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研究揭示超保守有害外显子的重要性和抑癌活性
作者:小柯机器人 发布时间:2020/1/9 14:48:12

美国福瑞德·哈金森癌症研究中心Robert K. Bradley小组利用RNA亚型筛选揭示了超保守有害外显子的重要性和抑癌活性。相关论文于2020年1月7日在线发表于国际学术期刊《自然—遗传学》。

研究人员报道了pgFARM(成对向导RNA用于可变外显子去除),这是一种基于CRISPR–Cas9的方法,其不依赖于基因失活来操纵亚型。这种方法能够在多克隆环境中快速抑制外显子识别,从而鉴定单个外显子的功能,例如调节泛癌内含子保留的SMNDC1盒外显子。研究人员将这种方法推广到一个集合筛选中,以测量“有害”盒外显子的功能相关性,这会破坏其宿主基因的阅读框,但通常是超保守的。许多有害外显子对于培养的细胞和肺腺癌异种移植物的生长都是必不可少的,而其中一部分具有临床相关的肿瘤抑制活性。有害外显子的必要性以及与癌症的相关性可能会导致其异常高的保守性,并与其他对于存活不可或缺的超保守元件形成对比。

据了解,尽管RNA-seq能够对替代剪接进行全面定量,但目前不存在用于功能性研究单个亚型的高通量检测方法。

附:英文原文

Title: RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons

Author: James D. Thomas, Jacob T. Polaski, Qing Feng, Emma J. De Neef, Emma R. Hoppe, Maria V. McSharry, Joseph Pangallo, Austin M. Gabel, Andrea E. Belleville, Jacqueline Watson, Naomi T. Nkinsi, Alice H. Berger, Robert K. Bradley

Issue&Volume: 2020-01-07

Abstract: While RNA-seq has enabled comprehensive quantification of alternative splicing, no correspondingly high-throughput assay exists for functionally interrogating individual isoforms. We describe pgFARM (paired guide RNAs for alternative exon removal), a CRISPR–Cas9-based method to manipulate isoforms independent of gene inactivation. This approach enabled rapid suppression of exon recognition in polyclonal settings to identify functional roles for individual exons, such as an SMNDC1 cassette exon that regulates pan-cancer intron retention. We generalized this method to a pooled screen to measure the functional relevance of ‘poison’ cassette exons, which disrupt their host genes’ reading frames yet are frequently ultraconserved. Many poison exons were essential for the growth of both cultured cells and lung adenocarcinoma xenografts, while a subset had clinically relevant tumor-suppressor activity. The essentiality and cancer relevance of poison exons are likely to contribute to their unusually high conservation and contrast with the dispensability of other ultraconserved elements for viability.

DOI: 10.1038/s41588-019-0555-z

Source: https://www.nature.com/articles/s41588-019-0555-z

期刊信息

Nature Genetics:《自然—遗传学》,创刊于1992年。隶属于施普林格·自然出版集团,最新IF:25.455
官方网址:https://www.nature.com/ng/
投稿链接:https://mts-ng.nature.com/cgi-bin/main.plex