Journal: Molecular cell

Article Title: CRAMP1 drives linker histone expression to enable Polycomb repression.

doi: 10.1016/j.molcel.2025.05.031

Figure Lengend Snippet: Figure 1. A genome-wide CRISPR-Cas9 genetic screen identifies an essential requirement for CRAMP1 and histone H1.4 in PRC2-mediated reporter repression (A) Schematic representation of GFP reporter repression by the PRC2 complex. (B) The GFP reporter is derepressed upon CRISPR-Cas9-mediated gene disruption of any of the three core PRC2 subunits, as assayed by flow cytometry. (C) A genome-wide CRISPR-Cas9 screen to identify factors required for PRC2 function. Following Cas9 expression in KBM-7 cells harboring the PRC2-sensitive GFP reporter, genome-wide mutagenesis was carried out with the Sabatini/Lander single guide RNA (sgRNA) library, 36 and GFP + cells isolated through two sequential rounds of FACS. ‘‘Significance’’ on the y axis represents the negative log of the ‘‘pos|score’’ metric reported by Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK). 37

Article Snippet: Single guide RNA (sgRNA) sequences were selected from the Sabatini/Lander Human CRISPR Pooled Library (Addgene #1000000100, kindly deposited by David Sabatini and Eric Lander 81 ) or the Brunello Human CRISPR Knockout Pooled Library (Addgene #73178, kindly deposited by David Root and John Doench 82 ).

Techniques: Genome Wide, CRISPR, Disruption, Flow Cytometry, Expressing, Mutagenesis, Isolation, Knock-Out

Journal: Molecular cell

Article Title: CRAMP1 drives linker histone expression to enable Polycomb repression.

doi: 10.1016/j.molcel.2025.05.031

Figure Lengend Snippet: Figure 5. Linker histones are not enriched at regions marked by H3K9me3 (A–D) Lack of linker histone enrichment at H3K9me3-marked genomic regions. (A) Tornado plots depicting linker histone CUT&Tag signal across H3K9me3 peaks from the ENCODE project; average signal intensity is shown in (B). (C) Heatmap depicting the lack of correlation between linker histone occupancy and H3K9me3. Cells are annotated with pairwise Spearman correlation coefficients. An example locus is shown in (D). (E) CUT&Tag faithfully profiles H3K9me3. Example loci comparing CUT&Tag versus H3K9me3 ChIP-seq data (ENCODE) are shown. (F and G) Linker histone insufficiency does not impair H3K9me3-dependent LINE-1 silencing by the HUSH complex. (F) Schematic representation of the dual- color reporter cell line designed to monitor both H3K9me3-dependent repression by the HUSH complex and linker histone-mediated PRC2-reporter repression. (G) HUSH-mediated LINE-1 silencing is unaffected upon CRAMP1 depletion. The indicated CRISPR sgRNAs were expressed in the dual-color reporter cell line, and GFP and iRFP fluorescence assayed by flow cytometry. See also Figure S5 and Table S2.

Article Snippet: Single guide RNA (sgRNA) sequences were selected from the Sabatini/Lander Human CRISPR Pooled Library (Addgene #1000000100, kindly deposited by David Sabatini and Eric Lander 81 ) or the Brunello Human CRISPR Knockout Pooled Library (Addgene #73178, kindly deposited by David Root and John Doench 82 ).

Techniques: ChIP-sequencing, CRISPR, Fluorescence, Flow Cytometry

Journal: mBio

Article Title: Evolutionary dynamics of heparan sulfate utilization by SARS-CoV-2

