular eukaryotic organism Tetrahymena thermophila
inferredcites →https://doi.org/10.1016/j.molcel.2009.07.027openalex-snapshot
A Method for Genetically Installing Site-Specific Acetylation in Recombinant Histones Defines the Effects of H3 K56 Acetylation
inferredcites →https://doi.org/10.1016/j.molcel.2010.01.037openalex-snapshot
The Histone Chaperone Nap1 Promotes Nucleosome Assembly by Eliminating Nonnucleosomal Histone DNA Interactions
inferredcites →https://doi.org/10.1016/j.ymeth.2003.10.018openalex-snapshot
Measurement of histone–DNA interaction free energy in nucleosomes
inferredcites →https://doi.org/10.1016/s0021-9258(17)38193-0openalex-snapshot
Effects of methylation on the stability of nucleic acid conformations. Studies at the polymer level.
inferredcites →https://doi.org/10.1016/s0021-9258(18)54150-8openalex-snapshot
Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 “tail” to DNA.
inferredcites →https://doi.org/10.1016/s0076-6879(99)04003-3openalex-snapshot
Preparation of nucleosome core particle from recombinant histones
inferredcites →https://doi.org/10.1016/s0092-8674(00)80321-9openalex-snapshot
ACF, an ISWI-Containing and ATP-Utilizing Chromatin Assembly and Remodeling Factor
inferredcites →https://doi.org/10.1016/s0092-8674(00)81063-6openalex-snapshot
Tetrahymena Histone Acetyltransferase A: A Homolog to Yeast Gcn5p Linking Histone Acetylation to Gene Activation
inferredcites →https://doi.org/10.1016/s0092-8674(00)81720-1openalex-snapshot
Crystal Structure of the Oxytricha nova Telomere End Binding Protein Complexed with Single Strand DNA
inferredcites →https://doi.org/10.1016/s0092-8674(02)00941-8openalex-snapshot
Methylation of Histone H3 at Lysine 9 Targets Programmed DNA Elimination in Tetrahymena
inferredcites →https://doi.org/10.1038/nature07667openalex-snapshot
The DNA-encoded nucleosome organization of a eukaryotic genome
inferredcites →https://doi.org/10.1038/nature17640openalex-snapshot
DNA methylation on N6-adenine in mammalian embryonic stem cells
inferredcites →https://doi.org/10.1038/nbt.1508openalex-snapshot
Design and analysis of ChIP-seq experiments for DNA-binding proteins
inferredcites →https://doi.org/10.1038/nchembio.2008openalex-snapshot
A two-state activation mechanism controls the histone methyltransferase Suv39h1
inferredcites →https://doi.org/10.1038/nchembio.2235openalex-snapshot
Ubiquitin utilizes an acidic surface patch to alter chromatin structure
inferredcites →https://doi.org/10.1038/nchembio.501openalex-snapshot
Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction
inferredcites →https://doi.org/10.1038/ncomms13052openalex-snapshot
Abundant DNA 6mA methylation during early embryogenesis of zebrafish and pig
inferredcites →https://doi.org/10.1038/ng.3859openalex-snapshot
Widespread adenine N6-methylation of active genes in fungi
inferredcites →https://doi.org/10.1038/nmeth.1226openalex-snapshot
Mapping and quantifying mammalian transcriptomes by RNA-Seq
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nrm4076openalex-snapshot
DNA N6-methyladenine: a new epigenetic mark in eukaryotes?
