Koç Baran, Fucile Geoffrey, Schmucki Roland, Giroud Nicolas, Bergauer Tobias, Hall Benjamin J
Faculty of Science, University of Basel, Basel, Switzerland.
Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
Front Mol Neurosci. 2021 Feb 25;14:624881. doi: 10.3389/fnmol.2021.624881. eCollection 2021.
Genome-wide sequencing technologies have greatly contributed to our understanding of the genetic basis of neurodevelopmental disorders such as autism spectrum disorder (ASD). Interestingly, a number of ASD-related genes express natural antisense transcripts (NATs). In some cases, these NATs have been shown to play a regulatory role in sense strand gene expression and thus contribute to brain function. However, a detailed study examining the transcriptional relationship between ASD-related genes and their NAT partners is lacking. We performed strand-specific, deep RNA sequencing to profile expression of sense and antisense reads with a focus on 100 ASD-related genes in medial prefrontal cortex (mPFC) and striatum across mouse post-natal development (P7, P14, and P56). Using transcriptome assembly, we generated a comprehensive long non-coding RNA (lncRNA) transcriptome. We conducted BLAST analyses to compare the resultant transcripts with the human genome and identified transcripts with high sequence similarity and coverage. We assembled 32861 antisense transcripts mapped to 12182 genes, of which 1018 are annotated by Ensembl as lncRNA. We validated the expression of a subset of selected ASD-related transcripts by PCR, including and . Our analyses revealed that more than 70% (72/100) of the examined ASD-related genes have one or more expressed antisense transcripts, suggesting more ASD-related genes than previously thought could be subject to NAT-mediated regulation in mice. We found that expression levels of antisense contigs were mostly positively correlated with their cognate coding sense strand RNA transcripts across developmental age. A small fraction of the examined transcripts showed brain region specific enrichment, indicating possible circuit-specific roles. Our BLAST analyses identified 110 of 271 ASD-related transcripts with >90% identity to the human genome at >90% coverage. These findings, which include an assembled antisense transcriptome, contribute to the understanding of NAT regulation of ASD-related genes in mice and can guide NAT-mediated gene regulation strategies in preclinical investigations toward the ultimate goal of developing novel therapeutic targets for ASD.
全基因组测序技术极大地促进了我们对诸如自闭症谱系障碍（ASD）等神经发育障碍的遗传基础的理解。有趣的是，许多与ASD相关的基因表达天然反义转录本（NATs）。在某些情况下，这些NATs已被证明在有义链基因表达中发挥调节作用，从而对脑功能有贡献。然而，缺乏一项详细研究来检验与ASD相关的基因与其NAT伙伴之间的转录关系。我们进行了链特异性深度RNA测序，以分析有义链和反义链 reads 的表达情况，重点关注小鼠出生后发育阶段（P7、P14和P56）内侧前额叶皮质（mPFC）和纹状体中的100个与ASD相关的基因。通过转录组组装，我们生成了一个全面的长链非编码RNA（lncRNA）转录组。我们进行了BLAST分析，将所得转录本与人类基因组进行比较，并鉴定出具有高序列相似性和覆盖率的转录本。我们组装了32861个映射到12182个基因的反义转录本，其中1018个被Ensembl注释为lncRNA。我们通过PCR验证了一部分选定的与ASD相关的转录本的表达，包括 和 。我们的分析表明，超过70%（72/100）的被检测的与ASD相关的基因有一个或多个表达的反义转录本，这表明在小鼠中，可能有比以前认为的更多的与ASD相关的基因受到NAT介导的调控。我们发现，在整个发育年龄中，反义重叠群的表达水平大多与其同源的编码有义链RNA转录本呈正相关。一小部分被检测的转录本显示出脑区特异性富集，表明可能具有特定回路的作用。我们的BLAST分析在271个与ASD相关的转录本中鉴定出110个在覆盖率>90%时与人类基因组的同一性>90%。这些发现，包括一个组装的反义转录组，有助于理解小鼠中与ASD相关的基因的NAT调控，并可指导临床前研究中NAT介导的基因调控策略，以实现为ASD开发新型治疗靶点的最终目标。
