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Evidence of transcription at polyT short tandem repeats

https://doi.org/10.1101/634261
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What this work says

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

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Sox9 transactivation and testicular expression of a novel human gene, KIAA0800
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Functional repeat‐derived RNAs often originate from retrotransposon‐propagated ncRNAs
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ggplot2: Elegant Graphics for Data Analysis
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Detecting Expressed Genes Using CAGE
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ggplot2
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Low diversity, activity, and density of transposable elements in five avian genomes
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Satellite non-coding RNAs: the emerging players in cells, cellular pathways and cancer
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The “initiator” as a transcription control element
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Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
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Genomic Nucleosome Organization Reconstituted with Pure Proteins
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The TOMM40 poly-T rs10524523 variant is associated with cognitive performance among non-demented elderly with type 2 diabetes
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The cis ‐regulatory effect of an Alzheimer's disease‐associated poly‐T locus on expression of TOMM40 and apolipoprotein E genes
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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
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Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin
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A TOMM40 poly-T variant modulates gene expression and is associated with vocabulary ability and decline in nonpathologic aging
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Mislocalization of neuronal tau in the absence of tangle pathology in phosphomutant tau knockin mice
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Polymorphism in the TOMM40 gene modifies the risk of developing sporadic inclusion body myositis and the age of onset of symptoms
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Poly(dA:dT) tracts: major determinants of nucleosome organization
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Functional consequences of bidirectional promoters
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A unified architecture of transcriptional regulatory elements
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Role of poly(A) tail length in Alu retrotransposition
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H3K4me2 reliably defines transcription factor binding regions in different cells
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
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Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
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Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs
inferredcites →https://doi.org/10.1038/nature11233openalex-snapshot
Landscape of transcription in human cells
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An integrated encyclopedia of DNA elements in the human genome
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An atlas of active enhancers across human cell types and tissues
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A promoter-level mammalian expression atlas
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Intragenic DNA methylation prevents spurious transcription initiation
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An atlas of human long non-coding RNAs with accurate 5′ ends
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Interactive visualization and analysis of large-scale sequencing datasets using ZENBU
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An integrated expression atlas of miRNAs and their promoters in human and mouse
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Nuclear stability and transcriptional directionality separate functionally distinct RNA species
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Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
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Abundant contribution of short tandem repeats to gene expression variation in humans
inferredcites →https://doi.org/10.1038/ng836openalex-snapshot
A polymorphic microsatellite that mediates induction of PIG3 by p53
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ChromHMM: automating chromatin-state discovery and characterization
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Unsupervised pattern discovery in human chromatin structure through genomic segmentation
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Comprehensive analysis of lncRNA-mRNA co-expression patterns identifies immune-associated lncRNA biomarkers in ovarian cancer malignant progression
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A new avenue for obtaining insight into the functional characteristics of long noncoding RNAs associated with estrogen receptor signaling
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The dark matter rises: the expanding world of regulatory RNAs
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Microsatellite instability regulates transcription factor binding and gene expression
