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The genomic false shuffle: epigenetic maintenance of topological domains in the rearranged gibbon genome

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What this work says

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

inferredcites →https://doi.org/10.1002/ajmg.a.20072openalex-snapshot

Melorheostosis in a family with autosomal dominant osteopoikilosis: Report of a third family

inferredcites →https://doi.org/10.1002/ajmg.a.38253openalex-snapshot

Clinical and molecular characterization of a second family with the 12q14 microdeletion syndrome and review of the literature

inferredcites →https://doi.org/10.1002/humu.23146openalex-snapshot

Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation

inferredcites →https://doi.org/10.1006/geno.1995.9875openalex-snapshot

Genomic Reorganization in the Concolor Gibbon (Hylobates concolor) Revealed by Chromosome Painting

inferredcites →https://doi.org/10.1016/0955-0674(91)90069-bopenalex-snapshot

DNA repair and the role of chromatin structure

inferredcites →https://doi.org/10.1016/j.ajhg.2017.06.011openalex-snapshot

Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements

inferredcites →https://doi.org/10.1016/j.cell.2013.04.053openalex-snapshot

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

inferredcites →https://doi.org/10.1016/j.cell.2014.02.019openalex-snapshot

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

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.2015.04.004openalex-snapshot

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

inferredcites →https://doi.org/10.1016/j.cell.2015.07.048openalex-snapshot

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

inferredcites →https://doi.org/10.1016/j.cell.2017.06.034openalex-snapshot

Genome Organization Drives Chromosome Fragility

inferredcites →https://doi.org/10.1016/j.celrep.2015.02.004openalex-snapshot

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

inferredcites →https://doi.org/10.1016/j.celrep.2015.02.046openalex-snapshot

The 3D Organization of Chromatin Explains Evolutionary Fragile Genomic Regions

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.molcel.2010.05.004openalex-snapshot

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

inferredcites →https://doi.org/10.1016/j.tig.2016.01.003openalex-snapshot

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

inferredcites →https://doi.org/10.1038/ejhg.2011.199openalex-snapshot

Severe intellectual disability and autistic features associated with microduplication 2q23.1

inferredcites →https://doi.org/10.1038/emboj.2013.85openalex-snapshot

The transcription factor Hmx1 and growth factor receptor activities control sympathetic neurons diversification

inferredcites →https://doi.org/10.1038/nature08514openalex-snapshot

Human DNA methylomes at base resolution show widespread epigenomic differences

inferredcites →https://doi.org/10.1038/nature11049openalex-snapshot

Spatial partitioning of the regulatory landscape of the X-inactivation centre

inferredcites →https://doi.org/10.1038/nature11082openalex-snapshot

Topological domains in mammalian genomes identified by analysis of chromatin interactions

inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot

An integrated encyclopedia of DNA elements in the human genome

inferredcites →https://doi.org/10.1038/nature13679openalex-snapshot

Gibbon genome and the fast karyotype evolution of small apes

inferredcites →https://doi.org/10.1038/nature13986openalex-snapshot

Topologically associating domains are stable units of replication-timing regulation

inferredcites →https://doi.org/10.1038/nature19356openalex-snapshot

High-throughput discovery of novel developmental phenotypes

inferredcites →https://doi.org/10.1038/nature19800openalex-snapshot

Formation of new chromatin domains determines pathogenicity of genomic duplications

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/ng.2653openalex-snapshot

The Genotype-Tissue Expression (GTEx) project

inferredcites →https://doi.org/10.1038/ng.3282openalex-snapshot

Mutations in KCNH1 and ATP6V1B2 cause Zimmermann-Laband syndrome

inferredcites →https://doi.org/10.1038/ng.3720openalex-snapshot

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

inferredcites →https://doi.org/10.1038/ng.496openalex-snapshot

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

inferredcites →https://doi.org/10.1038/ng1453openalex-snapshot

Loss-of-function mutations in LEMD3 result in osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis

