Ottawa Hospital Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada.
Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
Cell Death Dis. 2023 Oct 25;14(10):701. doi: 10.1038/s41419-023-06224-x.
Neurodegenerative diseases are accompanied by dynamic changes in gene expression, including the upregulation of hallmark stress-responsive genes. While the transcriptional pathways that impart adaptive and maladaptive gene expression signatures have been the focus of intense study, the role of higher order nuclear organization in this process is less clear. Here, we examine the role of the nuclear lamina in genome organization during the degeneration of rod photoreceptors. Two proteins had previously been shown to be necessary and sufficient to tether heterochromatin at the nuclear envelope. The lamin B receptor (Lbr) is expressed during development, but downregulates upon rod differentiation. A second tether is the intermediate filament lamin A (LA), which is not normally expressed in murine rods. Here, we show that in the rd1 model of retinitis pigmentosa, LA ectopically upregulates in rod photoreceptors at the onset of degeneration. LA upregulation correlated with increased heterochromatin tethering at the nuclear periphery in rd1 rods, suggesting that LA reorganizes the nucleus. To determine how heterochromatin tethering affects the genome, we used in vivo electroporation to misexpress LA or Lbr in mature rods in the absence of degeneration, resulting in the restoration of conventional nuclear architecture. Using scRNA-seq, we show that reorganizing the nucleus via LA/Lbr misexpression has relatively minor effects on rod gene expression. Next, using ATAC-seq, we show that LA and Lbr both lead to marked increases in genome accessibility. Novel ATAC-seq peaks tended to be associated with stress-responsive genes. Together, our data reveal that heterochromatin tethers have a global effect on genome accessibility, and suggest that heterochromatin tethering primes the photoreceptor genome to respond to stress.
神经退行性疾病伴随着基因表达的动态变化，包括标志性应激反应基因的上调。虽然赋予适应性和失调性基因表达特征的转录途径一直是研究的重点，但核高级组织在这个过程中的作用还不太清楚。在这里，我们研究了核层在杆状光感受器变性过程中对基因组组织的作用。以前已经证明两种蛋白足以将异染色质固定在核膜上。核层 B 受体（Lbr）在发育过程中表达，但在杆状分化后下调。另一种固定蛋白是中间丝层蛋白 A（LA），它在正常情况下不在鼠杆状细胞中表达。在这里，我们发现，在色素性视网膜炎 rd1 模型中，LA 在变性开始时在杆状光感受器中异常上调。LA 的上调与 rd1 杆状细胞中核周异染色质固定的增加相关，表明 LA 重新组织了细胞核。为了确定异染色质固定如何影响基因组，我们在没有变性的情况下使用体内电穿孔在成熟的杆状细胞中异常表达 LA 或 Lbr，导致常规核结构的恢复。通过 scRNA-seq，我们表明通过 LA/Lbr 异常表达重新组织核具有相对较小的对杆状细胞基因表达的影响。接下来，通过 ATAC-seq，我们表明 LA 和 Lbr 都导致基因组可及性显著增加。新的 ATAC-seq 峰往往与应激反应基因相关。总之，我们的数据揭示了异染色质固定对基因组可及性有全局影响，并表明异染色质固定使光感受器基因组能够对应激做出反应。
