Department of Biology, College of Staten Island, City University of New York (CUNY), 2800 Victory Boulevard, Staten Island, NY, 10314, USA.
PhD Programs in Biology and Biochemistry at the City University of New York (CUNY), Graduate Center, 365 Fifth Avenue, New York, NY, 10016, USA.
Genetics. 2023 Oct 4;225(2). doi: 10.1093/genetics/iyad145.
Transcriptional regulatory elements (TREs) are the primary nodes that control developmental gene regulatory networks. In embryo stages, larvae, and adult differentiated red spherule cells of the sea urchin Strongylocentrotus purpuratus, transcriptionally engaged TREs are detected by Precision Run-On Sequencing (PRO-seq), which maps genome-wide at base pair resolution the location of paused or elongating RNA polymerase II (Pol II). In parallel, TRE accessibility is estimated by the Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq). Our analysis identifies surprisingly early and widespread TRE accessibility in 4-cell cleavage embryos that is not necessarily followed by concurrent or subsequent transcription. TRE transcriptional differences identified by PRO-seq provide more contrast among embryonic stages than ATAC-seq accessibility differences, in agreement with the apparent excess of accessible but inactive TREs during embryogenesis. Global TRE accessibility reaches a maximum around the 20-hour late blastula stage, which coincides with the consolidation of major embryo regionalizations and peak histone variant H2A.Z expression. A transcriptional potency model based on labile nucleosome TRE occupancy driven by DNA sequences and the prevalence of histone variants is proposed in order to explain the basal accessibility of transcriptionally inactive TREs during embryogenesis. However, our results would not reconcile well with labile nucleosome models based on simple A/T sequence enrichment. In addition, a large number of distal TREs become transcriptionally disengaged during developmental progression, in support of an early Pol II paused model for developmental gene regulation that eventually resolves in transcriptional activation or silencing. Thus, developmental potency in early embryos may be facilitated by incipient accessibility and transcriptional pause at TREs.
转录调控元件 (TREs) 是控制发育基因调控网络的主要节点。在海胆 Strongylocentrotus purpuratus 的胚胎期、幼虫期和成年分化的红色球形体细胞中，通过精确运行测序 (PRO-seq) 检测到转录活跃的 TREs，该方法以碱基对分辨率绘制全基因组范围内暂停或延伸的 RNA 聚合酶 II (Pol II) 的位置。同时，通过转座酶可及染色质的测定 (ATAC-seq) 来估计 TRE 的可及性。我们的分析在 4 细胞分裂胚胎中发现了令人惊讶的早期和广泛的 TRE 可及性，而这种可及性不一定伴随着同时或随后的转录。PRO-seq 鉴定的 TRE 转录差异比 ATAC-seq 可及性差异在胚胎阶段之间提供了更多的对比，这与胚胎发生过程中明显存在大量可及但无活性的 TRE 相符。TRE 的全局可及性在 20 小时晚期囊胚期达到最大值，这与主要胚胎区域化的巩固和组蛋白变体 H2A.Z 表达的峰值相吻合。为了解释在胚胎发生过程中转录无活性 TRE 的基础可及性，提出了一种基于由 DNA 序列驱动的不稳定核小体 TRE 占有率和组蛋白变体的普遍性的转录潜能模型。然而，我们的结果与基于简单 A/T 序列富集的不稳定核小体模型不太一致。此外，大量的远端 TRE 在发育进程中失去转录活性，支持早期 Pol II 暂停模型用于发育基因调控，该模型最终在转录激活或沉默中得到解决。因此，早期胚胎中的发育潜能可能是通过 TRE 的初始可及性和转录暂停来促进的。
