Biology subjects

Real, T. D.

Publications and source records attributed to Real, T. D..

4 recordsLinked to original sources

bioRxiv2026

Single-molecule variation in telomeric sequence and structure across humans

The repetitive architectures of telomeric and subtelomeric regions have obscured studies of their genetic variation and chromatin organization across the human population. Here, we integrate near-complete diploid genome assemblies from 212 individuals with matched long-read sequencing data to construct an atlas of 316,146 telomere-spanning molecules across 12,080 chromosome-end-resolved telomere arrays. This atlas reveals that nearly every chromosome end harbors a structured and unique pattern of telomere variant repeats (TVR), or TVR code, with subtelomere-proximal TVR codes being heritable, somatically stable, and influenced by subtelomeric TAR1 regulatory elements. Despite ongoing cycles of telomere shortening and elongation in the germline, proximal TVR codes are maintained across the human population. These TVR codes expose rare telomerase-independent events that lengthen telomeres in the germline, including interchromosomal telomere exchange and recurrent internal duplications within telomere arrays. Furthermore, single-molecule chromatin fiber sequencing across 26,972 molecules spanning the telomere-subtelomere boundary confirms that TVR-rich regions adopt telomeric chromatin but introduce discrete discontinuities into otherwise compact telomeric chromatin fibers. Together, our results link chromosome-end sequence variation to telomere cap formation and telomerase-independent telomere extension mechanisms in the human germline.

genomics↗

bioRxiv2026

Evaluating genome assemblies with HMM-Flagger

HMM-Flagger is a reference-free tool for detecting structural errors in haplotype-resolved genome assemblies based upon the coverage of mapped reads. It models read coverage with a hidden Markov model augmented by a Gaussian autoregressive process, which enables classifying coverage anomalies as erroneous blocks, false duplications, or collapsed blocks. Trained and tested on synthetic misassemblies, it detected synthetic errors using Pacific Biosciences HiFi and Oxford Nanopore Technologies R10 data with F1 scores of 78.4% and 60.4% respectively. When applied to six HG002 assemblies it revealed multiple large misassemblies including false duplications and collapse events in human satellites. Applied to assemblies from the Human Pangenome Reference Consortium (HPRC), HMM-Flagger demonstrated substantial improvements from release 1 (0.94% error rate) to release 2 (0.38%), reflecting technological advances. HMM-Flagger also validated NOTCH2NL assemblies in HPRC release 2 and confirmed the correctness of three novel structural configurations.

bioinformatics↗

bioRxiv2025

Genetic diversity and regulatory features of human-specific NOTCH2NL duplications

NOTCH2NL (NOTCH2-N-terminus-like) genes arose from ape-specific chromosome 1 segmental duplications implicated in human brain cortical expansion, including an incomplete NOTCH2 gene. Genetic characterization of these loci and their regulation is complicated because they are embedded in large, nearly identical duplications that predispose to recurrent microdeletion syndromes. Using near-complete long-read assemblies generated from 70 human and 12 ape haploid genomes, we show independent recurrent duplication among apes with protein-coding copies emerging in humans 2.2-3.7 million years ago. We distinguish NOTCH2NL paralogs present in every human haplotype (NOTCH2NLA) from copy number variable ones. We also characterize large-scale structural variation, including gene conversion, for 28% of haplotypes leading to a previously undescribed paralog, NOTCH2tv. Finally, we apply Fiber-seq and long-read transcript sequencing to human dorsal forebrain organoids to characterize the regulatory landscape and find that the most fixed paralogs, NOTCH2 and NOTCH2NLA, harbor the greatest number of paralog-specific elements potentially driving their regulation.

genomics↗

bioRxiv2023

Conservation of chromatin organization within human and primate centromeres

The focal attachment of the kinetochore to the centromere is essential for genome maintenance, yet the highly repetitive nature of satellite regional centromeres, such as those in humans, limits our understanding of their chromatin organization. We demonstrate that single-molecule chromatin fiber sequencing (Fiber-seq) can uniquely co-resolve kinetochore and surrounding chromatin architectures along point centromeres, revealing largely homogeneous single-molecule kinetochore occupancy along each chromosome. In contrast, extension of Fiber-seq to regional satellite centromeres exposed marked per-molecule heterogeneity in their chromatin organization. Regional CENP-A-marked centromere cores uniquely contain a dichotomous chromatin organization (dichromatin) composed of compacted nucleosome arrays punctuated with highly accessible chromatin patches. CENP-B occupancy phases dichromatin to the underlying alpha-satellite repeat within centromere cores, but is not necessary for dichromatin formation. Centromere core dichromatin is a conserved feature between humans despite the marked divergence of their underlying alpha-satellite organization and is similarly a conserved feature along regional centromeres that lack satellite repeats in gibbon. Overall, the chromatin organization of regional centromeres is defined by marked per-molecule heterogeneity, likely buffering kinetochore attachment against sequence and structural variability within regional centromeres. HighlightsO_LIDichotomous accessible and compacted chromatin (dichromatin) marks centromere cores C_LIO_LIHighly accessible chromatin patches punctuate sites of kinetochore attachment C_LIO_LIDichromatin can form irrespective of CENP-B occupancy C_LIO_LIConservation within centromeres is mediated at the level of chromatin, not DNA C_LI

genomics↗