Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Ricardo De Paoli-Iseppi, Shweta S. Joshi, Josie Gleeson, Yair D. J. Prawer, Yupei You, Ria Agarwal, Anran Li, Anthea Hull, Eloise M. Whitehead, Yoonji Seo, Rhea Kujawa, Raphael Chang, Mriga Dutt, Catriona McLean, Benjamin L. Parker, Michael B. Clark
{"title":"Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain","authors":"Ricardo De Paoli-Iseppi, Shweta S. Joshi, Josie Gleeson, Yair D. J. Prawer, Yupei You, Ria Agarwal, Anran Li, Anthea Hull, Eloise M. Whitehead, Yoonji Seo, Rhea Kujawa, Raphael Chang, Mriga Dutt, Catriona McLean, Benjamin L. Parker, Michael B. Clark","doi":"10.1186/s13059-025-03724-1","DOIUrl":null,"url":null,"abstract":"Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or RNA isoforms made by risk genes. However, how these genes contribute to disease risk and onset through altered expression and RNA splicing is not well understood. Combining our new bioinformatic pipeline IsoLamp with nanopore long-read amplicon sequencing, we deeply profile the RNA isoform repertoire of 31 high-confidence neuropsychiatric disorder risk genes in Human brain. We show most risk genes are more complex than previously reported, identifying 363 novel isoforms and 28 novel exons, including isoforms which alter protein domains, and genes such as ATG13 and GATAD2A where most expression was from previously undiscovered isoforms. The greatest isoform diversity is detected in the schizophrenia risk gene ITIH4. Mass spectrometry of brain protein isolates confirms translation of a novel exon skipping event in ITIH4, suggesting a new regulatory mechanism for this gene in the brain. Our results emphasize the widespread presence of previously undetected RNA and protein isoforms in the human brain and provide an effective approach to address this knowledge gap. Uncovering the isoform repertoire of candidate neuropsychiatric risk genes will underpin future analyses of the functional impact these isoforms have on neuropsychiatric disorders, enabling the translation of genomic findings into a pathophysiological understanding of disease.\n","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"190 1","pages":""},"PeriodicalIF":10.1000,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genome Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s13059-025-03724-1","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or RNA isoforms made by risk genes. However, how these genes contribute to disease risk and onset through altered expression and RNA splicing is not well understood. Combining our new bioinformatic pipeline IsoLamp with nanopore long-read amplicon sequencing, we deeply profile the RNA isoform repertoire of 31 high-confidence neuropsychiatric disorder risk genes in Human brain. We show most risk genes are more complex than previously reported, identifying 363 novel isoforms and 28 novel exons, including isoforms which alter protein domains, and genes such as ATG13 and GATAD2A where most expression was from previously undiscovered isoforms. The greatest isoform diversity is detected in the schizophrenia risk gene ITIH4. Mass spectrometry of brain protein isolates confirms translation of a novel exon skipping event in ITIH4, suggesting a new regulatory mechanism for this gene in the brain. Our results emphasize the widespread presence of previously undetected RNA and protein isoforms in the human brain and provide an effective approach to address this knowledge gap. Uncovering the isoform repertoire of candidate neuropsychiatric risk genes will underpin future analyses of the functional impact these isoforms have on neuropsychiatric disorders, enabling the translation of genomic findings into a pathophysiological understanding of disease.
长读测序揭示了人类大脑中神经精神风险基因的RNA异构体库
神经精神疾病是一种高度复杂的疾病,发展成一种疾病的风险与数百种基因组变异有关,这些变异会改变由风险基因产生的表达和/或RNA同种异构体。然而,这些基因如何通过改变表达和RNA剪接来促进疾病风险和发病尚不清楚。结合我们新的生物信息学管道IsoLamp和纳米孔长读扩增子测序,我们深入分析了人类大脑中31个高置信度神经精神疾病风险基因的RNA异型库。我们发现大多数风险基因比以前报道的更复杂,鉴定出363种新的异构体和28种新的外显子,包括改变蛋白质结构域的异构体,以及像ATG13和GATAD2A这样的基因,其中大多数表达来自以前未发现的异构体。在精神分裂症风险基因ITIH4中检测到最大的同种异构体多样性。脑蛋白分离物的质谱分析证实了ITIH4中一个新的外显子跳变事件的翻译,这表明该基因在脑中的一种新的调控机制。我们的研究结果强调了以前未被发现的RNA和蛋白质亚型在人脑中的广泛存在,并提供了解决这一知识差距的有效方法。揭示候选神经精神风险基因的同工异构体将支持这些同工异构体对神经精神疾病的功能影响的未来分析,使基因组研究结果转化为对疾病的病理生理学理解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信