Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
Genes (Basel). 2023 Mar 28;14(4):815. doi: 10.3390/genes14040815.
The incubation behavior of geese seriously affects their egg production performance. Studies on incubation behavior have identified functional genes, but the regulatory architecture relationship between functional genes and chromatin accessibility remains poorly understood. Here, we present an integrated analysis of open chromatin profiles and transcriptome to identify the cis-regulatory element and their potential transcription factors involved in regulating incubation behavior in goose pituitary. Assay for transposase-accessible chromatin sequencing (ATAC-seq) revealed that open chromatin regions increased in the pituitary during the transition from incubation behavior to laying. We identified 920 significant differential accessible regions (DARs) in the pituitary. Compared to the laying stage, most DARs had higher chromatin accessibility in the brooding stage. Motif analysis of open DARs showed that the most significant transcription factor (TF) occupied sites predominantly enriched in motifs binding to the RFX family (RFX5, RFX2, and RFX1). While the majority of TF motifs enriched under sites of the nuclear receptor (NR) family (ARE, GRE, and PGR) in closed DARs at the incubation behavior stage. Footprint analysis indicated that the transcription factor RFX family exhibited higher binding on chromatin at the brooding stage. To further elucidate the effect of changes in chromatin accessibility on gene expression levels, a comparison of the transcriptome revealed 279 differentially expressed genes (DEGs). The transcriptome changes were associated with processes of steroid biosynthesis. By integrating ATAC-seq and RNA-seq, few DARs directly affect incubation behavior by regulating the transcription levels of genes. Five DAR-related DEGs were found to be closely related to maintaining the incubation behavior in geese. Footprinting analysis revealed a set of transcription factors (RFX1, RFX2, RFX3, RFX5, BHLHA15, SIX1, and DUX) which displayed the highest activity at the brooding stage. SREBF2 was predicted to be the unique differentially expressed transcription factor whose mRNA level was down-regulated and enriched in hyper-accessible regions of PRL in the broody stage. In the present study, we comprehensively profiled the transcriptome and chromatin accessibility in the pituitary related to incubation behavior. Our findings provided insight into the identification and analysis of regulatory elements in goose incubation behavior. The epigenetic alterations profiled here can help decipher the epigenetic mechanisms that contribute to the regulation of incubation behavior in birds.
鹅的孵化行为严重影响其产蛋性能。对孵化行为的研究已经确定了功能基因，但功能基因与染色质可及性之间的调控结构关系仍知之甚少。在这里，我们对开放染色质图谱和转录组进行了综合分析，以鉴定参与调节鹅垂体孵化行为的顺式调控元件及其潜在转录因子。转座酶可及性染色质测序（ATAC-seq）分析表明，在从孵化行为到产卵的过渡过程中，垂体中的开放染色质区域增加。我们在垂体中鉴定出 920 个显著差异可及区域（DAR）。与产卵阶段相比，大多数 DAR 在孵育阶段具有更高的染色质可及性。开放 DAR 的基序分析表明，最显著的转录因子（TF）占据的位点主要富集在与 RFX 家族（RFX5、RFX2 和 RFX1）结合的基序中。而在孵化行为阶段，大多数核受体（NR）家族（ARE、GRE 和 PGR）的封闭 DAR 中富含的 TF 基序。足迹分析表明，在孵育阶段，RFX 家族的转录因子在染色质上表现出更高的结合。为了进一步阐明染色质可及性变化对基因表达水平的影响，对转录组的比较揭示了 279 个差异表达基因（DEG）。转录组的变化与类固醇生物合成过程有关。通过整合 ATAC-seq 和 RNA-seq，少数 DAR 通过调节基因的转录水平直接影响孵化行为。发现五个与维持鹅孵化行为密切相关的 DAR 相关 DEG。足迹分析揭示了一组转录因子（RFX1、RFX2、RFX3、RFX5、BHLHA15、SIX1 和 DUX），它们在孵育阶段表现出最高的活性。预测 SREBF2 是唯一差异表达的转录因子，其 mRNA 水平下调，并在孵育阶段的 PRL 高可及区域富集。在本研究中，我们全面分析了与孵化行为相关的垂体转录组和染色质可及性。我们的研究结果为鉴定和分析鹅孵化行为的调控元件提供了新的视角。这里描绘的表观遗传变化有助于破译促进鸟类孵化行为调控的表观遗传机制。