doi: 10.1128/mbio.01303-25

Figure Lengend Snippet: ACE2-independent binding of the Omicron RBD to cell surface HS. ( A ) CRISPR KO library screening scheme to identify Omicron RBD binding molecules expressed on HEK293T cells. ( B ) Binding of CRISPR KO library-transduced HEK293T cells with (red line) or without (shaded gray) Omicron RBD-Fc, before and after sorting. ( C ) Number of sgRNA sequences identified in Omicron RBD-Fc non-binding cells after sorting. Red: GAG-synthesis-related genes; black: other expressed genes; gray: non-expressed genes in HEK293T cells. ( D ) HS biosynthetic pathway highlighting SLC35B2 and B3GAT3. PAPS, 3'-phosphoadenosine-5'-phosphosulfate; Xyl, xylose; Gal, galactose; GlcNAc, N-acetylglucosamine; GlcA, glucuronic acid; IdoA, iduronic acid. ( E ) Binding of BA.1 RBD-Fc, anti-HS Ab, or anti-CS Ab to mock (black line), or SLC35B2 or B3GAT3 KO (red line) HEK293T cells. ( F ) Binding of WT or BA.1 RBD-Fc, PILRα-Fc, anti-HS Ab, or anti-CS Ab to ACE2 KO HEK293T cells pretreated with (+) or without (–) heparinase or chondroitinase. ( G ) Binding of WT or BA.1 RBD-Fc to HEK293T cells at different heparin concentrations. RBD-Fc binding was normalized to binding in the absence of heparin. ( H ) Immunofluorescence of human nasal tissue with anti-HS Ab and 4', 6-diamidino-2-phenylindole (DAPI). Scale bar, 200 µm. ( I ) Binding of WT or BA.1 RBD-Fc, anti-ACE2 Ab, or anti-HS Ab to cell lines. Data are mean ± SEM of three to four technical replicates. Statistical analysis was performed using two-way ANOVA with Sidak’s multiple comparison tests in panel F ; * P < 0.05, ** P < 0.01, and **** P < 0.0001; ns, not significant. Data are representative of two to three independent experiments.

Article Snippet: CRISPR KO library-transduced HEK293T cells were generated by lentivirus-mediated transduction using the Human CRISPR KO Pooled Library (GeCKO v2; Addgene, 1000000048).

Techniques: Binding Assay, CRISPR, Library Screening, Immunofluorescence, Comparison

Journal: Cells

Article Title: Rapid and Robust Generation of Homozygous Fluorescent Reporter Knock-In Cell Pools by CRISPR-Cas9

doi: 10.3390/cells14151165

Figure Lengend Snippet: Overview of CRISPR-Cas9-based strategies for generating fluorescent reporter cell lines via in-frame knock-in. ( A ) Schematic illustration of the general strategy for generating fluorescent knock-in reporter cell lines. Cas9-expressing cells are transduced with a gene-specific sgRNA to introduce a double-stranded break at the target locus. A donor DNA template containing a fluorescent reporter is provided for homology-directed repair (HDR), enabling precise insertion of the reporter sequence into the genomic locus of interest. Created with BioRender.com. ( B ) Schematic representation of the dual-plasmid and single-plasmid systems. In the dual-plasmid system, the sgRNA and the donor DNA template are delivered by two separate vectors. The sgRNA plasmid features a doxycycline-inducible sgRNA expression cassette and a miRFP670 fluorescent reporter as a marker for transient expression of the plasmid. The donor DNA vector includes a 5′ homology arm, a fluorescent reporter in frame with a T2A peptide and lacking a start codon, and a 3′ homology arm. In the single-plasmid system, a multiple cloning site (MCS) was engineered into the sgRNA plasmid to enable subcloning of the donor DNA template. Other than expressing sgRNA induced by doxycycline, this plasmid also acts as the donor DNA for HDR within a limited time window after infection. Moreover, cells expressing the miRFP670 reporter from randomly integrated donor DNA can be eliminated by FACS sorting from a few days post-infection onwards. Created with BioRender.com.

Article Snippet: The Human Two Plasmid Activity-Optimized CRISPR Knockout sgRNA Library, developed by David Sabatini, Eric Lander and colleagues, was obtained from Addgene (Cat# 1000000095, Watertown, MA, USA) [ ].

Techniques: CRISPR, Knock-In, Expressing, Transduction, Introduce, Sequencing, Plasmid Preparation, Marker, Cloning, Subcloning, Infection

Journal: Cells

Article Title: Rapid and Robust Generation of Homozygous Fluorescent Reporter Knock-In Cell Pools by CRISPR-Cas9

