Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
Anyang Institute of Technology, Anyang, Henan, 455000, China.
BMC Biol. 2023 Jul 31;21(1):165. doi: 10.1186/s12915-023-01665-4.
The development of cotton fiber is regulated by the orchestrated binding of regulatory proteins to cis-regulatory elements associated with developmental genes. The cis-trans regulatory dynamics occurred throughout the course of cotton fiber development are elusive. Here we generated genome-wide high-resolution DNase I hypersensitive sites (DHSs) maps to understand the regulatory mechanisms of cotton ovule and fiber development.
We generated DNase I hypersensitive site (DHS) profiles from cotton ovules at 0 and 3 days post anthesis (DPA) and fibers at 8, 12, 15, and 18 DPA. We obtained a total of 1185 million reads and identified a total of 199,351 DHSs through ~ 30% unique mapping reads. It should be noted that more than half of DNase-seq reads mapped multiple genome locations and were not analyzed in order to achieve a high specificity of peak profile and to avoid bias from repetitive genomic regions. Distinct chromatin accessibilities were observed in the ovules (0 and 3 DPA) compared to the fiber elongation stages (8, 12, 15, and 18 DPA). Besides, the chromatin accessibility during ovules was particularly elevated in genomic regions enriched with transposable elements (TEs) and genes in TE-enriched regions were involved in ovule cell division. We analyzed cis-regulatory modules and revealed the influence of hormones on fiber development from the regulatory divergence of transcription factor (TF) motifs. Finally, we constructed a reliable regulatory network of TFs related to ovule and fiber development based on chromatin accessibility and gene co-expression network. From this network, we discovered a novel TF, WRKY46, which may shape fiber development by regulating the lignin content.
Our results not only reveal the contribution of TEs in fiber development, but also predict and validate the TFs related to fiber development, which will benefit the research of cotton fiber molecular breeding.
棉纤维的发育是通过调节蛋白与与发育基因相关的顺式调控元件的有序结合来调控的。棉纤维发育过程中整个发生的顺-反式调控动态难以捉摸。在这里，我们生成了全基因组高分辨率的 DNA 酶 I 超敏位点（DHS）图谱，以了解棉花胚珠和纤维发育的调控机制。
我们从授粉后 0 和 3 天的棉花胚珠和 8、12、15 和 18 天的纤维中生成了 DNA 酶 I 超敏位点（DHS）图谱。我们共获得了 1.185 亿个读数，通过约 30%的唯一映射读数总共鉴定了 199351 个 DHS。需要注意的是，超过一半的 DNA 酶测序读数映射到多个基因组位置，为了实现峰图的高特异性并避免来自重复基因组区域的偏差，这些位置未进行分析。与纤维伸长阶段（8、12、15 和 18 天）相比，胚珠（0 和 3 天）中观察到明显不同的染色质可及性。此外，富含转座元件（TE）的基因组区域中胚珠的染色质可及性特别升高，TE 富集区域中的基因参与胚珠细胞分裂。我们分析了顺式调控模块，并从转录因子（TF）基序的调控分歧中揭示了激素对纤维发育的影响。最后，我们基于染色质可及性和基因共表达网络构建了与胚珠和纤维发育相关的可靠 TF 调控网络。从这个网络中，我们发现了一个新的 TF，WRKY46，它可能通过调节木质素含量来塑造纤维发育。
我们的结果不仅揭示了 TEs 在纤维发育中的贡献，还预测和验证了与纤维发育相关的 TFs，这将有助于棉花纤维分子育种的研究。
