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The impact of endogenous retroviruses on nuclear organization and gene expression

https://doi.org/10.1101/295329
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/bies.201300040openalex-snapshot
Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?
inferredcites →https://doi.org/10.1002/bies.201700155openalex-snapshot
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re‐Visiting the “Gene‐Battery” Model
inferredcites →https://doi.org/10.1007/978-1-4939-3372-3_4openalex-snapshot
Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans
inferredcites →https://doi.org/10.1016/b978-0-12-391938-0.00004-5openalex-snapshot
4C Technology: Protocols and Data Analysis
inferredcites →https://doi.org/10.1016/j.bbagrm.2017.05.003openalex-snapshot
Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions
inferredcites →https://doi.org/10.1016/j.ceb.2014.04.004openalex-snapshot
Models of chromosome structure
inferredcites →https://doi.org/10.1016/j.cell.2010.10.019openalex-snapshot
Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome
inferredcites →https://doi.org/10.1016/j.cell.2011.11.058openalex-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.2015.03.026openalex-snapshot
Ubiquitous L1 Mosaicism in Hippocampal Neurons
inferredcites →https://doi.org/10.1016/j.cell.2016.02.007openalex-snapshot
The 3D Genome as Moderator of Chromosomal Communication
inferredcites →https://doi.org/10.1016/j.cell.2016.09.037openalex-snapshot
Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
inferredcites →https://doi.org/10.1016/j.cell.2016.10.024openalex-snapshot
Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control
inferredcites →https://doi.org/10.1016/j.cell.2017.09.043openalex-snapshot
Multiscale 3D Genome Rewiring during Mouse Neural Development
inferredcites →https://doi.org/10.1016/j.celrep.2016.05.073openalex-snapshot
A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination
inferredcites →https://doi.org/10.1016/j.chom.2017.09.007openalex-snapshot
GBPs Inhibit Motility of Shigella flexneri but Are Targeted for Degradation by the Bacterial Ubiquitin Ligase IpaH9.8
inferredcites →https://doi.org/10.1016/j.devcel.2016.10.015openalex-snapshot
The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances
inferredcites →https://doi.org/10.1016/j.gde.2016.01.001openalex-snapshot
How retrotransposons shape genome regulation
inferredcites →https://doi.org/10.1016/j.gde.2016.01.002openalex-snapshot
The three-dimensional cancer genome
inferredcites →https://doi.org/10.1016/j.molcel.2012.06.036openalex-snapshot
Close Proximity to Igh Is a Contributing Factor to AID-Mediated Translocations
inferredcites →https://doi.org/10.1016/j.molcel.2014.05.029openalex-snapshot
Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.molcel.2017.04.010openalex-snapshot
Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation
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.stem.2015.01.005openalex-snapshot
Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells
inferredcites →https://doi.org/10.1016/j.stem.2016.08.004openalex-snapshot
MED12 Regulates HSC-Specific Enhancers Independently of Mediator Kinase Activity to Control Hematopoiesis
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/10.1016/j.ymeth.2017.04.004openalex-snapshot
Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation
inferredcites →https://doi.org/10.1038/nature10413openalex-snapshot
Mouse genomic variation and its effect on phenotypes and gene regulation
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/nature11244openalex-snapshot
Embryonic stem cell potency fluctuates with endogenous retrovirus activity
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature12644openalex-snapshot
A high-resolution map of the three-dimensional chromatin interactome in human cells
inferredcites →https://doi.org/10.1038/nature13417openalex-snapshot
Enhancer loops appear stable during development and are associated with paused polymerase
inferredcites →https://doi.org/10.1038/nature14308openalex-snapshot
Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells
inferredcites →https://doi.org/10.1038/ncb3573openalex-snapshot
Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo
inferredcites →https://doi.org/10.1038/ncomms10286openalex-snapshot
Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells
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.3286openalex-snapshot
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
inferredcites →https://doi.org/10.1038/ng.3935openalex-snapshot
Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation
inferredcites →https://doi.org/10.1038/ng.3945openalex-snapshot
LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo
inferredcites →https://doi.org/10.1038/ng0598-19openalex-snapshot
The impact of L1 retrotransposons on the human genome
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.2173openalex-snapshot
Robust 4C-seq data analysis to screen for regulatory DNA interactions
inferredcites →https://doi.org/10.1038/nmeth.3664openalex-snapshot
Multiplexed analysis of chromosome conformation at vastly improved sensitivity
inferredcites →https://doi.org/10.1038/nrc.2017.35openalex-snapshot
Transposable elements in cancer
inferredcites →https://doi.org/10.1038/nrg.2016.112openalex-snapshot
Organization and function of the 3D genome