inferredcites →https://doi.org/10.1038/nsmb.2506openalex-snapshot
Determinants of nucleosome positioning
inferredcites →https://doi.org/10.1038/nsmb.3145openalex-snapshot
Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications
inferredcites →https://doi.org/10.1073/pnas.1106264108openalex-snapshot
Histone fold modifications control nucleosome unwrapping and disassembly
inferredcites →https://doi.org/10.1073/pnas.75.10.4992openalex-snapshot
Macronuclear DNA of the hypotrichous ciliate Oxytricha fallax
inferredcites →https://doi.org/10.1073/pnas.95.13.7480openalex-snapshot
Phosphorylation of histone H3 at serine 10 is correlated with chromosome condensation during mitosis and meiosis in Tetrahymena
inferredcites →https://doi.org/10.1073/pnas.96.26.14967openalex-snapshot
Methylation of histone H3 at lysine 4 is highly conserved and correlates with transcriptionally active nuclei in Tetrahymena
inferredcites →https://doi.org/10.1074/jbc.274.46.33020openalex-snapshot
Nucleosome Positioning Is Independent of Histone H1in Vivo
inferredcites →https://doi.org/10.1074/mcp.m114.046011openalex-snapshot
EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra*
inferredcites →https://doi.org/10.1083/jcb.56.3.697openalex-snapshot
[6N]METHYL ADENINE IN THE NUCLEAR DNA OF A EUCARYOTE, TETRAHYMENA PYRIFORMIS
inferredcites →https://doi.org/10.1093/nar/25.14.2877openalex-snapshot
The telomere binding protein of Euplotes crassus prevents non-specific transcription initiation but has no role in positioning transcription initiation complexes
inferredcites →https://doi.org/10.1093/nar/gkq900openalex-snapshot
The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association
inferredcites →https://doi.org/10.1093/nar/gkv054openalex-snapshot
CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses
inferredcites →https://doi.org/10.1093/nar/gkw1107openalex-snapshot
InterPro in 2017—beyond protein family and domain annotations
inferredcites →https://doi.org/10.1101/gad.1544207openalex-snapshot
RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena
inferredcites →https://doi.org/10.1101/gr.139618.112openalex-snapshot
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
inferredcites →https://doi.org/10.1101/gr.188516.114openalex-snapshot
DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome
inferredcites →https://doi.org/10.1101/gr.4086505openalex-snapshot
Galaxy: A platform for interactive large-scale genome analysis
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The Gene-size DNA Molecules in Oxytricha
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Nucleosome Phasing in Tetrahymena Macronuclei1
inferredcites →https://doi.org/10.1128/jb.135.3.1156-1157.1978openalex-snapshot
Comparative study of DNA methylation in three unicellular eucaryotes
inferredcites →https://doi.org/10.1128/jb.150.2.993-996.1982openalex-snapshot
Sequence specificity of DNA adenine methylase in the protozoan Tetrahymena thermophila
inferredcites →https://doi.org/10.1128/mcb.01070-14openalex-snapshot
Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density
inferredcites →https://doi.org/10.1128/mcb.1.7.600openalex-snapshot
Deoxyribonucleic acid methylation and chromatin organization in Tetrahymena thermophila.
inferredcites →https://doi.org/10.1128/microbiolspec.mdna3-0025-2014openalex-snapshot
Programmed Genome Rearrangements in the CiliateOxytricha
inferredcites →https://doi.org/10.1128/mr.58.2.233-267.1994openalex-snapshot
The DNA of ciliated protozoa
inferredcites →https://doi.org/10.1146/annurev.biochem.77.062706.153223openalex-snapshot
The Biology of Chromatin Remodeling Complexes
inferredcites →https://doi.org/10.1186/1471-2164-9-562openalex-snapshot
Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure
inferredcites →https://doi.org/10.1186/gb-2010-11-11-140openalex-snapshot
Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology
inferredcites →https://doi.org/10.1186/gb-2010-11-8-r86openalex-snapshot
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
inferredcites →https://doi.org/10.1371/journal.pbio.0040286openalex-snapshot
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
inferredcites →https://doi.org/10.1371/journal.pbio.1001473openalex-snapshot
The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes
inferredcites →https://doi.org/10.1371/journal.pgen.1003541openalex-snapshot
DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria
inferredcites →https://doi.org/10.1371/journal.pone.0030630openalex-snapshot
Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing
inferredcites →https://doi.org/10.1534/genetics.114.163279openalex-snapshot
Transcription-Independent Functions of an RNA Polymerase II Subunit, Rpb2, During Genome Rearrangement in the Ciliate, Oxytricha trifallax
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