inferredcites →https://doi.org/10.1038/ng1891openalex-snapshot

Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions

inferredcites →https://doi.org/10.1038/nsmb.2089openalex-snapshot

DNA secondary structures and epigenetic determinants of cancer genome evolution

inferredcites →https://doi.org/10.1038/s41588-018-0195-8openalex-snapshot

Integrative detection and analysis of structural variation in cancer genomes

inferredcites →https://doi.org/10.1074/jbc.m512757200openalex-snapshot

Specification of SUMO1- and SUMO2-interacting Motifs

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btr167openalex-snapshot

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btw368openalex-snapshot

TADtool: visual parameter identification for TAD-calling algorithms

inferredcites →https://doi.org/10.1093/hmg/ddu278openalex-snapshot

The impact of chromosomal rearrangements on regulation of gene expression

inferredcites →https://doi.org/10.1093/jmcb/mju038openalex-snapshot

Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation

inferredcites →https://doi.org/10.1093/nar/gkv693openalex-snapshot

The interplay between DNA methylation and sequence divergence in recent human evolution

inferredcites →https://doi.org/10.1101/191213openalex-snapshot

Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries

inferredcites →https://doi.org/10.1101/gr.086041.108openalex-snapshot

Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

inferredcites →https://doi.org/10.1101/gr.136184.111openalex-snapshot

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

inferredcites →https://doi.org/10.1101/gr.138651.112openalex-snapshot

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

inferredcites →https://doi.org/10.1101/gr.229102openalex-snapshot

The Human Genome Browser at UCSC

inferredcites →https://doi.org/10.1101/gr.3896805openalex-snapshot

Hotspots of mutation and breakage in dog and human chromosomes

inferredcites →https://doi.org/10.1101/gr.6052507openalex-snapshot

Molecular refinement of gibbon genome rearrangements

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/10.1126/science.aad9024openalex-snapshot

Activation of proto-oncogenes by disruption of chromosome neighborhoods

inferredcites →https://doi.org/10.1159/000076292openalex-snapshot

Characterization of two novel KRAB-domain-containing zinc finger genes, ZNF460 and ZNF461, on human chromosome 19q13.1→q13.4

inferredcites →https://doi.org/10.1186/1471-2164-10-335openalex-snapshot

Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

inferredcites →https://doi.org/10.1186/gb-2012-13-10-r83openalex-snapshot

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

inferredcites →https://doi.org/10.1186/s13059-017-1253-8openalex-snapshot

Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours

inferredcites →https://doi.org/10.1371/journal.pgen.0020223openalex-snapshot

A High-Resolution Map of Synteny Disruptions in Gibbon and Human Genomes

inferredcites →https://doi.org/10.1371/journal.pgen.1000538openalex-snapshot

Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution

inferredcites →https://doi.org/10.1371/journal.pgen.1002692openalex-snapshot

Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome

inferredcites →https://doi.org/10.1371/journal.pone.0004999openalex-snapshot

A Chromosomal Inversion Unique to the Northern White-Cheeked Gibbon

inferredcites →https://doi.org/10.1371/journal.pone.0056955openalex-snapshot

Loss of GGN Leads to Pre-Implantation Embryonic Lethality and Compromised Male Meiotic DNA Double Strand Break Repair in the Mouse

inferredcites →https://doi.org/10.1534/g3.113.008680openalex-snapshot

Large-Scale Quality Analysis of Published ChIP-seq Data

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.cels.2019.05.011openalex-snapshot

Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF

inferred← citeshttps://doi.org/10.1038/s41438-021-00494-2openalex-snapshot

Bioinformatic analysis of chromatin organization and biased expression of duplicated genes between two poplars with a common whole-genome duplication

inferred← citeshttps://doi.org/10.1073/pnas.1808631116openalex-snapshot

Chromatin features constrain structural variation across evolutionary timescales

inferred← citeshttps://doi.org/10.1101/272245openalex-snapshot

Most regulatory interactions are not in linkage disequilibrium

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