Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain
Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain
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DOI：
10.1371/journal.pgen.1008265
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发表时间：
2019-07-01
期刊：
影响因子：
4.5
通讯作者：
Merlin, Christine
中科院分区：
文献类型：
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作者：
Lugena, Aldrin B.;Zhang, Ying;Merlin, Christine
北美东部的帝王蝶以其壮观的季节性长距离迁徙而闻名。近年来，它还作为一种新的系统出现，用于研究动物生物钟如何跟踪时间，并调节与生态相关的日常节奏活动和季节性行为输出。然而，与果蝇和老鼠不同的是，在帝王身上几乎没有做过什么工作来在全基因组水平上识别节律基因，并阐明它们日常表达的调节。在这里，我们使用RNA测序和转座酶可访问染色质(ATAC)测序的方法来分析野生型君主和具有时钟功能受损的君主大脑中的日常转录组、开放染色质区域和转录因子(TF)足迹，包括隐色素2(Cry2)、时钟(CLK)和周期样功能丧失突变体。我们在帝王的大脑中发现了217个有节奏地表达的基因，其中许多参与了对大脑功能至关重要的生物过程的调节，如葡萄糖代谢和神经传递。令人惊讶的是，我们没有发现大脑中染色质的可及性随时间和基因型的显著变化。相反，我们发现在野生型君主大脑中节律基因附近的开放染色质区域内，存在着对TF占有率的时间调节，这在时钟缺陷突变体中被破坏。总而言之，这项工作首次确定了在帝王大脑中调节昼夜转录节奏的节律基因和调控模式。它还说明了ATAC测序的力量，以描述全基因组调节元件和TF结合在尚未获得TF特异性抗体的非模式生物体中。
The Eastern North American monarch butterfly, Danaus plexippus, is famous for its spectacular seasonal long-distance migration. In recent years, it has also emerged as a novel system to study how animal circadian clocks keep track of time and regulate ecologically relevant daily rhythmic activities and seasonal behavioral outputs. However, unlike in Drosophila and the mouse, little work has been undertaken in the monarch to identify rhythmic genes at the genome-wide level and elucidate the regulation of their diurnal expression. Here, we used RNA-sequencing and Assay for Transposase-Accessible Chromatin (ATAC)-sequencing to profile the diurnal transcriptome, open chromatin regions, and transcription factor (TF) footprints in the brain of wild-type monarchs and of monarchs with impaired clock function, including Cryptochrome 2 (Cry2), Clock (Clk), and Cycle-like loss-of-function mutants. We identified 217 rhythmically expressed genes in the monarch brain; many of them were involved in the regulation of biological processes key to brain function, such as glucose metabolism and neurotransmission. Surprisingly, we found no significant time-of-day and genotype-dependent changes in chromatin accessibility in the brain. Instead, we found the existence of a temporal regulation of TF occupancy within open chromatin regions in the vicinity of rhythmic genes in the brains of wild-type monarchs, which is disrupted in clock deficient mutants. Together, this work identifies for the first time the rhythmic genes and modes of regulation by which diurnal transcription rhythms are regulated in the monarch brain. It also illustrates the power of ATAC-sequencing to profile genome-wide regulatory elements and TF binding in a non-model organism for which TF-specific antibodies are not yet available.