Leila Haj Abdullah Alieh, Beatriz Cardoso de Toledo, Anna Hadarovich, Agnes Toth-Petroczy, Federico Calegari
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Here, we capitalize on the use of a validated reporter mouse line to isolate neural stem cells, neurogenic progenitors and neurons during corticogenesis and combine the use of short- and long-read sequencing to reconstruct the full transcriptome diversity characterizing neurogenic commitment. Extending available transcriptional profiles of the mammalian brain by nearly 50,000 new isoforms, we found that neurogenic commitment is characterized by a progressive increase in exon inclusion resulting in the profound remodeling of the transcriptional profile of specific cortical cell types. Most importantly, we computationally infer the biological significance of AS on protein structure by using AlphaFold2, revealing how radical protein conformational changes can arise from subtle changes in isoforms sequence. Together, our study reveals that AS has a greater potential to impact protein diversity and function than previously thought, independently from changes in gene expression.</p>","PeriodicalId":9216,"journal":{"name":"Biology Open","volume":"13 10","pages":""},"PeriodicalIF":1.8000,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11554263/pdf/","citationCount":"0","resultStr":"{\"title\":\"Characterization of alternative splicing during mammalian brain development reveals the extent of isoform diversity and potential effects on protein structural changes.\",\"authors\":\"Leila Haj Abdullah Alieh, Beatriz Cardoso de Toledo, Anna Hadarovich, Agnes Toth-Petroczy, Federico Calegari\",\"doi\":\"10.1242/bio.061721\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Regulation of gene expression is critical for fate commitment of stem and progenitor cells during tissue formation. 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引用次数: 0
摘要
基因表达调控对组织形成过程中干细胞和祖细胞的命运承诺至关重要。在哺乳动物大脑发育的背景下,大量研究描述了单个基因表达的变化如何在整个本体发育和系统发育过程中描述细胞类型的特征。然而,人们很少关注任何给定基因可通过替代剪接(AS)产生不同的转录本这一事实。替代剪接被认为是进化过程中扩大转录组多样性的一个关键机制,但评估替代剪接对同工酶多样性和蛋白质功能的全部潜力一直是众所周知的难题。在这里,我们利用经过验证的报告小鼠品系来分离皮质发生过程中的神经干细胞、神经原祖细胞和神经元,并结合使用短线程和长线程测序来重建神经原承诺的全部转录组多样性。通过对哺乳动物大脑近 50,000 个新同工形式的转录谱进行扩展,我们发现神经原承诺的特点是外显子包容性的逐渐增加,从而导致特定皮质细胞类型的转录谱发生深刻的重塑。最重要的是,我们利用 AlphaFold2 计算推断了 AS 对蛋白质结构的生物学意义,揭示了异构体序列的微妙变化如何导致蛋白质构象的根本性改变。总之,我们的研究揭示了AS对蛋白质多样性和功能的影响潜力比以前想象的要大,而不依赖于基因表达的变化。
Characterization of alternative splicing during mammalian brain development reveals the extent of isoform diversity and potential effects on protein structural changes.
Regulation of gene expression is critical for fate commitment of stem and progenitor cells during tissue formation. In the context of mammalian brain development, a plethora of studies have described how changes in the expression of individual genes characterize cell types across ontogeny and phylogeny. However, little attention has been paid to the fact that different transcripts can arise from any given gene through alternative splicing (AS). Considered a key mechanism expanding transcriptome diversity during evolution, assessing the full potential of AS on isoform diversity and protein function has been notoriously difficult. Here, we capitalize on the use of a validated reporter mouse line to isolate neural stem cells, neurogenic progenitors and neurons during corticogenesis and combine the use of short- and long-read sequencing to reconstruct the full transcriptome diversity characterizing neurogenic commitment. Extending available transcriptional profiles of the mammalian brain by nearly 50,000 new isoforms, we found that neurogenic commitment is characterized by a progressive increase in exon inclusion resulting in the profound remodeling of the transcriptional profile of specific cortical cell types. Most importantly, we computationally infer the biological significance of AS on protein structure by using AlphaFold2, revealing how radical protein conformational changes can arise from subtle changes in isoforms sequence. Together, our study reveals that AS has a greater potential to impact protein diversity and function than previously thought, independently from changes in gene expression.
期刊介绍:
Biology Open (BiO) is an online Open Access journal that publishes peer-reviewed original research across all aspects of the biological sciences. BiO aims to provide rapid publication for scientifically sound observations and valid conclusions, without a requirement for perceived impact.