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A constitutive heterochromatic region shapes genome organization and impacts gene expression in Neurospora crassa.
BMC Genomics
December 2024
Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.
Background: Organization of the eukaryotic genome is essential for proper function, including gene expression. In metazoans, chromatin loops and Topologically Associated Domains (TADs) organize genes into transcription factories, while chromosomes occupy nuclear territories in which silent heterochromatin is compartmentalized at the nuclear periphery and active euchromatin localizes to the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation typified by heterochromatic centromeres and telomeres independently clustering at the nuclear membrane, while interspersed heterochromatic loci aggregate across Megabases of linear genomic distance to loop chromatin in TAD-like structures.
View Article and Find Full Text PDF3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization.
Nat Commun
November 2024
Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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.
View Article and Find Full Text PDFComputational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ).
J Comput Aided Mol Des
October 2024
Department of Biomedical Engineering, Izmir University of Economics, İzmir, Turkey.
G-quadruplexes refer to a large group of nucleic acid-based structures. In recent years, they have been attracting attention due to their biological roles in the telomeres and promoter regions. These structures show wide diversity in topology, however, development of methods for structural classification of G-quadruplexes has been evaded for a long time.
View Article and Find Full Text PDFDe novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes.
Genome Res
October 2024
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA;
Understanding the evolution of chromatin conformation among species is fundamental to elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly distant loci regulate gene function in species-specific patterns, affecting genome function, evolution, and, ultimately, speciation. Yet, data from nonmodel organisms are scarce.
View Article and Find Full Text PDFA Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression in .
bioRxiv
October 2024
Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO 80918, USA.
Background: Organization of the eukaryotic genome is essential for proper function, including gene expression. In metazoans, chromatin loops and Topologically Associated Domains (TADs) organize genes into transcription factories, while chromosomes occupy nuclear territories in which silent heterochromatin is compartmentalized at the nuclear periphery and active euchromatin localizes to the nucleus center. A similar hierarchical organization occurs in the fungus where its seven chromosomes form a Rabl conformation typified by heterochromatic centromeres and telomeres independently clustering at the nuclear membrane, while interspersed heterochromatic loci aggregate across Megabases of linear genomic distance to loop chromatin in TAD-like structures.
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