Gifford is a founder of Think Therapeutics, Inc.Ī large fraction of genetic variation associated with human disease lies in the non-coding region of the human genome. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: David K. All other relevant data are available in the manuscript and its Supporting Information files.įunding: We acknowledge funding from NIH grants 1R01HG008363 (D.K.G.), 1R01HG008754 (D.K.G.), and 1K01DK101684-01 (R.I.S.) the Human Frontier Science Program, Netherlands Organisation for Scientific Research, Brigham Research Institute, and Harvard Stem Cell Institute (R.I.S.) and the Agency for Science, Technology and Research Graduate Academy (G.H.T.Y.). This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: Raw and processed single-cell RNA-sequencing data are available from GEO (accession number GSE117053). Received: AugAccepted: FebruPublished: March 12, 2021Ĭopyright: © 2021 Yeo et al. Leslie, Memorial Sloan-Kettering Cancer Center, UNITED STATES PLoS Comput Biol 17(3):Įditor: Christina S. (2021) Detection of gene cis-regulatory element perturbations in single-cell transcriptomes. We analyze how the power to detect the consequences of changes to the regulatory genome depends on factors such as number of cells receiving a gRNA, the extent of a knock-out, and the baseline gene expression in the control.Ĭitation: Yeo GHT, Juez O, Chen Q, Banerjee B, Chu L, Shen MW, et al. We find that in contrast to ORF targeting, altering regulatory regions rarely results in total knock-out of the targeted gene. We develop an assay for directly observing CRISPR/Cas9 guide RNAs (gRNAs) in scRNA-seq, and apply it to monitoring gene expression changes induced by perturbations to the regulatory genome. However, existing studies coupling CRISPR screens with scRNA-seq have focused on perturbations to open reading frames (ORFs). More recently, CRISPR/Cas9 based screens have been combined with single-cell RNA-sequencing (scRNA-seq) technology to provide cellular transcriptomes as screen readouts. CRISPR/Cas9 enables programmable and scalable alteration of genomic regions of interest. Predicting how mutations in non-coding regions impact gene expression is an important step towards understanding how non-coding variants contribute to human variation and disease.
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