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Genome-wide rules of nucleosome phasing

https://doi.org/10.1101/093666
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Assembly of spaced chromatin promoted by DNA synthesis in extracts from Xenopus eggs.
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Nucleosome positioning in yeasts: methods, maps, and mechanisms
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Assembly of SV40 chromatin in a cell-free system from Xenopus eggs
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A drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation
inferredcites →https://doi.org/10.1016/0092-8674(95)90216-3openalex-snapshot
Purification and properties of an ATP-dependent nucleosome remodeling factor
inferredcites →https://doi.org/10.1016/j.cell.2007.01.030openalex-snapshot
Chromatin Challenges during DNA Replication and Repair
inferredcites →https://doi.org/10.1016/j.cell.2009.02.043openalex-snapshot
Mechanisms that Specify Promoter Nucleosome Location and Identity
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Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
inferredcites →https://doi.org/10.1016/j.cell.2012.04.036openalex-snapshot
Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers
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Genomic Nucleosome Organization Reconstituted with Pure Proteins
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Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping
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Evolutionarily Conserved Principles Predict 3D Chromatin Organization
inferredcites →https://doi.org/10.1016/j.ydbio.2009.06.012openalex-snapshot
Nucleosome positioning: How is it established, and why does it matter?
inferredcites →https://doi.org/10.1016/j.ydbio.2016.01.039openalex-snapshot
A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis
inferredcites →https://doi.org/10.1016/s0021-9258(19)85258-4openalex-snapshot
Nucleosome assembly during complementary DNA strand synthesis in extracts from mammalian cells
inferredcites →https://doi.org/10.1016/s0076-6879(03)71037-4openalex-snapshot
Chromatin Assembly In Vitro with Purified Recombinant ACF and NAP-1
inferredcites →https://doi.org/10.1016/s0091-679x(08)60916-4openalex-snapshot
Chapter 13 The Soluble Nuclear Fraction, a Highly Efficient Transcription Extract from Drosophila Embryos
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/s0304-419x(98)00008-0openalex-snapshot
The use of chromatin templates to recreate transcriptional regulatory phenomena in vitro
inferredcites →https://doi.org/10.1038/330221a0openalex-snapshot
The structure of an oligo(dA)·oligo(dT) tract and its biological implications
inferredcites →https://doi.org/10.1038/38444openalex-snapshot
Crystal structure of the nucleosome core particle at 2.8 Å resolution
inferredcites →https://doi.org/10.1038/41587openalex-snapshot
Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II
inferredcites →https://doi.org/10.1038/emboj.2009.301openalex-snapshot
Histone H1 binding is inhibited by histone variant H3.3
inferredcites →https://doi.org/10.1038/emboj.2011.112openalex-snapshot
The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4
inferredcites →https://doi.org/10.1038/nature06929openalex-snapshot
Nucleosome organization in the Drosophila genome
inferredcites →https://doi.org/10.1038/nature09725openalex-snapshot
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
inferredcites →https://doi.org/10.1038/nature10002openalex-snapshot
Determinants of nucleosome organization in primary human cells
inferredcites →https://doi.org/10.1038/nature13380openalex-snapshot
Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA
inferredcites →https://doi.org/10.1038/nature15545openalex-snapshot
Transcriptional regulators form diverse groups with context-dependent regulatory functions
inferredcites →https://doi.org/10.1038/nbt.1511openalex-snapshot
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
inferredcites →https://doi.org/10.1038/ng.1064openalex-snapshot
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
inferredcites →https://doi.org/10.1038/nprot.2007.261openalex-snapshot
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
inferredcites →https://doi.org/10.1038/nsmb.2419openalex-snapshot
Genome-wide nucleosome positioning during embryonic stem cell development
inferredcites →https://doi.org/10.1038/nsmb.2506openalex-snapshot
Determinants of nucleosome positioning
inferredcites →https://doi.org/10.1038/nsmb1170openalex-snapshot
The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing
inferredcites →https://doi.org/10.1038/s41467-017-02525-wopenalex-snapshot
High-resolution TADs reveal DNA sequences underlying genome organization in flies
inferredcites →https://doi.org/10.1073/pnas.83.16.5889openalex-snapshot
Affinity purification of sequence-specific DNA binding proteins.
