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Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia

https://doi.org/10.1101/772954
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What this work says

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

inferredcites →https://doi.org/10.1002/1878-0261.12407openalex-snapshot
The expression signature of cancer‐associated KRAB ‐ ZNF factors identified in TCGA pan‐cancer transcriptomic data
inferredcites →https://doi.org/10.1002/gcc.22794openalex-snapshot
Transcriptional networks in acute myeloid leukemia
inferredcites →https://doi.org/10.1002/jcb.27645openalex-snapshot
Prognostic role of TPD52 in acute myeloid leukemia: A retrospective multicohort analysis
inferredcites →https://doi.org/10.1002/mc.22794openalex-snapshot
Decreased SCIN expression, associated with promoter methylation, is a valuable predictor for prognosis in acute myeloid leukemia
inferredcites →https://doi.org/10.1016/j.ccell.2014.10.012openalex-snapshot
Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia
inferredcites →https://doi.org/10.1016/j.ccr.2009.11.020openalex-snapshot
DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia
inferredcites →https://doi.org/10.1016/j.ccr.2014.02.008openalex-snapshot
A Remote GATA2 Hematopoietic Enhancer Drives Leukemogenesis in inv(3)(q21;q26) by Activating EVI1 Expression
inferredcites →https://doi.org/10.1016/j.cell.2013.02.022openalex-snapshot
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
inferredcites →https://doi.org/10.1016/j.cell.2013.10.001openalex-snapshot
A Retrotransposon-Driven Dicer Isoform Directs Endogenous Small Interfering RNA Production in Mouse Oocytes
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.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.celrep.2018.12.098openalex-snapshot
Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes
inferredcites →https://doi.org/10.1016/j.gde.2016.03.011openalex-snapshot
Genetic and epigenetic heterogeneity in acute myeloid leukemia
inferredcites →https://doi.org/10.1016/j.prp.2013.08.004openalex-snapshot
Expression of cancer/testis (CT) antigens in squamous cell carcinoma of the head and neck: Evaluation as markers of squamous dysplasia
inferredcites →https://doi.org/10.1016/j.stem.2019.03.012openalex-snapshot
Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs
inferredcites →https://doi.org/10.1016/s0021-9258(18)68638-7openalex-snapshot
Two copies of the human apolipoprotein C-I gene are linked closely to the apolipoprotein E gene.
inferredcites →https://doi.org/10.1017/s0094837300004310openalex-snapshot
Exaptation—a Missing Term in the Science of Form
inferredcites →https://doi.org/10.1038/nature21683openalex-snapshot
KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks
inferredcites →https://doi.org/10.1038/nbt.3122openalex-snapshot
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
inferredcites →https://doi.org/10.1038/ng.2553openalex-snapshot
Endogenous retroviruses function as species-specific enhancer elements in the placenta
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/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/nm.2129openalex-snapshot
Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
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/onc.2015.308openalex-snapshot
Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma
inferredcites →https://doi.org/10.1038/oncsis.2015.49openalex-snapshot
Lipid metabolic reprogramming in cancer cells
inferredcites →https://doi.org/10.1038/s41375-018-0010-7openalex-snapshot
ANP32A regulates histone H3 acetylation and promotes leukemogenesis
inferredcites →https://doi.org/10.1038/s41375-018-0311-xopenalex-snapshot
Global long terminal repeat activation participates in establishing the unique gene expression programme of classical Hodgkin lymphoma
inferredcites →https://doi.org/10.1038/s41587-019-0201-4openalex-snapshot
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
inferredcites →https://doi.org/10.1038/s41588-018-0270-1openalex-snapshot
Subtype-specific regulatory network rewiring in acute myeloid leukemia
inferredcites →https://doi.org/10.1038/s41588-019-0373-3openalex-snapshot
Transposable elements drive widespread expression of oncogenes in human cancers