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/nrg3117openalex-snapshot
Repetitive DNA and next-generation sequencing: computational challenges and solutions
inferredcites →https://doi.org/10.1038/nrm.2016.104openalex-snapshot
Genome-wide mapping and analysis of chromosome architecture
inferredcites →https://doi.org/10.1038/nrm.2016.138openalex-snapshot
Regulation of disease-associated gene expression in the 3D genome
inferredcites →https://doi.org/10.1073/pnas.0611223104openalex-snapshot
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
inferredcites →https://doi.org/10.1073/pnas.1422187112openalex-snapshot
The histone methyltransferase SETDB1 represses endogenous and exogenous retroviruses in B lymphocytes
inferredcites →https://doi.org/10.1083/jcb.200305013openalex-snapshot
Visualization of chromatin domains created by the gypsy insulator of Drosophila
inferredcites →https://doi.org/10.1093/molbev/msw281openalex-snapshot
MBE Citation Classics (2017 Edition)
inferredcites →https://doi.org/10.1093/molbev/msx219openalex-snapshot
Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints
inferredcites →https://doi.org/10.1093/nar/gkv1292openalex-snapshot
The 3D folding of metazoan genomes correlates with the association of similar repetitive elements
inferredcites →https://doi.org/10.1101/083980openalex-snapshot
Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape
inferredcites →https://doi.org/10.1101/gad.281964.116openalex-snapshot
The second decade of 3C technologies: detailed insights into nuclear organization
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.218149.116openalex-snapshot
Transposable elements are the primary source of novelty in primate gene regulation
inferredcites →https://doi.org/10.1101/sqb.1951.016.01.004openalex-snapshot
CHROMOSOME ORGANIZATION AND GENIC EXPRESSION
inferredcites →https://doi.org/10.1101/sqb.1956.021.01.017openalex-snapshot
Controlling Elements and the Gene
inferredcites →https://doi.org/10.1109/tvcg.2014.2346248openalex-snapshot
UpSet: Visualization of Intersecting Sets
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.1262088openalex-snapshot
CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation
inferredcites →https://doi.org/10.1126/science.aad5497openalex-snapshot
Regulatory evolution of innate immunity through co-option of endogenous retroviruses
inferredcites →https://doi.org/10.1128/microbiolspec.mdna3-0009-2014openalex-snapshot
Mammalian Endogenous Retroviruses
inferredcites →https://doi.org/10.1128/mmbr.00006-15openalex-snapshot
An Overview of Genome Organization and How We Got There: from FISH to Hi-C
inferredcites →https://doi.org/10.1146/annurev-cellbio-100814-125514openalex-snapshot
The Developmental Control of Transposable Elements and the Evolution of Higher Species
inferredcites →https://doi.org/10.1146/annurev-genet-110711-155616openalex-snapshot
Active Transposition in Genomes
inferredcites →https://doi.org/10.1146/annurev-genet-110711-155621openalex-snapshot
Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes
inferredcites →https://doi.org/10.1158/0008-5472.can-15-3502openalex-snapshot
Nutritional Stress Induced by Tryptophan-Degrading Enzymes Results in ATF4-Dependent Reprogramming of the Amino Acid Transporter Profile in Tumor Cells
inferredcites →https://doi.org/10.1186/1759-8753-3-9openalex-snapshot
C-GATE - catalogue of genes affected by transposable elements
inferredcites →https://doi.org/10.1186/gb-2012-13-6-r45openalex-snapshot
The genomic landscape shaped by selection on transposable elements across 18 mouse strains
inferredcites →https://doi.org/10.1186/s12977-015-0173-5openalex-snapshot
Retrotransposons shape species-specific embryonic stem cell gene expression
inferredcites →https://doi.org/10.1186/s13059-016-0992-2openalex-snapshot
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
inferredcites →https://doi.org/10.1186/s13100-015-0041-9openalex-snapshot
Repbase Update, a database of repetitive elements in eukaryotic genomes
inferredcites →https://doi.org/10.1186/s13100-016-0080-xopenalex-snapshot
Endogenous retroviral promoter exaptation in human cancer
inferredcites →https://doi.org/10.12688/f1000research.7334.1openalex-snapshot
HiCUP: pipeline for mapping and processing Hi-C data
inferredcites →https://doi.org/10.1371/journal.pcbi.1004780openalex-snapshot
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
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/10.15252/embr.201642198openalex-snapshot
Capture‐C reveals preformed chromatin interactions between HIF‐binding sites and distant promoters
inferredcites →https://doi.org/10.15252/embr.201642743openalex-snapshot
CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome
inferredcites →https://doi.org/10.2217/epi-2017-0157openalex-snapshot
Enhancer Talk
inferredcites →https://doi.org/10.2217/epi.15.25openalex-snapshot
Breaking TADs: Insights into Hierarchical Genome Organization
inferredcites →https://doi.org/10.7554/elife.10565openalex-snapshot
Genomic DNA transposition induced by human PGBD5
inferredcites →https://doi.org/10.7554/elife.13926openalex-snapshot
Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci
inferredcites →https://doi.org/10.7554/elife.21926openalex-snapshot
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells
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