Biology subjects

Thieme, C. J.

Publications and source records attributed to Thieme, C. J..

5 recordsLinked to original sources

bioRxiv2026

Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes

Resolving the three-dimensional structure of chromatin with haplotype specificity remains a fundamental challenge for understanding genetic and epigenetic contributions to gene regulation in healthy development and in disease. Phasing of chromatin contacts derived by ligation-dependent methods relies on high single-nucleotide variant (SNV) density, which limits its applicability in human genomes where SNVs are sparse. Here, we present CoPhasing, a strategy that leverages the intrinsic haplotype fidelity of Genome Architecture Mapping (GAM), a ligation-free method that inherently captures haplotype-matched genomic neighborhoods in thin nuclear slices. CoPhasing assigns SNV-free reads to their haplotype through proximity to informative reads, enabling efficient and accurate phasing even in SNV-sparse regions. Applying CoPhasing genome-wide reveals extensive, previously inaccessible structural heterogeneity between human homologous chromosomes, demonstrating the power of GAM CoPhasing to investigate allele-specific differences in 3D genome organization and their relevance to gene regulation and disease.

genomics↗

bioRxiv2024

An integrated view of the structure and function of the human 4D nucleome

The dynamic three-dimensional (3D) organization of the human genome (the "4D Nucleome") is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view of human 3D genome organization in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We provide extensive benchmarking of 3D genome mapping assays and integrate these diverse datasets to annotate spatial genomic features across scales. The data reveal a rich complexity of chromatin domains and their sub-nuclear positions, and over one hundred thousand structural loops and promoter-enhancer interactions. We developed 3D models of population-based and individual cell-to-cell variation in genome structure, establishing connections between chromosome folding, nuclear organization, chromatin looping, gene transcription, and DNA replication. We demonstrate the use of computational methods to predict genome folding from DNA sequence, uncovering potential effects of genetic variants on genome structure and function. Together, this comprehensive analysis contributes insights into human genome organization and enhances our understanding of connections between the regulation of genome function and 3D genome organization in general.

genomics↗

bioRxiv2024

Extensive folding variability between homologous chromosomes in mammalian cells

Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.

genomics↗

bioRxiv2022

3D genome topologies distinguish pluripotent epiblast and primitive endoderm cells in the mouse blastocyst

The development of embryonic cell lineages is tightly controlled by transcription factors that regulate gene expression and chromatin organisation. To investigate the specialisation of 3D genome structure in pluripotent or extra-embryonic endoderm lineages, we applied Genome Architecture Mapping (GAM) in embryonic stem (ES) cells, extra-embryonic endoderm (XEN) stem cells, and in their in vivo counterparts, the epiblast (Epi) and primitive endoderm (PrE) cells, respectively. We discover extensive differences in 3D genome topology including the formation domain boundaries that differ between Epi and PrE lineages, both in vivo and in vitro, at lineage commitment genes. In ES cells, Sox2 contacts other active regions enriched for NANOG and SOX2 binding sites. PrE-specific genes, such as Lama1 and Gata6, form repressive chromatin hubs in ES cells. Lama1 activation in XEN or PrE cells coincides with its extensive decondensation. Putative binding sites for OCT4 and SNAIL, or GATA4/6, distinguish chromatin contacts unique to embryonic or extra-embryonic lineages, respectively. Overall, 3D genome folding is highly specialised in early development, especially at genes encoding factors driving lineage identity. HighlightsO_LIES and XEN cells have specialised 3D genome structures C_LIO_LIGAM applied in the blastocyst distinguishes Epi and PrE genome structures C_LIO_LILineage specific genes establish cell-type specific chromatin contacts C_LIO_LISpecific chromatin contacts feature putative bindings sites for GATA4/6 in XEN cells and SNAIL in ES cells C_LI

developmental biology↗

bioRxiv2020

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C

Technologies for measuring 3D genome topology are increasingly important for studying mechanisms of gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of Genome Architecture Mapping (GAM), a ligation-free technique to map chromatin contacts genome-wide. We perform a detailed comparison of contacts obtained by multiplex-GAM and Hi-C using mouse embryonic stem (mES) cells. We find that both methods detect similar topologically associating domains (TADs). However, when examining the strongest contacts detected by either method, we find that only one third of these are shared. The strongest contacts specifically found in GAM often involve "active" regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain "inactive" regions. Our work shows that active genomic regions are involved in extensive complex contacts that currently go under-estimated in genome-wide ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies.

molecular biology↗