The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America.
PLoS Genet. 2019 Nov 6;15(11):e1008397. doi: 10.1371/journal.pgen.1008397. eCollection 2019 Nov.
In animals, circadian rhythms are driven by oscillations in transcription, translation, and proteasomal degradation of highly conserved genes, resulting in diel cycles in the expression of numerous clock-regulated genes. Transcription is largely regulated through the binding of transcription factors to cis-regulatory elements within accessible regions of the chromatin. Chromatin remodeling is linked to circadian regulation in mammals, but it is unknown whether cycles in chromatin accessibility are a general feature of clock-regulated genes throughout evolution. To assess this, we applied an ATAC-seq approach using Nematostella vectensis, grown under two separate light regimes (light:dark (LD) and constant darkness (DD)). Based on previously identified N. vectensis circadian genes, our results show the coupling of chromatin accessibility and circadian transcription rhythmicity under LD conditions. Out of 180 known circadian genes, we were able to list 139 gene promoters that were highly accessible compared to common promoters. Furthermore, under LD conditions, we identified 259 active enhancers as opposed to 333 active enhancers under DD conditions, with 171 enhancers shared between the two treatments. The development of a highly reproducible ATAC-seq protocol integrated with published RNA-seq and ChIP-seq databases revealed the enrichment of transcription factor binding sites (such as C/EBP, homeobox, and MYB), which have not been previously associated with circadian signaling in cnidarians. These results provide new insight into the regulation of cnidarian circadian machinery. Broadly speaking, this supports the notion that the association between chromatin remodeling and circadian regulation arose early in animal evolution as reflected in this non-bilaterian lineage.
在动物中，昼夜节律是由转录、翻译和蛋白酶体降解高度保守基因的波动驱动的，导致许多时钟调节基因的表达出现昼夜节律。转录主要通过转录因子与染色质可及区域内的顺式调节元件结合来调节。染色质重塑与哺乳动物的昼夜节律调节有关，但尚不清楚染色质可及性的循环是否是整个进化过程中时钟调节基因的普遍特征。为了评估这一点，我们应用了一种 ATAC-seq 方法，使用 Nematostella vectensis，在两种不同的光照条件下（光照：黑暗（LD）和持续黑暗（DD））进行培养。基于先前鉴定的 N. vectensis 昼夜节律基因，我们的结果表明在 LD 条件下，染色质可及性和昼夜转录节律性的耦合。在 180 个已知的昼夜节律基因中，我们能够列出 139 个与常见启动子相比高度可及的基因启动子。此外，在 LD 条件下，我们鉴定出 259 个活性增强子，而在 DD 条件下鉴定出 333 个活性增强子，两种处理之间有 171 个增强子共享。与已发表的 RNA-seq 和 ChIP-seq 数据库相结合的高度可重复的 ATAC-seq 方案的开发揭示了转录因子结合位点（如 C/EBP、同源盒和 MYB）的富集，这些结合位点以前与刺胞动物的昼夜信号没有关联。这些结果为刺胞动物昼夜节律机制的调节提供了新的见解。广义上讲，这支持了这样一种观点，即染色质重塑和昼夜节律调节之间的关联在动物进化的早期就出现了，这在这个非双侧动物谱系中得到了反映。
