Spatial organisation of the genome is essential for regulating gene activity, yet the mechanisms that shape this three-dimensional organisation in eukaryotes are far from understood. Here, we combine bioinformatic determination of chromatin states during normal growth and heat shock, and computational polymer modelling of genome structure, with quantitative microscopy and Hi-C to demonstrate that differential mobility of yeast chromosome segments leads to spatial self-organisation of the genome. We observe that more than forty percent of chromatin-associated proteins display a poised and heterogeneous distribution along the chromosome, creating a heteropolymer. This distribution changes upon heat shock in a concerted, state-specific manner. Simulating yeast chromosomes as heteropolymers, in which the mobility of each segment depends on its cumulative protein occupancy, results in functionally relevant structures, which match our experimental data. This thermodynamically driven self-organisation achieves spatial clustering of poised genes and mechanistically contributes to the directed relocalisation of active genes to the nuclear periphery upon heat shock. One Sentence Summary:Unequal protein occupancy and chromosome segment mobility drive 3D organisation of the genome.Main Text: Eukaryotic genomes are highly organised in three dimensions ( 1 , 2 ) and this spatial organisation has to be maintained in order to achieve the correct gene expression profiles ( 3 -6 ) . The 3D organisation of the genome is thus central to many aspects of cell biology and has been intensely investigated during normal growth ( 7 -9 ) , differentiation ( 10 -12 ) , cell division ( 13 ) , senescence ( 14 ) , and disease ( 5 , 6 , 15 ) , and has been shown to arise independently of transcription ( 16 ) . In the budding yeast Saccharomyces cerevisiae , target genes of most transcription factors are enriched in specific regions along the chromosome in one dimension ( 17 ) , or in the genome in three dimensions ( 18 ) . A central question in the field is by which mechanisms this 3D organisation is achieved.Any mechanism that organises genome structure has to do so in a highly dynamic and crowded nucleoplasm ( 19 , 20 ) . The prevalent view is that 3D genome organisation comes about despite the known intrinsic fluctuations of the chromatin fibre. Most studies focus on stable interactions between DNA-bound proteins that connect two chromatin loci ( 9 , 21 -27 ) . Here, we propose and validate a fundamentally different mechanism: The mobility of the chromatin fibre is not uniform, but heterogeneous, along its length, as a result of the unequal distribution of protein binding along the genome. This leads to thermodynamically driven self-organisation, which we observe experimentally, and which we show to have important functional implications.Determination and characterisation of chromatin states. In order to analyse the global effects of protein binding on spatial organisation of yeast chromosomes, and incorporate these data into pe...
Snorc (Small NOvel Rich in Cartilage) has been identified as a chondrocyte-specific gene in the mouse. Yet little is known about the SNORC protein biochemical properties, and mechanistically how the gene is regulated transcriptionally in a tissue-specific manner. The goals of the present study were to shed light on those important aspects. The chondrocyte nature of Snorc expression was confirmed in mouse and rat tissues, in differentiated (day 7) ATDC5, and in RCS cells where it was constitutive. Topological mapping and biochemical analysis brought experimental evidences that SNORC is a type I protein carrying a chondroitin sulfate (CS) attached to serine 44. The anomalous migration of SNORC on SDS-PAGE was due to its primary polypeptide features, suggesting no additional post-translational modifications apart from the CS glycosaminoglycan. A highly conserved SOX9-binding enhancer located in intron 1 was necessary to drive transcription of Snorc in the mouse, rat, and human. The enhancer was active independently of orientation and whether located in a heterologous promoter or intron. Crispr-mediated inactivation of the enhancer in RCS cells caused reduction of Snorc. Transgenic mice carrying the intronic multimerized enhancer drove high expression of a βGeo reporter in chondrocytes, but not in the hypertrophic zone. Altogether these data confirmed the chondrocyte-specific nature of Snorc and revealed dependency on the intronic enhancer binding of SOX9 for transcription.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.