Topology regulatory elements: From shaping genome architecture to gene regulation

ProOvErlap: Assessing feature proximity/overlap and testing statistical significance from genomic intervals

Feature overlap is a critical concept in bioinformatics and occurs when two genomic intervals, usually represented as BED files, are located in the same genomic regions. Instead, feature proximity refers to the spatial proximity of genomic elements. For example, promoters typically overlap or are close to the genes they regulate. Overlap and proximity are also important in epigenetic studies. Here, the overlap of regions enriched for specific epigenetic modifications or accessible chromatin can elucidate complex molecular phenotypes. Consequently, the ability to analyze and interpret feature overlap and proximity is essential for understanding the biological processes that contribute to a given phenotype. To address this need, we present a computational method capable of analyzing data represented in the BED format. This method aims to quantitatively assess the degree of proximity or overlap between genomic features and to determine the statistical significance of these events in the context of a non-parametric randomization test. The aim is to understand whether the observed state differs from what would be expected by chance. The method is designed to be easy to use, requiring only a single command line to run, allowing straightforward overlap and proximity analysis. It also provides clear visualizations and publication-quality figures. In conclusion, this study highlights the importance of feature overlap and proximity in epigenetic studies and presents a method to improve the systematic assessment and interpretation of these features. A new resource for identifying biologically significant interactions between genomic features in both healthy and disease states.

Loop Catalog: a comprehensive HiChIP database of human and mouse samples

HiChIP enables cost-effective and high-resolution profiling of chromatin loops. To leverage the increasing number of HiChIP datasets, we developed Loop Catalog (https://loopcatalog.lji.org), a web-based database featuring loop calls from 1000+ distinct human and mouse HiChIP samples from 152 studies plus 44 high-resolution Hi-C samples. We demonstrate its utility for interpreting GWAS and eQTL variants through SNP-to-gene linking, identifying enriched sequence motifs and motif pairs, and generating regulatory networks and 2D representations of chromatin structure. Our catalog spans over 4.19M unique loops, and with embedded analysis modules, constitutes an important resource for the field.

3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization

Nuclear three dimensional (3D) folding of chromatin structure has been linked to gene expression regulation and correct developmental programs, but little is known about the 3D architecture of sex chromosomes within the nucleus, and how that impacts their role in sex determination. Here, we determine the sex-specific 3D organization of the model brown alga Ectocarpus chromosomes at 2 kb resolution, by mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report that Ectocarpus interphase chromatin exhibits a non-Rabl conformation, with strong contacts among telomeres and among centromeres, which feature centromere-specific LTR retrotransposons. The Ectocarpus chromosomes do not contain large local interactive domains that resemble TADs described in animals, but their 3D genome organization is largely shaped by post-translational modifications of histone proteins. We show that the sex determining region (SDR) within the U and V chromosomes are insulated and span the centromeres and we link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of the U and V chromosomes. Finally, we uncover the unique conformation of a large genomic region on chromosome 6 harboring an endogenous viral element, providing insights regarding the impact of a latent giant dsDNA virus on the host genome's 3D chromosomal folding.

Epigenetic regulation in adult neural stem cells

Neural stem cells (NSCs) exhibit self-renewing and multipotential properties. Adult NSCs are located in two neurogenic regions of adult brain: the ventricular-subventricular zone (V-SVZ) of the lateral ventricle and the subgranular zone of the dentate gyrus in the hippocampus. Maintenance and differentiation of adult NSCs are regulated by both intrinsic and extrinsic signals that may be integrated through expression of some key factors in the adult NSCs. A number of transcription factors have been shown to play essential roles in transcriptional regulation of NSC cell fate transitions in the adult brain. Epigenetic regulators have also emerged as key players in regulation of NSCs, neural progenitor cells and their differentiated progeny via epigenetic modifications including DNA methylation, histone modifications, chromatin remodeling and RNA-mediated transcriptional regulation. This minireview is primarily focused on epigenetic regulations of adult NSCs during adult neurogenesis, in conjunction with transcriptional regulation in these processes.