doi: 10.3390/cells14151165

Figure Lengend Snippet: Generation of biallelic knockout cells with fluorescent knock-in reporter as a surrogate of gene disruption. ( A ) Workflow for generating TSPAN8 knock-out cell lines with a GFP knock-in reporter. The donor DNA template consists of an 800 bp 5′ homology arm, T2A-GFP sequence, SV40 polyA signal, and an 800 bp 3′ homology arm flanking exon 2 of the TSPAN8 gene. The TSPAN8 sgRNA target site was abolished in this donor template to prevent further DNA breaks after integration. Cas9-expressing cells were transfected with dual plasmids (sgRNA and donor template) by electroporation. Immediately following transfection, cells were treated with doxycycline (Dox) to induce sgRNA expression for 48 h. After 7–10 days of culture, cells were enriched based on GFP expression levels to isolate targeted populations. ( B ) Representative FACS plot showing the initial sorting of cells. Only cells transfected with TSPAN8 sgRNA exhibit a GFP + population, confirming successful targeting and reporter integration. The GFP + population was gated and sorted for subsequent analyses and enrichment. Both MEC and JHH5 cells were used in this experiment, with 20 µg of total plasmids (1:1 ratio of sgRNA and donor template plasmids) transfected per million cells. ( C ) FACS plot showing TSPAN8 protein expression in relation to GFP expression in the initially sorted cell population (GFP + cells gated in ( B )). Notably, the majority of GFP high cells exhibited an absence of TSPAN8 expression, confirming the efficacy of the reporter enrichment strategy. GFP high cells were sorted to further enrich the homozygous reporter cell population and establish the final cell line. ( D ) FACS analysis demonstrates that most cells in the final homozygous cell line derived from the sorted GFP high population were TSPAN8-negative. ( E ) Western blotting validates the absence of TSPAN8 protein in the homozygous reporter cell line. An established TSPAN8 knockout (KO) and non-targeting (NT) cells generated in our previous study were used as negative and positive controls, respectively, for TSPAN8 expression.

Article Snippet: The Human Two Plasmid Activity-Optimized CRISPR Knockout sgRNA Library, developed by David Sabatini, Eric Lander and colleagues, was obtained from Addgene (Cat# 1000000095, Watertown, MA, USA) [ ].

Techniques: Knock-Out, Knock-In, Disruption, Sequencing, Expressing, Transfection, Electroporation, Derivative Assay, Western Blot, Generated

Journal: Cells

Article Title: Rapid and Robust Generation of Homozygous Fluorescent Reporter Knock-In Cell Pools by CRISPR-Cas9

doi: 10.3390/cells14151165

Figure Lengend Snippet: Establishment of biallelic knock-in reporter cells retaining endogenous protein expression. ( A ) Schematic illustration of the targeting strategy for the TSPAN8 gene locus by CRISPR-Cas9. In this strategy, the stop codon of the human TSPAN8 gene is replaced with a T2A-eGFP sequence. The resulting mRNA from the modified allele encodes two separate proteins: TSPAN8 and GFP. ( B ) Representative FACS analysis of electroporated cells. Different dosages of plasmids were tested on MEC cells. Notably, in the absence of TSPAN8 sgRNA (i.e., non-target sgRNA), no GFP-positive cells were observed. ( C ) Representative FACS plots of the reporter cell line generated after multiple rounds of sorting of the GFP high population. The established reporter cell line exhibits high GFP and intact TSPAN8 expression. ( D ) PCR genotyping analysis of the established reporter cell line. The total GFP + cells exhibited two bands corresponding to knock-in (KI) and wild-type (WT) alleles, respectively. The WT allele is absent in the reporter cell line established from the GFP high population.

Article Snippet: The Human Two Plasmid Activity-Optimized CRISPR Knockout sgRNA Library, developed by David Sabatini, Eric Lander and colleagues, was obtained from Addgene (Cat# 1000000095, Watertown, MA, USA) [ ].

Techniques: Knock-In, Expressing, CRISPR, Sequencing, Modification, Generated

Journal: Cells

Article Title: Rapid and Robust Generation of Homozygous Fluorescent Reporter Knock-In Cell Pools by CRISPR-Cas9

doi: 10.3390/cells14151165

Figure Lengend Snippet: Generation of knock-in reporter cells using a single-plasmid system integrating both sgRNA and donor DNA. ( A ) Workflow for generating GFP knock-in cell lines using a single plasmid. Cas9-expressing MEC cells were transfected with the single plasmid by electroporation and cultured for 7–10 days. GFP + /miRFP670 − populations were enriched by FACS. ( B ) Representative FACS plots for cells electroporated with different amounts of single plasmid and analysed 10 days post-transduction. Transduced cells with the single plasmid lacking TSPAN8 sgRNA (i.e., non-target sgRNA) were also tested as a negative control. ( C ) Representative FACS plots of the knock-in reporter cell line generated after multiple rounds of GFP high sorting. ( D ) PCR genotyping of the established reporter cell line. The total GFP + cells exhibited bands corresponding to both knock-in (KI) and wild-type (WT) alleles. The WT allele is absent in the reporter cell line derived from the GFP high population.

