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Single cell analysis reveals dynamics of transposable element transcription following epigenetic de-repression

https://doi.org/10.1101/462853
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What this work says

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

inferredcites →https://doi.org/10.1006/dbio.2001.0501openalex-snapshot
Dynamic Reprogramming of DNA Methylation in the Early Mouse Embryo
inferredcites →https://doi.org/10.1016/j.cell.2015.07.011openalex-snapshot
Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses
inferredcites →https://doi.org/10.1016/j.cell.2015.07.056openalex-snapshot
DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts
inferredcites →https://doi.org/10.1016/j.cell.2018.05.019openalex-snapshot
Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq
inferredcites →https://doi.org/10.1016/j.cell.2018.05.052openalex-snapshot
LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade
inferredcites →https://doi.org/10.1016/j.cell.2018.09.051openalex-snapshot
Targeting CDK9 Reactivates Epigenetically Silenced Genes in Cancer
inferredcites →https://doi.org/10.1016/j.molcel.2015.04.005openalex-snapshot
The Technology and Biology of Single-Cell RNA Sequencing
inferredcites →https://doi.org/10.1016/j.stem.2011.04.004openalex-snapshot
DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs
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.tibtech.2016.04.004openalex-snapshot
Multi-Omics of Single Cells: Strategies and Applications
inferredcites →https://doi.org/10.1016/j.tig.2018.06.006openalex-snapshot
Nimble and Ready to Mingle: Transposon Outbursts of Early Development
inferredcites →https://doi.org/10.1016/j.ymeth.2015.06.021openalex-snapshot
Computational assignment of cell-cycle stage from single-cell transcriptome data
inferredcites →https://doi.org/10.1016/s0168-9525(02)00006-9openalex-snapshot
Origin of a substantial fraction of human regulatory sequences from transposable elements
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature13458openalex-snapshot
Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells
inferredcites →https://doi.org/10.1038/nature21350openalex-snapshot
Scaling single-cell genomics from phenomenology to mechanism
inferredcites →https://doi.org/10.1038/nature23884openalex-snapshot
The 4D nucleome project
inferredcites →https://doi.org/10.1038/ng.368openalex-snapshot
The regulated retrotransposon transcriptome of mammalian cells
inferredcites →https://doi.org/10.1038/ng.3889openalex-snapshot
DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats
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/nrg.2016.93openalex-snapshot
Targeting the cancer epigenome for therapy
inferredcites →https://doi.org/10.1038/nrg2072openalex-snapshot
Transposable elements and the epigenetic regulation of the genome
inferredcites →https://doi.org/10.1038/nrg2337openalex-snapshot
Transposable elements and the evolution of regulatory networks
inferredcites →https://doi.org/10.1038/nrg3542openalex-snapshot
Single-cell sequencing-based technologies will revolutionize whole-organism science
inferredcites →https://doi.org/10.1038/s41467-017-00039-zopenalex-snapshot
Reconstructing cell cycle pseudo time-series via single-cell transcriptome data
inferredcites →https://doi.org/10.1073/pnas.82.7.1946openalex-snapshot
Expression of a mouse long terminal repeat is cell cycle-linked.
inferredcites →https://doi.org/10.1080/2162402x.2015.1122160openalex-snapshot
Unraveling the molecular pathways of DNA-methylation inhibitors: human endogenous retroviruses induce the innate immune response in tumors
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/nar/gks1215openalex-snapshot
INTERFEROME v2.0: an updated database of annotated interferon-regulated genes
inferredcites →https://doi.org/10.1101/gad.234294.113openalex-snapshot
DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos
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.191031.115openalex-snapshot
CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
inferredcites →https://doi.org/10.1101/gr.209601.116openalex-snapshot
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
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/10.1159/000084975openalex-snapshot
Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differences
inferredcites →https://doi.org/10.1172/jci69735openalex-snapshot
Aging and epigenetic drift: a vicious cycle
inferredcites →https://doi.org/10.1186/s13059-019-1812-2openalex-snapshot
MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions
inferredcites →https://doi.org/10.18632/oncotarget.9255openalex-snapshot
LTR12 promoter activation in a broad range of human tumor cells by HDAC inhibition
inferredcites →https://doi.org/10.7554/elife.35989openalex-snapshot
Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation

What points at this work

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

inferred← citeshttps://doi.org/10.1016/b978-0-12-819414-0.00006-9openalex-snapshot
Bisulfite PCR of repetitive genomic sequences
inferred← citeshttps://doi.org/10.1016/j.celrep.2023.112401openalex-snapshot
Cell-to-cell variability in Myc dynamics drives transcriptional heterogeneity in cancer cells
inferred← citeshttps://doi.org/10.1038/s41576-020-0251-yopenalex-snapshot
Measuring and interpreting transposable element expression
inferred← citeshttps://doi.org/10.1038/s41587-021-01093-1openalex-snapshot
Locus-specific expression of transposable elements in single cells with CELLO-seq
inferred← citeshttps://doi.org/10.1038/s41588-020-0645-yopenalex-snapshot
Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells
inferred← citeshttps://doi.org/10.1098/rstb.2019.0345openalex-snapshot
Mobile genomics: tools and techniques for tackling transposons
inferred← citeshttps://doi.org/10.1101/2020.10.02.322073openalex-snapshot
Transposable element expression at unique loci in single cells with CELLO-seq
inferred← citeshttps://doi.org/10.1101/2023.07.12.548732openalex-snapshot
Transposable elements regulate thymus development and function
inferred← citeshttps://doi.org/10.1101/gr.265173.120openalex-snapshot
Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data
inferred← citeshttps://doi.org/10.7554/elife.91037openalex-snapshot
Transposable elements regulate thymus development and function
inferred← citeshttps://doi.org/10.7554/elife.91037.1openalex-snapshot
Transposable elements regulate thymus development and function
inferred← citeshttps://doi.org/10.7554/elife.91037.2openalex-snapshot
Transposable elements regulate thymus development and function
inferred← citeshttps://doi.org/10.7554/elife.91037.3openalex-snapshot
Transposable elements regulate thymus development and function
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