inferredcites →https://doi.org/10.1038/sj.onc.1210951openalex-snapshot
Apolipoprotein C-1 maintains cell survival by preventing from apoptosis in pancreatic cancer cells
inferredcites →https://doi.org/10.1056/nejmoa1301689openalex-snapshot
Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
inferredcites →https://doi.org/10.1073/pnas.1004139107openalex-snapshot
Long-range function of an intergenic retrotransposon
inferredcites →https://doi.org/10.1073/pnas.1602886113openalex-snapshot
A distant trophoblast-specific enhancer controls HLA-G expression at the maternal–fetal interface
inferredcites →https://doi.org/10.1074/jbc.m006557200openalex-snapshot
Long Terminal Repeats Are Used as Alternative Promoters for the Endothelin B Receptor and Apolipoprotein C-I Genes in Humans
inferredcites →https://doi.org/10.1084/jem.20130624openalex-snapshot
RHEX, a novel regulator of human erythroid progenitor cell expansion and erythroblast development
inferredcites →https://doi.org/10.1093/bioinformatics/btn480openalex-snapshot
F-Seq: a feature density estimator for high-throughput sequence tags
inferredcites →https://doi.org/10.1093/emboj/17.13.3714openalex-snapshot
Hoxa9 transforms primary bone marrow cells through specific collaboration with Meis1a but not Pbx1b
inferredcites →https://doi.org/10.1093/nar/gkt1036openalex-snapshot
BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells
inferredcites →https://doi.org/10.1093/nar/gkv1272openalex-snapshot
The Dfam database of repetitive DNA families
inferredcites →https://doi.org/10.1093/nar/gkv416openalex-snapshot
The MEME Suite
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/pdb.prot5384openalex-snapshot
DNase-seq: A High-Resolution Technique for Mapping Active Gene Regulatory Elements across the Genome from Mammalian Cells
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/jvi.02216-06openalex-snapshot
Rate of Recombinational Deletion among Human Endogenous Retroviruses
inferredcites →https://doi.org/10.1128/jvi.79.19.12507-12514.2005openalex-snapshot
Genomewide Screening Reveals High Levels of Insertional Polymorphism in the Human Endogenous Retrovirus Family HERV-K(HML2): Implications for Present-Day Activity
inferredcites →https://doi.org/10.1128/microbiolspec.mdna3-0009-2014openalex-snapshot
Mammalian Endogenous Retroviruses
inferredcites →https://doi.org/10.1158/2159-8290.cd-16-1032openalex-snapshot
Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers
inferredcites →https://doi.org/10.1158/2326-6066.cir-13-0124openalex-snapshot
Cancer–Testis Antigen Expression in Digestive Tract Carcinomas: Frequent Expression in Esophageal Squamous Cell Carcinoma and Its Precursor Lesions
inferredcites →https://doi.org/10.1159/000479837openalex-snapshot
High Expression of AHSP, EPB42, GYPC and HEMGN Predicts Favorable Prognosis in FLT3-ITD-Negative Acute Myeloid Leukemia
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/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1186/s13059-017-1381-1openalex-snapshot
RNA virus interference via CRISPR/Cas13a system in plants
inferredcites →https://doi.org/10.1186/s13100-016-0080-xopenalex-snapshot
Endogenous retroviral promoter exaptation in human cancer
inferredcites →https://doi.org/10.1186/s13100-018-0142-3openalex-snapshot
Variation in proviral content among human genomes mediated by LTR recombination
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/10.2147/cmar.s192529openalex-snapshot
Apolipoprotein C1 (APOC1) promotes tumor progression via MAPK signaling pathways in colorectal cancer
inferredcites →https://doi.org/10.3324/haematol.2013.092007openalex-snapshot
Epigenetics in the hematologic malignancies
inferredcites →https://doi.org/10.5281/zenodo.438045openalex-snapshot
Apocrita - High Performance Computing Cluster For Queen Mary University Of London
inferredcites →https://doi.org/10.7554/elife.35989openalex-snapshot
Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation
inferredcites →https://doi.org/10.7554/elife.44344openalex-snapshot
Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells

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

inferred← citeshttps://doi.org/10.1186/s13059-023-03085-7openalex-snapshot
Statistical learning quantifies transposable element-mediated cis-regulation
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