Article Snippet: The Human Two Plasmid Activity-Optimized CRISPR Knockout sgRNA Library, developed by David Sabatini, Eric Lander and colleagues, was obtained from Addgene (Cat# 1000000095, Watertown, MA, USA) [ ].

Techniques: Knock-In, Plasmid Preparation, Expressing, Transfection, Electroporation, Cell Culture, Transduction, Negative Control, Generated, Derivative Assay

Journal: Cells

Article Title: Rapid and Robust Generation of Homozygous Fluorescent Reporter Knock-In Cell Pools by CRISPR-Cas9

doi: 10.3390/cells14151165

Figure Lengend Snippet: Generation of knock-in reporter cells by the IDLV system. ( A ) Workflow for generating GFP knock-in cell lines using the IDLV system. Cas9-expressing MEC cells were infected with lentivirus packaged by the IDLV system. Following infection, cells were treated immediately with doxycycline to induce sgRNA expression. GFP + /miRFP670 − populations were enriched by FACS. ( B ) Representative FACS plots of cells at 10 days post-infection with the indicated amount of lentivirus generated by the IDLV system. Lentivirus lacking sgRNA was used as a negative control. ( C ) Representative FACS plots showing a uniform GFP expression in the established knock-in reporter cells, established by multiple rounds of sorting of the GFP high population. ( D ) Validation of correct integration of GFP reporter into the TSPAN8 locus. Two distinct sgRNAs targeting early exons of TSPAN8 were used for validation. ( E ) PCR analysis of random integration. PCR analysis was conducted using indicated primers targeting the sequences spanning the plasmid backbone and homology arms. Unsorted cells after transduction or the established reporter cell lines by single-plasmid electroporation or IDLV were analysed. ( F ) Droplet digital PCR (ddPCR) analysis of GFP and TSPAN8 was performed to determine their genomic copy numbers. Primers targeting the GFP insert and the endogenous TSPAN8 locus were used to assess the relative abundance of each sequence. Each sample was analysed in triplicate.

Article Snippet: The Human Two Plasmid Activity-Optimized CRISPR Knockout sgRNA Library, developed by David Sabatini, Eric Lander and colleagues, was obtained from Addgene (Cat# 1000000095, Watertown, MA, USA) [ ].

Techniques: Knock-In, Expressing, Infection, Generated, Negative Control, Biomarker Discovery, Plasmid Preparation, Transduction, Electroporation, Digital PCR, Sequencing

Journal: Cells

Article Title: Rapid and Robust Generation of Homozygous Fluorescent Reporter Knock-In Cell Pools by CRISPR-Cas9

doi: 10.3390/cells14151165

Figure Lengend Snippet: Genome-wide CRISPR-Cas9 screen for transcriptional regulators of TSPAN8. ( A ) Schematic illustrating the workflow of the genome-scale CRISPR/Cas9 loss-of-function screen to enrich the GFP low cells. JHH5 reporter cells stably expressing Cas9 were transduced with a lentiviral sgRNA library. The GFP low cell population was enriched through repeated rounds of sorting and culture. The enriched sgRNAs were identified via next-generation sequencing (NGS). ( B ) FACS plots showing sequential enrichment of the cells with reduced GFP expression. The GFP low cells were sorted over multiple rounds, with one week of expansion between rounds. ( C ) Candidate genes were identified by comparing the sgRNA read counts between the initial pool and the final GFP low population. ( D ) Scatterplot displaying the sgRNA enrichment for selected candidate genes. ( E – G ) Representative FACS plots showing the reduction in both cell-surface TSPAN8 ( E ) and GFP reporter expression ( G ) following knockout of NF2, DYRK1A, and SOX9. ( H , I ) FACS and qPCR analysis showing that knockout of SOX9 in JHH5 parental cells significantly downregulates TSPAN8 expression. ( J ) Representative FACS plots showing knockout of NF2, DYRK1A, and SOX9 reduced cell-surface TSPAN8 expression in the human HCC cell line SNU878.

Article Snippet: The Human Two Plasmid Activity-Optimized CRISPR Knockout sgRNA Library, developed by David Sabatini, Eric Lander and colleagues, was obtained from Addgene (Cat# 1000000095, Watertown, MA, USA) [ ].

Techniques: Genome Wide, CRISPR, Stable Transfection, Expressing, Transduction, Next-Generation Sequencing, Knock-Out