De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens
In: Nature Communications, Jg. 10 (2019), Heft 1, S. 1-10
Online
unknown
Zugriff:
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.
Tiling-sgRNA designs allow the in situ evaluation of protein domain functions. Here the authors present ProTiler - a computational method to predict CRISPR knockout hyper-sensitive regions, revealing previously unannotated domains.
Titel: |
De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens
|
---|---|
Autor/in / Beteiligte Person: | Zhang, Liang ; Chen, Taiping ; Xu, Han ; Shi, Xiaobing ; Bedford, Mark T. ; Dou, Jingzhuang ; Bartholomew, Blaine ; He, Wei ; Bedford, Ella ; Fu, Rongjie ; Patel, Anish Y. ; Villarreal, Oscar D. |
Link: | |
Zeitschrift: | Nature Communications, Jg. 10 (2019), Heft 1, S. 1-10 |
Veröffentlichung: | Nature Publishing Group, 2019 |
Medientyp: | unknown |
ISSN: | 2041-1723 (print) |
Schlagwort: |
|
Sonstiges: |
|