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A polymorphic dinucleotide repeat in the rat nucleolin gene forms Z-DNA and inhibits promoter activity
inferredcites →https://doi.org/10.1073/pnas.1318948111openalex-snapshot
Defining functional DNA elements in the human genome
inferredcites →https://doi.org/10.1093/bioinformatics/btp163openalex-snapshot
Biopython: freely available Python tools for computational molecular biology and bioinformatics
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
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/btu056openalex-snapshot
bwtool: a tool for bigWig files
inferredcites →https://doi.org/10.1093/database/bav082openalex-snapshot
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data
inferredcites →https://doi.org/10.1093/nar/26.17.4056openalex-snapshot
Distinct frequency-distributions of homopolymeric DNA tracts in different genomes
inferredcites →https://doi.org/10.1093/nar/29.1.308openalex-snapshot
dbSNP: the NCBI database of genetic variation
inferredcites →https://doi.org/10.1093/nar/gkv1222openalex-snapshot
ClinVar: public archive of interpretations of clinically relevant variants
inferredcites →https://doi.org/10.1093/nar/gkw257openalex-snapshot
deepTools2: a next generation web server for deep-sequencing data analysis
inferredcites →https://doi.org/10.1093/nar/gkx1092openalex-snapshot
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments
inferredcites →https://doi.org/10.1101/495226openalex-snapshot
Multi-tissue analysis reveals short tandem repeats as ubiquitous regulators of gene expression and complex traits
inferredcites →https://doi.org/10.1101/gad.1026202openalex-snapshot
The RNA polymerase II core promoter: a key component in the regulation of gene expression
inferredcites →https://doi.org/10.1101/gr.109389.110openalex-snapshot
A unique H3K4me2 profile marks tissue-specific gene regulation
inferredcites →https://doi.org/10.1101/gr.115469.110openalex-snapshot
Unamplified cap analysis of gene expression on a single-molecule sequencer
inferredcites →https://doi.org/10.1101/gr.132159.111openalex-snapshot
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
inferredcites →https://doi.org/10.1101/gr.136127.111openalex-snapshot
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inferredcites →https://doi.org/10.1101/gr.177774.114openalex-snapshot
The landscape of human STR variation
inferredcites →https://doi.org/10.1101/gr.189027.114openalex-snapshot
Regulation of the ESC transcriptome by nuclear long noncoding RNAs
inferredcites →https://doi.org/10.1101/gr.231449.117openalex-snapshot
Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome
inferredcites →https://doi.org/10.1101/gr.231753.117openalex-snapshot
Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
inferredcites →https://doi.org/10.1101/gr.236075.118openalex-snapshot
Systematic interrogation of human promoters
inferredcites →https://doi.org/10.1101/gr.384802openalex-snapshot
Active Alu Element “A-Tails”: Size Does Matter
inferredcites →https://doi.org/10.1109/bibm.2018.8621093openalex-snapshot
Fast and Accurate Genome-Scale Identification of DNA-Binding Sites
inferredcites →https://doi.org/10.1111/j.2517-6161.1996.tb02080.xopenalex-snapshot
Regression Shrinkage and Selection Via the Lasso
inferredcites →https://doi.org/10.1126/science.1112014openalex-snapshot
The Transcriptional Landscape of the Mammalian Genome
inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
inferredcites →https://doi.org/10.1126/science.aav1898openalex-snapshot
The chromatin accessibility landscape of primary human cancers
inferredcites →https://doi.org/10.1146/annurev-genet-110711-155459openalex-snapshot
Noncoding Transcription at Enhancers: General Principles and Functional Models
inferredcites →https://doi.org/10.1177/154405910408300516openalex-snapshot
Indian Hedgehog: A Mechanotransduction Mediator in Condylar Cartilage
inferredcites →https://doi.org/10.1186/s13100-016-0070-zopenalex-snapshot
Restricting retrotransposons: a review
inferredcites →https://doi.org/10.1371/journal.pgen.1007969openalex-snapshot
Transcription-driven chromatin repression of Intragenic transcription start sites
inferredcites →https://doi.org/10.1534/genetics.117.300095openalex-snapshot
Emerging Properties and Functional Consequences of Noncoding Transcription.
inferredcites →https://doi.org/10.25080/majora-92bf1922-00aopenalex-snapshot
Data Structures for Statistical Computing in Python
inferredcites →https://doi.org/10.3233/jad-130119openalex-snapshot
Role of TOMM40 rs10524523 Polymorphism in Onset of Alzheimer's Disease Caused by the PSEN1 M146L Mutation
inferredcites →https://doi.org/10.3233/jad-2011-110743openalex-snapshot
TOMM40 rs10524523 Polymorphism's Role in Late-Onset Alzheimer's Disease and in Longevity
inferredcites →https://doi.org/10.3389/fgene.2015.00002openalex-snapshot
Non-coding RNA: what is functional and what is junk?

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.mocell.2026.100363openalex-snapshot
Tandem repeats in human brain evolution and disease susceptibility
inferred← citeshttps://doi.org/10.1038/s41598-022-17267-zopenalex-snapshot
Detection of repeat expansions in large next generation DNA and RNA sequencing data without alignment
inferred← citeshttps://doi.org/10.1101/2021.04.05.438449openalex-snapshot
Ultrafast, alignment-free detection of repeat expansions in next-generation DNA and RNA sequencing data
inferred← citeshttps://doi.org/10.1212/nxg.0000000000000404openalex-snapshot
Use of local genetic ancestry to assess TOMM40 -523′ and risk for Alzheimer disease
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