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De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens.
Nat Commun. 2019 10 04; 10(1):4541.NC

Abstract

High-throughput CRISPR-Cas9 knockout screens using a tiling-sgRNA design permit in situ evaluation of protein domain function. Here, to facilitate de novo identification of essential protein domains from such screens, we propose ProTiler, a computational method for the robust mapping of CRISPR knockout hyper-sensitive (CKHS) regions, which refer to the protein regions associated with a strong sgRNA dropout effect in the screens. Applied to a published CRISPR tiling screen dataset, ProTiler identifies 175 CKHS regions in 83 proteins. Of these CKHS regions, more than 80% overlap with annotated Pfam domains, including all of the 15 known drug targets in the dataset. ProTiler also reveals unannotated essential domains, including the N-terminus of the SWI/SNF subunit SMARCB1, which is validated experimentally. Surprisingly, the CKHS regions are negatively correlated with phosphorylation and acetylation sites, suggesting that protein domains and post-translational modification sites have distinct sensitivities to CRISPR-Cas9 mediated amino acids loss.

Links

Authors+Show Affiliations

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA. The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.

Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA. The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA. The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.

Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA. hxu4@mdanderson.org. The Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. hxu4@mdanderson.org. Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. hxu4@mdanderson.org.

MeSH

AlgorithmsCRISPR-Cas SystemsCell Line, TumorComputational BiologyDatasets as TopicGene Knockout TechniquesHigh-Throughput Screening AssaysHumansModels, GeneticProtein DomainsProtein Processing, Post-TranslationalRNA, Guide, KinetoplastidaSMARCB1 ProteinSoftware

Pub Type(s)

Journal Article

Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

31586052

Citation

He, Wei, et al. "De Novo Identification of Essential Protein Domains From CRISPR-Cas9 tiling-sgRNA Knockout Screens." Nature Communications, vol. 10, no. 1, 2019, p. 4541.

He W, Zhang L, Villarreal OD, et al. De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nat Commun. 2019;10(1):4541.

He, W., Zhang, L., Villarreal, O. D., Fu, R., Bedford, E., Dou, J., Patel, A. Y., Bedford, M. T., Shi, X., Chen, T., Bartholomew, B., & Xu, H. (2019). De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. Nature Communications, 10(1), 4541. https://doi.org/10.1038/s41467-019-12489-8

He W, et al. De Novo Identification of Essential Protein Domains From CRISPR-Cas9 tiling-sgRNA Knockout Screens. Nat Commun. 2019 10 4;10(1):4541. PubMed PMID: 31586052.

* Article titles in AMA citation format should be in sentence-case

TY - JOUR T1 - De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens. AU - He,Wei, AU - Zhang,Liang, AU - Villarreal,Oscar D, AU - Fu,Rongjie, AU - Bedford,Ella, AU - Dou,Jingzhuang, AU - Patel,Anish Y, AU - Bedford,Mark T, AU - Shi,Xiaobing, AU - Chen,Taiping, AU - Bartholomew,Blaine, AU - Xu,Han, Y1 - 2019/10/04/ PY - 2019/03/18/received PY - 2019/09/02/accepted PY - 2019/10/6/entrez PY - 2019/10/6/pubmed PY - 2020/2/15/medline SP - 4541 EP - 4541 JF - Nature communications JO - Nat Commun VL - 10 IS - 1 N2 - High-throughput CRISPR-Cas9 knockout screens using a tiling-sgRNA design permit in situ evaluation of protein domain function. Here, to facilitate de novo identification of essential protein domains from such screens, we propose ProTiler, a computational method for the robust mapping of CRISPR knockout hyper-sensitive (CKHS) regions, which refer to the protein regions associated with a strong sgRNA dropout effect in the screens. Applied to a published CRISPR tiling screen dataset, ProTiler identifies 175 CKHS regions in 83 proteins. Of these CKHS regions, more than 80% overlap with annotated Pfam domains, including all of the 15 known drug targets in the dataset. ProTiler also reveals unannotated essential domains, including the N-terminus of the SWI/SNF subunit SMARCB1, which is validated experimentally. Surprisingly, the CKHS regions are negatively correlated with phosphorylation and acetylation sites, suggesting that protein domains and post-translational modification sites have distinct sensitivities to CRISPR-Cas9 mediated amino acids loss. SN - 2041-1723 UR - https://www.unboundmedicine.com/medline/citation/31586052/De_novo_identification_of_essential_protein_domains_from_CRISPR_Cas9_tiling_sgRNA_knockout_screens_ DB - PRIME DP - Unbound Medicine ER -