Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods
Abstract
How genomic changes translate into organismal novelties is often confounded by the multi-layered nature of genome architecture and the long evolutionary timescales over which molecular changes can accumulate. Coleoid cephalopods (squid, cuttlefish, and octopus) provide a unique system to study these processes due to a large-scale chromosomal rearrangement in the coleoid ancestor that gave rise to highly modified karyotypes, followed by lineage-specific repeat expansions, fusions, and translocations. How these events have shaped gene regulatory patterns underlying the evolution of coleoid innovations, including their large and elaborately structured nervous systems, novel organs, and complex behaviours, remains poorly understood. To address this, we integrate Micro-C, RNA-seq, and ATAC-seq across multiple coleoid species, developmental stages, and tissues. We find that while chromatin domains are broadly conserved, hundreds of chromatin loops are species- and context-specific, with distinct regulation signatures and dynamic expression profiles. CRISPR–Cas9 knockout of a putative regulatory sequence within a conserved region demonstrates the role of loops in neural development and the prevalence of long-range interactions that extend beyond chromatin domains. We propose that differential evolutionary constraints across the coleoid 3D genome allow macroevolutionary processes to shape genome topology in distinct ways, facilitating the emergence of novel regulatory entanglements and ultimately contributing to the evolution and maintenance of complex traits in the coleoids.
Related
- Mitotic centromeres organize in repeat-subunits with specialized histone landscape and multi-domain architecture as revealed by expansion microscopy
- Dynamic climate and ecological expansion drive body morphology evolution in fossil and extant neocoleoid cephalopods
- Melanoma suppresses galectin-9-glycan axis in dendritic cells and galectin-9 restoration limits T regulatory cell expansion
- A near-complete quail genome identifies heterochromatin expansion and chromosome architecture remodeling
- An amyloid-β/APP regulatory layer in human brown adipocyte recruitment identifies repurposable drugs for thermogenic fat expansion
BibTeX
@article{rogers2026genome,
title = {{Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods}},
author = {Thea F. Rogers and Jessica Stock and Natalie Grace Schulz and Gözde Yalçin and Simone Rencken and Anton Weissenbacher and Tereza Clarence and Darrin T. Schultz and Clifton W. Ragsdale and Caroline B. Albertin and Oleg Simakov},
journal = {Nature Communications},
year = {2026},
month = oct,
doi = {10.1038/s41467-026-77625-7},
url = {https://www.nature.com/articles/s41467-026-77625-7},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods
AU - Thea F. Rogers
AU - Jessica Stock
AU - Natalie Grace Schulz
AU - Gözde Yalçin
AU - Simone Rencken
AU - Anton Weissenbacher
AU - Tereza Clarence
AU - Darrin T. Schultz
AU - Clifton W. Ragsdale
AU - Caroline B. Albertin
AU - Oleg Simakov
PY - 2026
DA - 2026/10/09
JO - Nature Communications
DO - 10.1038/s41467-026-77625-7
UR - https://www.nature.com/articles/s41467-026-77625-7
AB - How genomic changes translate into organismal novelties is often confounded by the multi-layered nature of genome architecture and the long evolutionary timescales over which molecular changes can accumulate. Coleoid cephalopods (squid, cuttlefish, and octopus) provide a unique system to study these processes due to a large-scale chromosomal rearrangement in the coleoid ancestor that gave rise to highly modified karyotypes, followed by lineage-specific repeat expansions, fusions, and translocations. How these events have shaped gene regulatory patterns underlying the evolution of coleoid innovations, including their large and elaborately structured nervous systems, novel organs, and complex behaviours, remains poorly understood. To address this, we integrate Micro-C, RNA-seq, and ATAC-seq across multiple coleoid species, developmental stages, and tissues. We find that while chromatin domains are broadly conserved, hundreds of chromatin loops are species- and context-specific, with distinct regulation signatures and dynamic expression profiles. CRISPR–Cas9 knockout of a putative regulatory sequence within a conserved region demonstrates the role of loops in neural development and the prevalence of long-range interactions that extend beyond chromatin domains. We propose that differential evolutionary constraints across the coleoid 3D genome allow macroevolutionary processes to shape genome topology in distinct ways, facilitating the emergence of novel regulatory entanglements and ultimately contributing to the evolution and maintenance of complex traits in the coleoids.
SN - 2041-1723
ER -