Alternative transcription initiation (ATI) appears to be a ubiquitous regulatory mechanism of gene expression in eukaryotes. However, the extent to which it affects the products of gene expression and how it evolves and is regulated remain unknown. Here, we report genome-wide identification and analysis of transcription start sites (TSSs) in various soybean (Glycine max) tissues using a survey of transcription initiation at promoter elements with high-throughput sequencing (STRIPE-seq). We defined 193,579 TSS clusters/regions (TSRs) in 37,911 annotated genes, with 56.5% located in canonical regulatory regions and 43.5% from start codons to 3′ untranslated regions, which were responsible for changes in open reading frames of 24,131 genes. Strikingly, 6,845 genes underwent ATI within coding sequences (CDSs). These CDS-TSRs were tissue-specific, did not have TATA-boxes typical of canonical promoters, and were embedded in nucleosome-free regions flanked by nucleosomes with enhanced levels of histone marks potentially associated with intragenic transcriptional initiation, suggesting that ATI within CDSs was epigenetically tuned and associated with tissue-specific functions. Overall, duplicated genes possessed more TSRs, exhibited lower degrees of tissue specificity, and underwent stronger purifying selection than singletons. This study highlights the significance of ATI and the genomic and epigenomic factors shaping the distribution of ATI in CDSs in a paleopolyploid eukaryote.

中文翻译：

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非经典转录起始主要是组织特异性的，并且在古多倍体植物中进行了表观遗传调整


选择性转录起始 （ATI） 似乎是真核生物中普遍存在的基因表达调节机制。然而，它对基因表达产物的影响程度以及它如何进化和调节仍然未知。在这里，我们使用高通量测序启动子元件的转录起始调查 （STRIPE-seq） 报告了各种大豆 （Glycine max） 组织中转录起始位点 （TSS） 的全基因组鉴定和分析。我们在 37,911 个注释基因中定义了 193,579 个 TSS 簇/区域 （TSR），其中 56.5% 位于经典调控区，43.5% 位于起始密码子到 3' 非翻译区，这导致了 24,131 个基因的开放阅读框的变化。引人注目的是，6,845 个基因在编码序列 （CDS） 中经历了 ATI。这些 CDS-TSRs 是组织特异性的，没有典型启动子典型的 TATA 框，并且嵌入在无核小体区域，两侧是核小体，组蛋白标记水平增强，可能与基因内转录起始相关，表明 CDS 中的 ATI 是表观遗传调节的，并与组织特异性功能相关。总体而言，与单例相比，重复基因具有更多的 TSR，表现出较低的组织特异性，并且经历了更强的纯化选择。本研究强调了 ATI 的重要性以及塑造古多倍体真核生物 CDS 中 ATI 分布的基因组和表观基因组因素。