inferredcites →https://doi.org/10.1074/mcp.m115.053553openalex-snapshot
A Quantitative Proteomic Analysis of In Vitro Assembled Chromatin
inferredcites →https://doi.org/10.1093/bioinformatics/btr261openalex-snapshot
DREME: motif discovery in transcription factor ChIP-seq data
inferredcites →https://doi.org/10.1093/emboj/20.10.2518openalex-snapshot
Interactions between the Su(Hw) and Mod(mdg4) proteins required for gypsy insulator function
inferredcites →https://doi.org/10.1093/nar/11.5.1475openalex-snapshot
Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei
inferredcites →https://doi.org/10.1093/nar/16.14.6677openalex-snapshot
Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism
inferredcites →https://doi.org/10.1093/nar/gkt1239openalex-snapshot
Quantifying the role of steric constraints in nucleosome positioning
inferredcites →https://doi.org/10.1093/nar/gkt890openalex-snapshot
De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins
inferredcites →https://doi.org/10.1093/nar/gkt997openalex-snapshot
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
inferredcites →https://doi.org/10.1093/nar/gkx040openalex-snapshot
Deciphering the DNA code for the function of the Drosophila polydactyl zinc finger protein Suppressor of Hairy-wing
inferredcites →https://doi.org/10.1101/262899openalex-snapshot
Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions
inferredcites →https://doi.org/10.1101/gad.1139604openalex-snapshot
Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo
inferredcites →https://doi.org/10.1101/gad.176826.111openalex-snapshot
Pioneer transcription factors: establishing competence for gene expression
inferredcites →https://doi.org/10.1101/gr.138156.112openalex-snapshot
Nature and function of insulator protein binding sites in the Drosophila genome
inferredcites →https://doi.org/10.1101/gr.151878.112openalex-snapshot
Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators
inferredcites →https://doi.org/10.1101/gr.174169.114openalex-snapshot
Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin
inferredcites →https://doi.org/10.1126/science.1112178openalex-snapshot
Genome-Scale Identification of Nucleosome Positions in S. cerevisiae
inferredcites →https://doi.org/10.1126/science.1200508openalex-snapshot
A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome
inferredcites →https://doi.org/10.1126/science.1206097openalex-snapshot
A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization
inferredcites →https://doi.org/10.1126/science.1232542openalex-snapshot
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
inferredcites →https://doi.org/10.1128/mcb.12.5.2241openalex-snapshot
Cell-free system for assembly of transcriptionally repressed chromatin from Drosophila embryos.
inferredcites →https://doi.org/10.1128/mcb.21.14.4807-4817.2001openalex-snapshot
Insulation of Enhancer-Promoter Communication by a Gypsy Transposon Insert in the Drosophila cut Gene: Cooperation between Suppressor of Hairy-wing and Modifier of mdg4 Proteins
inferredcites →https://doi.org/10.1186/gb-2007-8-8-r167openalex-snapshot
Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1186/gb-2014-15-5-r82openalex-snapshot
Insulator function and topological domain border strength scale with architectural protein occupancy
inferredcites →https://doi.org/10.1371/journal.pgen.0030112openalex-snapshot
CTCF Genomic Binding Sites in Drosophila and the Organisation of the Bithorax Complex
inferredcites →https://doi.org/10.1371/journal.pgen.1000138openalex-snapshot
The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1005940openalex-snapshot
The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors
inferredcites →https://doi.org/10.26508/lsa.201800024openalex-snapshot
CHRAC/ACF contribute to the repressive ground state of chromatin
inferredcites →https://doi.org/10.7554/elife.20148openalex-snapshot
Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

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inferred← citeshttps://doi.org/10.26508/lsa.201800024openalex-snapshot
CHRAC/ACF contribute to the repressive ground state of chromatin
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