Biology subjects

Leuchtenberg, S.

Publications and source records attributed to Leuchtenberg, S..

2 recordsLinked to original sources

bioRxiv2026

Single-Platform Nanopore Sequencing Enables Diploid Telomere-to-Telomere Genome Assembly and Haplotype-Resolved 3D Chromatin Maps

Telomere-to-telomere (T2T) genome assembly has transformed human genomics by resolving centromeres, segmental duplications, and other previously inaccessible regions. However, most diploid T2T assemblies rely on the combination of multi-platform sequencing strategies including short read genome sequencing, PacBio HiFi, Oxford Nanopore ultra-long reads, and chromatin conformation capture data (Hi-C), limiting both scalability and accessibility. Here, we present a streamlined Nanopore-only workflow for diploid human T2T assembly using three ultra-long and one Pore-C PromethION flow cell per individual. Across 23 genetically diverse individuals, we generated 360 gapless chromosomes and 446 near-complete T2T scaffolds, achieving median consensus accuracy of QV50 without Duplex sequencing or hybrid polishing. Assembly continuity, gene completeness, and structural variant detection were comparable to multi-platform Human Pangenome Reference Consortium assemblies. Pore-C data enabled chromosome-scale haplotype phasing without parental information and supported generation of haplotype-resolved chromatin contact maps. Integrated methylation and 3D genome analyses revealed allele-specific chromatin organization at imprinted loci and clear signatures of X-chromosome inactivation. Our openly accessible dataset expands public T2T resources and demonstrates that reference-grade diploid assemblies, phased methylomes, and 3D genome maps can be derived from a single sequencing platform. This approach reduces technical barriers and supports scalable population and functional genomics in the T2T era.

genomics↗

bioRxiv2026

A molecular framework of chromatin extrusion in plants

Three-dimensional genome organization is a fundamental regulator of gene expression, yet the mechanisms shaping higher-order chromatin folding in plants remain poorly defined. Here, we identify the Arabidopsis cohesin regulator PDS5A as a central modulator of chromatin loop extrusion and topologically associating domain (TAD)-like architecture. Using Hi-C and Micro-C, we show that loss of PDS5A strongly enhances TAD-like domains and nucleosome-scale stripes and loops across chromosome arms, while leaving large-scale compartmentalization largely intact and revealing conserved TAD-like patterns across tissues and ploidy levels. Genetic analyses indicate that Arabidopsis TAD-like domain formation relies on the plant-specific kleisin SYN4 and is antagonized by WAPL1/2, with PDS5A acting as the dominant cohesin-unloading factor that limits loop extension. Biochemical experiments demonstrate that PDS5A physically associates with cohesin and that its function in suppressing TAD-like domains is independent of direct Tudor domain-mediated binding to H3K4me1-marked chromatin. Micro-C further resolves that chromatin loop and stripe anchors formed in pds5a are highly enriched at accessible, strongly transcribed promoters and are marked by the plant site II motif TGGGCC/T, implicating site II-binding transcription factors as plant-specific boundary elements analogous to CTCF in animals. Finally, mutational disruption of distal chromatin anchors shows that newly formed chromatin contacts in pds5a can act as cis-regulatory modules that influence target gene expression. Together, these findings identify a PDS5A-regulated chromatin extrusion module that shapes plant 3D genome architecture and uncover a promoter- and motif-based logic for loop anchoring and transcriptional control in plants.

genomics↗