Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline

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 transcriptrich 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.

Functional characterization of the TERRA transcriptome at damaged telomeres

“…RNA-seq experiments were performed on the TERRA-enriched RNA fraction and on total nuclear RNA (input) from wild-type or TRF2-depleted HeLa cells. The reads were mapped to the most complete assembly available of human subtelomeres (http://www.wistar.org/lab/harold-c-riethman-phd/page/subtelomere-assemblies) 31 and read density profiles were generated counting the number of reads aligned at each position along the subtelomeric regions. The TERRA transcripts stemming from different chromosome ends were identified based on their enriched read density in the UUAGGG-containing RNA fraction compared with the input material.…”

Nuclear respiratory factor 1 and endurance exercise promote human telomere transcription

“…1A and table S1) refers to subtelomeric sequences from the study by Stong et al . ( 13 ) that were either missing in the GRch38/hg38 assembly or lacking TTAGGG repeats at their 3′ ends. Sequences of p arms from acrocentric chromosomes are not available.…”

“…Missing subtelomeric sequences or sequences that did not have TTAGGG telomeric regions at the 3′ ends in GRCh38/hg38 assembly were obtained from the study by Stong et al . ( 13 ) and were classified as low confidence. Sequences of p arms from acrocentric 13, 14, 15, 21, and 22 chromosomes are missing.…”

Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4

“…Inter-chromosomal fusion events were identified from those discordant sequence read pairs that mapped to both a custom subtelomeric reference (comprised of 17p, XpYp, and the 21q family subtelomeric sequences appended with all known telomere variant repeats) (Jones et al 2014) and a modified human genome hg19 reference (supplemented with updated subtelomeric sequences and the 17p, XpYp, and 21q sequences) (Stong et al 2014).…”