Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP

被引：10

作者：

Lorenz, Daniel A. ^{[1
]}

Her, Hsuan-Lin ^{[2
,3
,4
]}

Shen, Kylie A. ^{[1
]}

Rothamel, Katie ^{[2
,3
,4
]}

Hutt, Kasey R. ^{[1
]}

Nojadera, Allan C. ^{[1
]}

Bruns, Stephanie C. ^{[1
]}

Manakov, Sergei A. ^{[1
]}

Yee, Brian A. ^{[2
,3
,4
]}

Chapman, Karen B. ^{[1
]}

Yeo, Gene W. ^{[2
,3
,4
]}

机构：

[1] Eclipse Bioinnovat, San Diego, CA 92121 USA

[2] Univ Calif San Diego, Dept Cellular & Mol Med, La Jolla, CA 92093 USA

[3] Univ Calif San Diego, Inst Genom Med, La Jolla, CA 92093 USA

[4] Univ Calif San Diego, Stem Cell Program, La Jolla, CA 92093 USA

来源：

NATURE METHODS | 2023年 / 20卷 / 01期

基金：

美国国家卫生研究院;

关键词：

CLIP; EXPRESSION; SEQ;

D O I：

10.1038/s41592-022-01708-8

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Ultraviolet crosslinking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the enhanced CLIP (eCLIP) protocol requires 4 days of hands-on time and lacks the ability to process several RBPs in parallel. We present a new method termed antibody-barcode eCLIP that utilizes DNA-barcoded antibodies and proximity ligation of the DNA oligonucleotides to RBP-protected RNA fragments to interrogate several RBPs simultaneously. We observe performance comparable with that of eCLIP with the advantage of dramatically increased scaling while maintaining the same material requirement of a single eCLIP experiment.

引用

页码：65 / +

页数：23

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