Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome.

Cell systems Pub Date : 2025-01-15 Epub Date: 2024-12-16 DOI:10.1016/j.cels.2024.12.002
Eli Metzner, Kaden M Southard, Thomas M Norman
{"title":"Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome.","authors":"Eli Metzner, Kaden M Southard, Thomas M Norman","doi":"10.1016/j.cels.2024.12.002","DOIUrl":null,"url":null,"abstract":"<p><p>Single-cell CRISPR screens link genetic perturbations to transcriptional states, but high-throughput methods connecting these induced changes to their regulatory foundations are limited. Here, we introduce Multiome Perturb-seq, extending single-cell CRISPR screens to simultaneously measure perturbation-induced changes in gene expression and chromatin accessibility. We apply Multiome Perturb-seq in a CRISPRi screen of 13 chromatin remodelers in human RPE-1 cells, achieving efficient assignment of sgRNA identities to single nuclei via an improved method for capturing barcode transcripts from nuclear RNA. We organize expression and accessibility measurements into coherent programs describing the integrated effects of perturbations on cell state, finding that ARID1A and SUZ12 knockdowns induce programs enriched for developmental features. Modeling of perturbation-induced heterogeneity connects accessibility changes to changes in gene expression, highlighting the value of multimodal profiling. Overall, our method provides a scalable and simply implemented system to dissect the regulatory logic underpinning cell state. A record of this paper's transparent peer review process is included in the supplemental information.</p>","PeriodicalId":93929,"journal":{"name":"Cell systems","volume":" ","pages":"101161"},"PeriodicalIF":0.0000,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11738662/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Cell systems","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1016/j.cels.2024.12.002","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/12/16 0:00:00","PubModel":"Epub","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0

Abstract

Single-cell CRISPR screens link genetic perturbations to transcriptional states, but high-throughput methods connecting these induced changes to their regulatory foundations are limited. Here, we introduce Multiome Perturb-seq, extending single-cell CRISPR screens to simultaneously measure perturbation-induced changes in gene expression and chromatin accessibility. We apply Multiome Perturb-seq in a CRISPRi screen of 13 chromatin remodelers in human RPE-1 cells, achieving efficient assignment of sgRNA identities to single nuclei via an improved method for capturing barcode transcripts from nuclear RNA. We organize expression and accessibility measurements into coherent programs describing the integrated effects of perturbations on cell state, finding that ARID1A and SUZ12 knockdowns induce programs enriched for developmental features. Modeling of perturbation-induced heterogeneity connects accessibility changes to changes in gene expression, highlighting the value of multimodal profiling. Overall, our method provides a scalable and simply implemented system to dissect the regulatory logic underpinning cell state. A record of this paper's transparent peer review process is included in the supplemental information.

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
多组扰动序列解锁可扩展的发现对转录组和表观基因组的综合扰动效应。
单细胞CRISPR筛选将遗传扰动与转录状态联系起来,但将这些诱导变化与其调控基础联系起来的高通量方法是有限的。在这里,我们引入了Multiome Perturb-seq,扩展了单细胞CRISPR筛选,同时测量扰动诱导的基因表达和染色质可及性的变化。我们将Multiome Perturb-seq应用于人类RPE-1细胞中13个染色质重塑子的CRISPRi筛选,通过从核RNA中捕获条形码转录本的改进方法,实现了sgRNA身份到单个细胞核的有效分配。我们将表达和可及性测量组织到描述扰动对细胞状态综合影响的连贯程序中,发现ARID1A和SUZ12敲低诱导了丰富发育特征的程序。微扰诱导异质性的建模将可及性变化与基因表达的变化联系起来,突出了多模态分析的价值。总的来说,我们的方法提供了一个可扩展和简单实现的系统来剖析支撑细胞状态的调节逻辑。本文的透明同行评议过程记录包含在补充信息中。
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 去求助
来源期刊
自引率
0.00%
发文量
0
期刊最新文献
Engineering highly active nuclease enzymes with machine learning and high-throughput screening. Multiplexed dynamic control of temperature to probe and observe mammalian cells. Self-resistance-gene-guided, high-throughput automated genome mining of bioactive natural products from Streptomyces. Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders. How well do contextual protein encodings learn structure, function, and evolutionary context?
×
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
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 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 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1