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Genome-wide analysis of the association of transposable elements with gene regulation suggests that Alu elements have the largest overall regulatory impact

https://doi.org/10.1101/142018

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What this work says

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

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Simultaneous Inference in General Parametric Models

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The impact of multiple splice sites in human L1 elements

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Endogenous retroviral LTRs as promoters for human genes: A critical assessment

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Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions

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Transposable element small RNAs as regulators of gene expression

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Transposable elements are found in a large number of human protein-coding genes

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Interspersed repeats and other mementos of transposable elements in mammalian genomes

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Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man

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Initial sequencing and analysis of the human genome

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Genetic and Pharmacogenetic Associations Between NOS3 Polymorphisms, Blood Pressure, and Cardiovascular Events in Hypertension

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Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes

inferredcites →https://doi.org/10.1038/nature09701openalex-snapshot

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

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Mapping and analysis of chromatin state dynamics in nine human cell types

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Systematic identification of abundant A-to-I editing sites in the human transcriptome

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Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes

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

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RNA truncation by premature polyadenylation attenuates human mobile element activity

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

inferredcites →https://doi.org/10.1038/nrg2072openalex-snapshot

Transposable elements and the epigenetic regulation of the genome

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The impact of retrotransposons on human genome evolution

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A new exon created by intronic insertion of a rearranged LINE-1 element as the cause of chronic granulomatous disease

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Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons

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Long Terminal Repeats Are Used as Alternative Promoters for the Endothelin B Receptor and Apolipoprotein C-I Genes in Humans

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Retroviral promoters in the human genome

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BEDTools: a flexible suite of utilities for comparing genomic features

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Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/gbe/evr015openalex-snapshot

Effect of the Transposable Element Environment of Human Genes on Gene Length and Expression

inferredcites →https://doi.org/10.1093/hmg/ddp152openalex-snapshot

Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes

inferredcites →https://doi.org/10.1093/molbev/mst045openalex-snapshot

Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

inferredcites →https://doi.org/10.1093/nar/gkl027openalex-snapshot

LINE-1 RNA splicing and influences on mammalian gene expression

inferredcites →https://doi.org/10.1093/nar/gkl842openalex-snapshot

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

inferredcites →https://doi.org/10.1093/nar/gkn540openalex-snapshot

Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes

inferredcites →https://doi.org/10.1093/nar/gkr1055openalex-snapshot

The UCSC Genome Browser database: extensions and updates 2011

inferredcites →https://doi.org/10.1093/nar/gks1048openalex-snapshot

The UCSC Genome Browser database: extensions and updates 2013

inferredcites →https://doi.org/10.1101/gad.17446611openalex-snapshot

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

inferredcites →https://doi.org/10.1101/gr.216150.116openalex-snapshot

Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes

inferredcites →https://doi.org/10.1101/gr.2745804openalex-snapshot

The human L1 promoter: Variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity

inferredcites →https://doi.org/10.1101/gr.282402openalex-snapshot

Mammalian Retroelements

inferredcites →https://doi.org/10.1101/gr.2855504openalex-snapshot

Widespread RNA Editing of EmbeddedAluElements in the Human Transcriptome

inferredcites →https://doi.org/10.1126/science.1237973openalex-snapshot

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

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/10.1159/000084979openalex-snapshot

Repbase Update, a database of eukaryotic repetitive elements

inferredcites →https://doi.org/10.1161/01.cir.100.14.1515openalex-snapshot

A Common Variant of the Endothelial Nitric Oxide Synthase (Glu298→Asp) Is a Major Risk Factor for Coronary Artery Disease in the UK

inferredcites →https://doi.org/10.1186/1471-2105-12-323openalex-snapshot

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

inferredcites →https://doi.org/10.1186/1471-2105-7-474openalex-snapshot

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

inferredcites →https://doi.org/10.1186/1471-2164-7-133openalex-snapshot

Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes

inferredcites →https://doi.org/10.1186/1471-2164-8-291openalex-snapshot

Exonization of the LTR transposable elements in human genome

inferredcites →https://doi.org/10.1186/1759-8753-5-14openalex-snapshot

Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression

inferredcites →https://doi.org/10.1186/gb-2003-4-5-p3openalex-snapshot

DAVID: Database for Annotation, Visualization, and Integrated Discovery

inferredcites →https://doi.org/10.1186/gb-2007-8-6-r127openalex-snapshot

Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome

inferredcites →https://doi.org/10.1186/gb-2011-12-12-236openalex-snapshot

Alu elements: know the SINEs

inferredcites →https://doi.org/10.1186/gb-2012-13-11-r107openalex-snapshot

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

inferredcites →https://doi.org/10.1371/journal.pgen.1003234openalex-snapshot

Transposable Elements Re-Wire and Fine-Tune the Transcriptome

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/10.1371/journal.pone.0004321openalex-snapshot

The Effect of Transposable Element Insertions on Gene Expression Evolution in Rodents

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Econometric Computing with HC and HAC Covariance Matrix Estimators

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The Intertwining of Transposable Elements and Non-Coding RNAs

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41598-025-15825-9openalex-snapshot

Genome-wide characterization of lumpy skin disease virus isolate from Bangladesh

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