Table 1:
Summary of CRISPR screens targeting the noncoding genome:
| Publication (year) | Perturbation Methods | sgRNA Libraries | Target Areas | Cell Types | Assay Methods | References |
|---|---|---|---|---|---|---|
| Canver et al. (2015) | Cas9 nuclease | 702 sgRNAs targeting 3 DHSs and non-targeting controls | Total of 4-kb sequences encompassing putative BCL11A enhancers | HUDEP-2 human umbilical cord blood-derived erythroid progenitor cell line | FACS-based on antibody staining | [25] |
| Korkmaz et al. (2016) | Cas9 nuclease | 1,116 sgRNAs for p53 enhancer and 97 sgRNAs for ERα enhancer | 685 p53 and 73 ERα bound enhancer regions | Human BJ fibroblast cells, MCF-7 and T47D breast cancer cell line | Cell proliferation | [39] |
| Sanjana et al. (2016) | Cas9 nuclease | 18,315 sgRNAs (6,682 sgRNAs for NF1, 6,934 sgRNAs for NF2 and 4,699 sgRNAs for CUL3) | 100-kb upstream and downstream of NF1, NF2 and CUL3 each | A375 human melanoma cell line | Cell survival after vemurafenib treatment | [36] |
| Rajagopal et al. (2016) | Cas9 nuclease | 3,908 tiling sgRNAs for each of Tdgf1, Nanog, Rpp25, and Zfp42 | Upstream regulatory regions of Tdgf1 (40-kb upstream), Nanog, (20-kb upstream + 92-Mb distal region) Rpp25 and Zfp42 (upstream regulators based on ChIA-PET) | Mouse embryonic stem cells | FACS-based on knock-in reporter | [23] |
| Diao et al. (2016) | Cas9 nuclease | 1,964 sgRNAs based on DHSs and ChIP-seq | 174 candidate regulatory regions within 1-Mb of POU5F1 | H1 human embryonic stem cells | FACS-based on transgenic reporter | [24] |
| Fulco et al. (2016) | dCas9-KRAB | 98,000 tiling sgRNAs | Total of ~1.29-Mb sequences around GATA1 and MYC | K562 human erythroleukemia cell line | Cell proliferation | [40] |
| Zhu et al. (2016) | Cas9 nuclease and dCas9- KRAB/dCas9- VP64 for validation | 12,472 sgRNA pairs | 647 IncRNA loci | Huh7.5 hepatocarcinoma cell line | Cell proliferation | [41] |
| Wallace et al. (2016) | Cas9 nuclease | GeCKO v2 library (123,411 sgRNAs for 19,050 protein coding genes), which also include 7,456 sgRNAs targeting 1,864 miRNAs | 1,864 miRNAs (4 sgRNA/miRNA) loci | MV4-11 myeloid leukemia cell line | Cell proliferation | [51] |
| Diao et al. (2017) | Cas9 nuclease | 11,570 sgRNA pairs | 2-Mb of POU5F1 cis-regulatory region | H1 human embryonic stem cells | FACS-based on transgenic reporter | [26] |
| Xie et al. (2017) | dCas9-KRAB | 51,448 sgRNAs | 71 targeted regions across 15 super enhancers | K562 human erythroleukemia cell line | scRNA-seq | [32] |
| Simeonov et al. (2017) | dCas9-VP64 | 10,780 sgRNAs for CD69 and 20,412 sgRNAs for IL2RA | 135-kb across CD69 and total of 178-kb upstream and downstream of IL2RA locus | Jurkat human T cell line | FACS-based on antibody staining | [27] |
| Klann et al. (2017) | dCas9-KRAB and dCas9-p300 | 12,472 sgRNAs targeting β-globin DHSs and 12,422 sgRNAs for HER2 DHSs | 4.5-Mb and 4-Mb, respectively, surrounding the β-globin and HER2 loci | K562 human erythroleukemia cell line, HEK293T, A431 human epidermoid carcinoma cell line | FACS-based on knock-in reporter | [22] |
| Liu et al. (2017) | dCas9-KRAB | 164,010 sgRNAs | 16,401 IncRNA loci | Cancer cell lines (K562, HeLa, U87, MCF7, MDA-MB-231) and human induced pluripotent stem cells | Cell proliferation | [42] |
| Joung et al. (2017) | dCas9-SAM | ~96,000 sgRNAs | 10,504 IncRNA loci | A375 human melanoma cell line | Cell survival after vemurafenib treatment | [43] |
| Chow et al. (2017) | Cas9 nuclease | 288 sgRNAs | 5 sgRNA each against 56 genes (49 tumor suppressor and 7 housekeeping genes) plus 8 nontargeting sgRNAs | In vivo screen using LSL-Cas9-GFP mice (for conditional Cas9 expression) | Cell proliferation | [50] |