CHyMErA Combinatorial Genome Editing System

Resources

Publications

Single-cell exon deletion profiling reveals splicing events that shape gene expression and cell state dynamics Kumari B., Damodaran A.P., Guiblet W.M., Xiao M.S., Behera A.K., On T.A., McIntosh C.E., Teszler M., Holloway C., Le S., Parab N., Zhao Y., Aregger M., Gonatopoulos-Pournatzis T. Nature Communications 17, 1218 (2026).

RNA-coupled CRISPR Screens Reveal ZNF207 as a Regulator of LMNA Aberrant Splicing in Progeria Behera A.K, Kim J.J., Kordale S., Pekovic F., Damodaran A. P., Kumari B., Vidak S., Dickson E., Xiao M.S., Duncan G., Andresson T., Misteli T., Valkov E., Gonatopoulos-Pournatzis T. Molecular Cell 86, 41–59.e15 (2025).

Genome-scale exon perturbation screens uncover exons critical for cell fitness Xiao M.S., Damodaran A.P., Kumari B., Dickson E., Xing K., On T.A., Parab N., King H.E., Perez A.R., Guiblet W.M., Duncan G., Chari R., Andresson T., Vidigal J.A., Weatheritt R.J., Aregger M., Gonatopoulos-Pournatzis T. Molecular Cell 84 (13), 2553 - 2572.e19 (2024).

Application of CHyMErA Cas9-Cas12a combinatorial genome editing platform for genetic interaction mapping and gene fragment deletion screening Aregger, M., Xing, K., Gonatopoulos-Pournatzis, T. Nature Protocols 16 (10), 4722–4765 (2021).

Analysis of combinatorial CRISPR screens with the Orthrus scoring pipeline Ward, H.N., Aregger, M., Gonatopoulos-Pournatzis, T., Billmann, M., Ohsumi, T.K., Brown, K.R., Blencowe, B.J., Moffat, J., Myers, C.L. Nature Protocols 16 (10), 4766–4798 (2021).

Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9–Cas12a platform Gonatopoulos-Pournatzis, T., Aregger, M., Brown, K.B., Farhangmehr S., Braunschweig U., Ward H., Ha K.C., Weiss A., Durbic T., Morris Q., Myers C., Blencowe B.J., Moffat J. Nature Biotechnology 38, 638–648 (2020).

Plasmids Required for CHyMErA Experiments

The plasmids required for CHyMErA experiments are available from Addgene:

  • Lenti-Cas9-2A-Blast: lentiviral expression construct for human codon-optimized N-terminal FLAG-tagged Streptococcus pyogenes (Sp)Cas9 nuclease with C-terminal NLS and Blasticidin S resistance.
  • pLenti-D156R LbCas12a-8xNLS Lentiviral vector expressing human codon-optimized D156R LbCas12a with 8xNLS and Neomycin/G418/Geneticin resistance.
  • pLenti-opCas12a-6xNLS Lentiviral vector expressing human codon-optimized (As) opCas12a with 6xNLS and Neomycin/G418/Geneticin resistance.
  • pLCHKOv6 Lentiviral backbone for expressing U6 driven hybrid guide (hg)RNAs with BveI cloning sites and puromycin selection marker.
  • Topo_SpCas9.tracr_LbCas12a.DR TOPO vector for the cloning of the SpCas9 tracrRNA - LbCas12a Direct Repeat (DR) fragment into the pLCHKO hgRNA vector.
  • Topo_SpCas9.tracr_AsCas12a.DR TOPO vector for the cloning of the SpCas9 tracrRNA - AsCas12a Direct Repeat (DR) fragment into the pLCHKO hgRNA vector.
  • pLCHKOv4 Lentiviral backbone for expressing U6-driven hybrid guide (hg)RNAs for scCHyMErA-Seq experiments.
  • Topo_SpCas9.tracrRNA-CS1_AsCas12a DRv10 TOPO vector for the cloning of the SpCas9 tracrRNA-CS1 - AsCas12a Direct Repeat (DR) v10 fragment into the pLCHKO_v4 hgRNA vector for scCHyMErA-Seq experiments.

Additional plasmids deposited as part of our CHyMErA manuscripts can be found at Addgene:

Selected Available CHyMErA Screening Libraries

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