CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries

Florian Heigwer; Tianzuo Zhan; Marco Breinig; Jan Winter; Dirk Brügemann; Svenja Leible; Michael Boutros

doi:10.1186/s13059-016-0915-2

CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries

Genome Biol. 2016 Mar 24:17:55. doi: 10.1186/s13059-016-0915-2.

Authors

Florian Heigwer¹, Tianzuo Zhan^{1

2}, Marco Breinig¹, Jan Winter¹, Dirk Brügemann¹, Svenja Leible¹, Michael Boutros³

Affiliations

¹ Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany.
² Department of Medicine II, University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
³ Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany. m.boutros@dkfz.de.

Abstract

Background: Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes.

Results: Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. To demonstrate its utility, we perform a pooled screen for modulators of the TNF-related apoptosis inducing ligand (TRAIL) pathway using a custom library of 12,471 sgRNAs.

Conclusion: CLD predicts a high fraction of functional sgRNAs and is publicly available at https://github.com/boutroslab/cld.

Keywords: Bioinformatics; CRISPR/Cas9; Functional genomics; Pooled screens; sgRNA design.

Publication types

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

MeSH terms

Animals
CRISPR-Cas Systems
Computational Biology / methods
Gene Library*
Humans
RNA, Guide, CRISPR-Cas Systems*
Software
TNF-Related Apoptosis-Inducing Ligand / genetics*

Substances

RNA, Guide, CRISPR-Cas Systems
TNF-Related Apoptosis-Inducing Ligand