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Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes and gene regulation

https://doi.org/10.1101/2022.02.01.475239

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What this work says

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

inferredcites →https://doi.org/10.1002/0471250953.bi0410s25openalex-snapshot

Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences

inferredcites →https://doi.org/10.1007/s00239-007-9028-6openalex-snapshot

Effect of Divergence Time and Recombination Rate on Molecular Evolution of Drosophila INE-1 Transposable Elements and Other Candidates for Neutrally Evolving Sites

inferredcites →https://doi.org/10.1016/j.cell.2005.01.001openalex-snapshot

Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse

inferredcites →https://doi.org/10.1016/j.cell.2009.06.001openalex-snapshot

CTCF: Master Weaver of the Genome

inferredcites →https://doi.org/10.1016/j.cell.2012.02.001openalex-snapshot

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

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.2017.05.004openalex-snapshot

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization

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.2015.02.004openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.celrep.2016.10.061openalex-snapshot

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

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.gpb.2020.06.025openalex-snapshot

AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-Seq Data Analysis

inferredcites →https://doi.org/10.1016/j.molcel.2017.08.006openalex-snapshot

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

inferredcites →https://doi.org/10.1016/j.molcel.2020.04.018openalex-snapshot

Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity

inferredcites →https://doi.org/10.1016/s0014-4827(03)00185-xopenalex-snapshot

The insulator binding protein CTCF associates with the nuclear matrix

inferredcites →https://doi.org/10.1038/cr.2012.15openalex-snapshot

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

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/nature18589openalex-snapshot

Structural organization of the inactive X chromosome in the mouse

inferredcites →https://doi.org/10.1038/nature23884openalex-snapshot

The 4D nucleome project

inferredcites →https://doi.org/10.1038/ncomms14550openalex-snapshot

Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus

inferredcites →https://doi.org/10.1038/ng.3963openalex-snapshot

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

inferredcites →https://doi.org/10.1038/ng.600openalex-snapshot

Transposable elements have rewired the core regulatory network of human embryonic stem cells

inferredcites →https://doi.org/10.1038/ng.917openalex-snapshot

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

inferredcites →https://doi.org/10.1038/nmeth.3543openalex-snapshot

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

inferredcites →https://doi.org/10.1038/nmeth.3999openalex-snapshot

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

inferredcites →https://doi.org/10.1038/nrg.2016.139openalex-snapshot

Regulatory activities of transposable elements: from conflicts to benefits

inferredcites →https://doi.org/10.1038/nrg2063openalex-snapshot

The evolutionary significance of cis-regulatory mutations

inferredcites →https://doi.org/10.1038/s41467-020-15520-5openalex-snapshot

Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes

inferredcites →https://doi.org/10.1038/s41586-019-1812-0openalex-snapshot

Key role for CTCF in establishing chromatin structure in human embryos

inferredcites →https://doi.org/10.1038/s41586-020-2493-4openalex-snapshot

Expanded encyclopaedias of DNA elements in the human and mouse genomes

inferredcites →https://doi.org/10.1038/s41588-018-0338-yopenalex-snapshot

EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains

inferredcites →https://doi.org/10.1038/s41588-019-0479-7openalex-snapshot

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

inferredcites →https://doi.org/10.1038/s41594-020-00539-5openalex-snapshot

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

inferredcites →https://doi.org/10.1073/pnas.1507253112openalex-snapshot

MIR retrotransposon sequences provide insulators to the human genome

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.1609643113openalex-snapshot

Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture

inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot

edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot

STAR: ultrafast universal RNA-seq aligner

inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot

HTSeq—a Python framework to work with high-throughput sequencing data

inferredcites →https://doi.org/10.1093/database/bax028openalex-snapshot

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

inferredcites →https://doi.org/10.1093/nar/gkj144openalex-snapshot

The UCSC Genome Browser Database: update 2006

inferredcites →https://doi.org/10.1093/nar/gkx1081openalex-snapshot

The Encyclopedia of DNA elements (ENCODE): data portal update

inferredcites →https://doi.org/10.1093/nar/gky354openalex-snapshot

CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens

inferredcites →https://doi.org/10.1093/nar/gky864openalex-snapshot

HACER: an atlas of human active enhancers to interpret regulatory variants

inferredcites →https://doi.org/10.1093/nar/gkz348openalex-snapshot

WashU Epigenome Browser update 2019

inferredcites →https://doi.org/10.1101/2020.04.18.047738openalex-snapshot

Three-dimensional Genome Organization Maps in Normal Haematopoietic Stem Cells and Acute Myeloid Leukemia

inferredcites →https://doi.org/10.1101/523712openalex-snapshot

Transposable elements drive reorganisation of 3D chromatin during early embryogenesis

inferredcites →https://doi.org/10.1101/gr.080663.108openalex-snapshot

Evolution of the mammalian transcription factor binding repertoire via transposable elements

inferredcites →https://doi.org/10.1101/gr.168872.113openalex-snapshot

Widespread contribution of transposable elements to the innovation of gene regulatory networks

inferredcites →https://doi.org/10.1101/gr.224576.117openalex-snapshot

The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes

inferredcites →https://doi.org/10.1101/gr.235747.118openalex-snapshot

Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions

inferredcites →https://doi.org/10.1101/gr.266528.120openalex-snapshot

Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize

inferredcites →https://doi.org/10.1126/science.1090005openalex-snapshot

Evolution at Two Levels in Humans and Chimpanzees

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-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/s13059-018-1598-7openalex-snapshot

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

inferredcites →https://doi.org/10.1186/s13059-019-1916-8openalex-snapshot

Co-opted transposons help perpetuate conserved higher-order chromosomal structures

inferredcites →https://doi.org/10.1186/s13059-021-02409-9openalex-snapshot

Evolution of mouse circadian enhancers from transposable elements

inferredcites →https://doi.org/10.1371/journal.pgen.1003504openalex-snapshot

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

inferredcites →https://doi.org/10.7554/elife.05899.013openalex-snapshot

Author response: Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

inferredcites →https://doi.org/10.7554/elife.52504openalex-snapshot

Derivation of trophoblast stem cells from naïve human pluripotent stem cells

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-3-032-04125-8_9openalex-snapshot

Transposable Elements and Hereditary Diseases

inferred← citeshttps://doi.org/10.1016/j.cell.2022.06.052openalex-snapshot

3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome

inferred← citeshttps://doi.org/10.1016/j.xgen.2023.100410openalex-snapshot

In silico discovery of repetitive elements as key sequence determinants of 3D genome folding

inferred← citeshttps://doi.org/10.1101/2022.10.25.513724openalex-snapshot

Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-κB binding

inferred← citeshttps://doi.org/10.1101/2024.03.11.584453openalex-snapshot

Sequence composition and conservation predict the phenotypic relevance of transposable elements

inferred← citeshttps://doi.org/10.3389/fnbeh.2022.923732openalex-snapshot

The Role of Transposable Elements in Sexual Development

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