If you are interested in CRISPRepi, please cite CRISPRepi: a multi-omic atlas for CRISPR-based epigenome editing.
Motivation of CRISPRepi
Epigenetic mechanisms play a pivotal role in gene regulation.
CRISPR-based epigenome editing is a technology that combines the precision targeting of the CRISPR-Cas system with the ability to modify epigenetic marks on the genome.
In contrast to traditional genome editing techniques (e.g., CRISPR-Cas9), epigenome editing does not directly alter the DNA sequence but rather influences gene expression by changing the chemical modification status of DNA or histone, making it tunable, reversible, and not involving DNA cleavage, effectively avoiding the cell toxicity associated with traditional gene editing.
Epigenome editing technologies provide researchers with a novel approach to explore gene expression regulatory mechanisms, making it a hotspot in therapeutic, genetic and gene function research.
Both CRISPR/Cas systems and epigenome editing systems may induce off-target activities, which impede the application of these techniques. To improve the editing efficiency and minimize the off-target effect, various epigenome editing systems have been developed and applied in different organisms and cell types.
As a result, a great number of epigenome editing information has been published subsequently. However, the detailed information is scattered, making it a big challenge for researchers to obtain all current available data to evaluate the precision of different epigenome editing systems and design the optimal small guide RNA sequences (sgRNAs) of target genes for further functional studies.
Herein, we developed CRISPRepi, a pioneering platform that consolidates extensive sequencing data from 671 meticulously curated RNA-seq, ChIP-seq, Bisulfite-seq, and ATAC-seq datasets in 87 cell types manipulated by 74 epigenome editing systems with 5 Cas proteins and 35 effector proteins. In total, CIRSPRepi has curated 5,962 sgRNAs associated with 283 target genes from 2,277 samples across six species. It covers diverse cell types related to human diseases such as cancers as well as normal cells from 103 published studies.
CRISPRepi provides putative editing precision of different systems by incorporating multiple annotations including “organisms”, “target gene”, “sgRNA sequences”, “sgRNA coordinate”, “sgRNA strand direction”, “editing substrate”, “cell/tissue name”, “editing systems” and “cis-regulator element type”. Therefore, CRISPRepi is an integrated database to systematically prioritize the sgRNA, editor systems and editing efficiency of target genes. Currently, we have analyzed editing data in more than 100 published studies and will regularly update the collection of epigenome editing data from other projects/literatures in the future. To our knowledge, CRISPRepi is the first integrated platform designed to present expression changes information and sgRNA designing of various CRISPR-based epigenome editing systems in multiple organisms. We believe CRISPRepi will help users to design suitable sgRNA according to different target genes in various organisms.
Workflow of CRISPRepi
CRISPRepi is a comprehensive database curating the outcome and evaluating editing efficiency of epigenome editors on various cell types and tissues in several species.