Deeply hidden genome organization directly mediated by SATB1

Mammalian genomes are organized by multi-layered chromatin folding. Whether and how three-dimensional genome organization contributes to cell-type specific transcription remains unclear. Here we uncover genome architecture formed by specialized sequences, base-unpairing regions (BURs), bound to a nuclear architectural protein, SATB1. SATB1 regulates cell-type specific transcription that underlies changes in cellular phenotypes. We developed a modified ChIP-seq protocol that stringently purifies genomic DNA only with its directly-associated proteins and unmasked previously-hidden BURs as direct SATB1 targets genome-wide. These SATB1-bound BURs are mutually exclusive from CTCF binding sites, and SATB1 is dispensable for CTCF/cohesion-mediated topologically associated domains (TADs). Instead, BURs largely overlap with lamina associated domains (LADs), and the fraction of BURs tethered to the SATB1 protein network in the nuclear interior is cell type-dependent. Our results reveal TAD-independent chromatin folding mediated by BUR sequences, which serve as genome architecture landmarks targeted by SATB1, to regulate cell-type specific gene expression.

Accessible Region Conformation Capture (ARC-C) gives high resolution insights into genome architecture and regulation

Nuclear organization and chromatin interactions are important for genome function, yet determining chromatin connections at high-resolution remains a major challenge. To address this, we developed Accessible Region Conformation Capture (ARC-C), which profiles interactions between regulatory elements genome-wide without a capture step. Applied to C. elegans, we identify ~15,000 significant interactions between regulatory elements at 500bp resolution. Of 105 TFs or chromatin regulators tested, we find that the binding sites of 60 are enriched for interacting with each other, making them candidates for mediating interactions. These include cohesin and condensin II. Applying ARC-C to a mutant of transcription factor BLMP-1 detected changes in interactions between its targets. ARC-C simultaneously profiles domain level architecture, and we observe that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) which interact with A/B (active/inactive) compartment-like structure. Furthermore, we discovered that inactive compartment interactions are dependent on H3K9 methylation. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution.

CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly

Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length > 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here.

Characterising genome architectures using Genome Decomposition Analysis

Genome architecture describes how genes and other features are arranged in genomes. These arrangements reflect the evolutionary pressures on genomes and underlie biological processes such as chromosomal segregation and the regulation of gene expression. We present a new tool called Genome Decomposition Analysis (GDA) that characterises genome architectures and acts as an accessible approach for discovering hidden features of a genome assembly. With the imminent deluge of high quality genome assemblies from projects such as the Darwin Tree of Life and the Earth BioGenome Project, GDA has been designed to facilitate their exploration and the discovery of novel genome biology. We highlight the effectiveness of our approach in characterising the genome architectures of single-celled eukaryotic parasites from the phylum Apicomplexa and show that it scales well to large genomes.SignificanceGenome sequencing has revealed that there are functionally important arrangements of genes, repetitive elements and regulatory sequences within chromosomes. Identifying these arrangements requires extensive computation and analysis. Furthermore, improvements in genome sequencing technology and the establishment of consortia aiming to sequence all species of eukaryotes mean that there is a need for high throughput methods for discovering new genome biology. Here we present a software pipeline, named GDA, which determines the patterns of genomic features across chromosomes and uses these to characterise genome architecture. We show that it recapitulates the known genome architecture of several Apicomplexan parasites and use it to identify features in a recently sequenced, less well-characterised genome. GDA scales well to large genomes and is freely available.