微小RNA（miRNA）是一类小型非编码RNA分子，能够结合到不同基因区域的靶位点，调控转录后基因表达。人类大约95%的多外显子基因可以选择性剪接，从而能够从单个基因中产生功能多样的转录本和蛋白质。通过选择性剪接，转录本可能丧失带有miRNA靶位点的外显子，从而无法对miRNA进行调控。为了验证这个假设，我们使用来自The Cancer Genome Atlas（TCGA）的六个癌症数据集和来自PPMI的帕金森病数据研究了miRNA靶位点在编码和非编码区域的作用。首先，我们使用TarPmiR根据转录本序列预测了mRNA上的miRNA靶位点。为了检查选择性剪接是否干扰了这种调控，我们训练了线性回归模型，从转录本表达预测miRNA表达。使用嵌套模型，我们比较了带有靶位点的转录本与没有靶位点的转录本的预测能力。结果显示，包含靶位点的转录本的模型表现显著更好。我们得出结论，通过跳过编码区域内带有miRNA靶位点的外显子，选择性剪接确实干扰了miRNA的调控。© 作者2023. 由牛津大学出版社代表NAR Genomics and Bioinformatics出版。

MicroRNAs (miRNAs) are small non-coding RNA molecules that bind to target sites in different gene regions and regulate post-transcriptional gene expression. Approximately 95% of human multi-exon genes can be spliced alternatively, which enables the production of functionally diverse transcripts and proteins from a single gene. Through alternative splicing, transcripts might lose the exon with the miRNA target site and become unresponsive to miRNA regulation. To check this hypothesis, we studied the role of miRNA target sites in both coding and non-coding regions using six cancer data sets from The Cancer Genome Atlas (TCGA) and Parkinson's disease data from PPMI. First, we predicted miRNA target sites on mRNAs from their sequence using TarPmiR. To check whether alternative splicing interferes with this regulation, we trained linear regression models to predict miRNA expression from transcript expression. Using nested models, we compared the predictive power of transcripts with miRNA target sites in the coding regions to that of transcripts without target sites. Models containing transcripts with target sites perform significantly better. We conclude that alternative splicing does interfere with miRNA regulation by skipping exons with miRNA target sites within the coding region.© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.