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The Hi-Culfite assay reveals relationships between chromatin contacts and DNA methylation state

https://doi.org/10.1101/481283
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What this work says

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

inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
inferredcites →https://doi.org/10.1016/j.cell.2017.09.026openalex-snapshot
Cohesin Loss Eliminates All Loop Domains
inferredcites →https://doi.org/10.1016/j.celrep.2016.03.001openalex-snapshot
Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors
inferredcites →https://doi.org/10.1016/j.cels.2015.07.012openalex-snapshot
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
inferredcites →https://doi.org/10.1016/j.cels.2016.07.002openalex-snapshot
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
inferredcites →https://doi.org/10.1038/35013100openalex-snapshot
Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene
inferredcites →https://doi.org/10.1038/35013106openalex-snapshot
CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus
inferredcites →https://doi.org/10.1038/nature08514openalex-snapshot
Human DNA methylomes at base resolution show widespread epigenomic differences
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature12593openalex-snapshot
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
inferredcites →https://doi.org/10.1038/nature16490openalex-snapshot
Insulator dysfunction and oncogene activation in IDH mutant gliomas
inferredcites →https://doi.org/10.1038/nature24281openalex-snapshot
Two independent modes of chromatin organization revealed by cohesin removal
inferredcites →https://doi.org/10.1038/ng.3811openalex-snapshot
Potential energy landscapes identify the information-theoretic nature of the epigenome
inferredcites →https://doi.org/10.1038/s41467-017-01724-9openalex-snapshot
DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes
inferredcites →https://doi.org/10.1038/sj.onc.1205699openalex-snapshot
5-Azacytidine and 5-aza-2′-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy
inferredcites →https://doi.org/10.1073/pnas.1518552112openalex-snapshot
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
inferredcites →https://doi.org/10.1073/pnas.89.5.1827openalex-snapshot
A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
inferredcites →https://doi.org/10.1093/bioinformatics/btr064openalex-snapshot
FIMO: scanning for occurrences of a given motif
inferredcites →https://doi.org/10.1093/bioinformatics/btu056openalex-snapshot
bwtool: a tool for bigWig files
inferredcites →https://doi.org/10.1093/nar/gks454openalex-snapshot
Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
inferredcites →https://doi.org/10.1093/nar/gkt067openalex-snapshot
Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub
inferredcites →https://doi.org/10.1093/nar/gkv1160openalex-snapshot
ENCODE data at the ENCODE portal
inferredcites →https://doi.org/10.1101/gr.229102openalex-snapshot
The Human Genome Browser at UCSC
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1186/gb-2012-13-10-r87openalex-snapshot
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
inferredcites →https://doi.org/10.15252/embj.201798004openalex-snapshot
Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41467-022-31857-5openalex-snapshot
Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery
inferred← citeshttps://doi.org/10.1101/833590openalex-snapshot
Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure
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