ArticleGenome research2014
Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 81 citations in OpenAlex.
- Article
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- KDM5 demethylases suppress R-loop-mediated 'viral mimicry' and DNA damage in breast cancer cells.eLife · 2025Article
- Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution.Nucleic acids research · 2025Article
- Genome assembly in the telomere-to-telomere era.Nature reviews. Genetics · 2024Review
- Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing.Cell genomics · 2024Article
- Digital telomere measurement by long-read sequencing distinguishes healthy aging from disease.Nature communications · 2024Article
- Human telomere length is chromosome end-specific and conserved across individuals.Science (New York, N.Y.) · 2024Article
- Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing.bioRxiv : the preprint server for biology · 2023Article
- Digital telomere measurement by long-read sequencing distinguishes healthy aging from disease.bioRxiv : the preprint server for biology · 2023Article
- Roles of Specialized Chromatin and DNA Structures at Subtelomeres inBiomolecules · 2023Review
- NPGREAT: assembly of human subtelomere regions with the use of ultralong nanopore reads and linked-reads.BMC bioinformatics · 2022Article
- Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers.Nucleic acids research · 2022Article
- Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres.Genome biology · 2022Article
- Telogator: a method for reporting chromosome-specific telomere lengths from long reads.Bioinformatics (Oxford, England) · 2022Article
- A complex network of interactions governs DNA methylation at telomeric regions.Nucleic acids research · 2022Article
- Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii.Nucleic acids research · 2021Article
- TERRA transcription destabilizes telomere integrity to initiate break-induced replication in human ALT cells.Nature communications · 2021Article
- Single-molecule telomere length characterization by optical mapping in nano-channel array: Perspective and review on telomere length measurement.Environmental toxicology and pharmacology · 2021Review
Corrections and comments
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Authors and funding
14 authors at 3 institutions in 1 country.
Funding
Abstract
Mapping genome-wide data to human subtelomeres has been problematic due to the incomplete assembly and challenges of low-copy repetitive DNA elements. Here, we provide updated human subtelomere sequence assemblies that were extended by filling telomere-adjacent gaps using clone-based resources. A bioinformatic pipeline incorporating multiread mapping for annotation of the updated assemblies using short-read data sets was developed and implemented. Annotation of subtelomeric sequence features as well as mapping of CTCF and cohesin binding sites using ChIP-seq data sets from multiple human cell types confirmed that CTCF and cohesin bind within 3 kb of the start of terminal repeat tracts at many, but not all, subtelomeres. CTCF and cohesin co-occupancy were also enriched near internal telomere-like sequence (ITS) islands and the nonterminal boundaries of subtelomere repeat elements (SREs) in transformed lymphoblastoid cell lines (LCLs) and human embryonic stem cell (ES) lines, but were not significantly enriched in the primary fibroblast IMR90 cell line. Subtelomeric CTCF and cohesin sites predicted by ChIP-seq using our bioinformatics pipeline (but not predicted when only uniquely mapping reads were considered) were consistently validated by ChIP-qPCR. The colocalized CTCF and cohesin sites in SRE regions are candidates for mediating long-range chromatin interactions in the transcript-rich SRE region. A public browser for the integrated display of short-read sequence-based annotations relative to key subtelomere features such as the start of each terminal repeat tract, SRE identity and organization, and subtelomeric gene models was established.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.