Reckard Andrew T, Pandeya Abhishek, Voris Jacob M, Gonzalez Cruz Carlos G, Oluwadare Oluwatosin, Klocko Andrew D
Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.
Department of Computer Science, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.
BMC Genomics. 2024 Dec 20;25(1):1215. doi: 10.1186/s12864-024-11110-7.
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. However, the role of individual heterochromatic loci in normal genome organization and function is unknown.
We examined the genome organization of a Neurospora strain harboring a ~ 47.4 kilobase deletion within a temporarily silent, facultative heterochromatic region, as well as the genome organization of a strain deleted of a 110.6 kilobase permanently silent constitutive heterochromatic region. While the facultative heterochromatin deletion minimally effects local chromatin structure or telomere clustering, the constitutive heterochromatin deletion alters local chromatin structure, the predicted three-dimensional chromosome conformation, and the expression of some genes, which are qualitatively repositioned into the nucleus center, while increasing Hi-C variability.
Our work elucidates how an individual constitutive heterochromatic region impacts genome organization and function. Specifically, one silent region indirectly assists in the hierarchical folding of the entire Neurospora genome by aggregating into the "typical" heterochromatin bundle normally observed in wild type nuclei, which may promote normal gene expression by positioning euchromatin in the nucleus center.
真核生物基因组的组织对于包括基因表达在内的正常功能至关重要。在后生动物中，染色质环和拓扑相关结构域（TADs）将基因组织成转录工厂，而染色体占据核区室，其中沉默的异染色质在核周边被分隔，活跃的常染色质定位于细胞核中心。在真菌粗糙脉孢菌中也存在类似的层次组织，其七条染色体形成拉布尔构象，其特征是异染色质着丝粒和端粒独立聚集在核膜处，而散布的异染色质位点在数百万碱基的线性基因组距离上聚集，形成类似TAD的结构来环化染色质。然而，单个异染色质位点在正常基因组组织和功能中的作用尚不清楚。
我们研究了一个粗糙脉孢菌菌株的基因组组织，该菌株在一个暂时沉默的兼性异染色质区域内有一个约47.4千碱基的缺失，以及一个缺失了110.6千碱基永久沉默的组成型异染色质区域的菌株的基因组组织。虽然兼性异染色质缺失对局部染色质结构或端粒聚集的影响最小，但组成型异染色质缺失改变了局部染色质结构、预测的三维染色体构象以及一些基因的表达，这些基因在性质上重新定位到细胞核中心，同时增加了Hi-C变异性。
我们的工作阐明了单个组成型异染色质区域如何影响基因组组织和功能。具体而言，一个沉默区域通过聚集形成野生型细胞核中通常观察到的“典型”异染色质束，间接协助整个粗糙脉孢菌基因组的层次折叠，这可能通过将常染色质定位在细胞核中心来促进正常基因表达。
