Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
Int J Mol Sci. 2020 May 25;21(10):3706. doi: 10.3390/ijms21103706.
tRNA and some other non-coding RNA genes are transcribed by RNA polymerase III (pol III), due to the presence of intragenic promoter, consisting of boxes A and B spaced by 30-40 bp. Such pol III promoters, called type 2, are also intrinsic to Short Interspersed Elements (SINEs). The contribution of 5'-flanking sequences to the transcription efficiency of genes containing type 2 promoters is still studied insufficiently. Here, we studied this issue, focusing on the genes of two small non-coding RNAs (4.5SH and 4.5SI), as well as B1 and B2 SINEs from the mouse genome. We found that the regions from position -31 to -24 may significantly influence the transcription of genes and SINEs. We studied the influence of nucleotide substitutions in these sites, representing TATA-like boxes, on transcription of 4.5SH and 4.5SI RNA genes. As a rule, the substitutions of A and T to G or C reduced the transcription level, although the replacement of C with A also lowered it. In 4.5SH gene, five distal nucleotides of -31/-24 box (TTCAAGTA) appeared to be the most important, while in the box -31/-24 of 4.5SI gene (CTACATGA), all nucleotides, except for the first one, contributed significantly to the transcription efficiency. Random sequences occurring at positions -31/-24 upstream of SINE copies integrated into genome, promoted their transcription with different efficacy. In the 5'-flanking sequences of 4.5SH and 4.5SI RNA genes, the recognition sites of CREB, C/EBP, and Sp1 factors were found, and their deletion decreased the transcription.
tRNA 和一些其他非编码 RNA 基因由 RNA 聚合酶 III（pol III）转录，这是由于存在内含子启动子，由间隔 30-40bp 的 A 和 B 框组成。这种 pol III 启动子，称为 2 型，也是短散布元件（SINEs）所固有的。5'-侧翼序列对含有 2 型启动子的基因转录效率的贡献仍研究不足。在这里，我们研究了这个问题，重点是两种小非编码 RNA（4.5SH 和 4.5SI）以及来自小鼠基因组的 B1 和 B2 SINE 基因。我们发现从位置-31 到-24 的区域可能会显著影响基因和 SINE 的转录。我们研究了这些位点的核苷酸取代对 4.5SH 和 4.5SI RNA 基因转录的影响，这些位点代表 TATA 样框。通常，A 和 T 到 G 或 C 的取代会降低转录水平，尽管 C 被 A 取代也会降低转录水平。在 4.5SH 基因中，-31/-24 框的五个远端核苷酸（TTCAAGTA）似乎是最重要的，而在 4.5SI 基因的-31/-24 框（CTACATGA）中，除了第一个核苷酸外，所有核苷酸都显著影响转录效率。随机序列出现在整合到基因组中的 SINE 拷贝的-31/-24 上游位置，以不同的效率促进它们的转录。在 4.5SH 和 4.5SI RNA 基因的 5'-侧翼序列中，发现了 CREB、C/EBP 和 Sp1 因子的识别位点，删除这些位点会降低转录。
