Research method
CRISPR-Cas9 Genome Editing
CRISPR in this library is two different objects that share a name. In bacteria it is an adaptive immune array of repeats and spacers; papers can catalogue those arrays without editing anything. In experimental cells and plants it is a programmable nuclease or RNA-targeting enzyme (Cas9, dCas9, Cas13a) used to cut, bind, or interfere with a chosen sequence. The student question 'what is CRISPR?' therefore has to ask which of those jobs the paper actually did.
Researchers reach for Cas enzymes when they need a targeted cut, a promoter pull-down, or sequence-specific viral interference; they reach for CRISPR-array scans when they are describing prokaryotic genomes. The method answers either 'what happens if we target this sequence?' or 'where are these arrays and what might they fold into?' Mixing those answers is the characteristic mistake this page exists to prevent. Native-array papers do not demonstrate genome editing; Cas-tool papers do not, by themselves, map every CRISPR locus in nature.
Evidence
What the evidence shows
Drawn from 9 studies in this library. Each finding starts with a plain-language takeaway, then the denser detail. Supports means evidence for a finding; Challenges means evidence against a stated position; Qualifies marks scope with a short note on each study’s contribution. Challenged positions are labeled — they are not findings.
Native CRISPR arrays can be studied as sequence and predicted RNA structure without any editing experiment. A scan of 439 genomes found 561 arrays in 195 genomes; some repeat clusters had consistently high folding potential, taken as support for RNA intermediates — computational structure, not a Cas9 knockout.
Cas13a can be programmed as an antiviral in plants. Targeting different TuMV genomic regions reduced GFP and viral accumulation, showing sequence-specific RNA-virus interference rather than a DNA double-strand break. Guide choice still mattered, and the paper is not a field deployment against all RNA viruses.
Catalytically dead Cas9 can be used as a locus-specific hook. dCas9 chromatin immunoprecipitation (CasIP) in MDA-MB231 cells pulled RNAs at the FLI1 promoter and helped identify FECR1, a FLI1 exonic circRNA that activates FLI1 and promotes invasion — a dCas9 affinity experiment, not a knockout screen.
Many papers in the CRISPR index mention CRISPR or Cas proteins in passing while the actual experiment is something else (APEX2 proximity labelling, pan-genome presence/absence, ChIP-seq of histone acylations, scRNA-seq of endoderm). Those hits show why a body-count lexicon over-recruits; they are not additional editing results.
- Mapping the faces of mitochondria and ER
- How open is the Listeria pan-genome?
- Histone acylations respond to plant stress
- What marks definitive endoderm progenitors in hESCs?
Study Role Design N Population Outcome Mapping the faces of mitochondria and ER Supports Animal / in-vitroAPEX2 proximity labeling of cytosol-facing OMM and ER membranes in living HEK 293T cells SILAC proteomic maps with two replicates per membrane — cell-resource study HEK 293T cells expressing OMM/ERM APEX2 fusions Proteomes of cytosol-facing outer mitochondrial and ER membranes How open is the Listeria pan-genome? Supports Computational / modellingExtended L. monocytogenes complete-genome set covering all serotypes for pan-genome analysis N=16 · 16 completely sequenced chromosomes (extended by 11 strains in this work) Listeria monocytogenes genomes across serotypes Pan-genome stability and accessory-gene hotspot dynamics Histone acylations respond to plant stress Supports Animal / in-vitroMS and ChIP-seq mapping of histone Kbu/Kcr in rice vs H3K9ac under metabolic stress Plant chromatin proteomics/ChIP-seq study — no single primary analytic N in stored text Rice (and related plants) under stress conditions Distribution and stress dynamics of histone butyrylation/crotonylation What marks definitive endoderm progenitors in hESCs? Supports Animal / in-vitroscRNA-seq of H1/H9 progenitors and oxygen-condition tests during definitive endoderm differentiation N=1018 · 1,018 single cells analysed (including H1 n=212, H9 n=162, HFFs n=159) Human embryonic stem cells and lineage-specific progenitors Single-cell regulators and hypoxia effects on definitive endoderm differentiation
Open questions
Tensions and limits
Some items are genuine disagreements on the same question. Others mark different assays, populations, or outcomes — limits on how far one study travels — not a forced fight between papers.
The strongest tension is naming. The 2007 array paper and the Listeria pan-genome treat CRISPR as a genomic feature of bacteria; the Cas13a and dCas9 papers treat CRISPR–Cas as a laboratory tool. Both usages are historically connected, but a finding about repeat RNA folding does not license a claim about editing a human promoter, and a CasIP result does not catalogue environmental CRISPR diversity.
- CRISPR repeats conserve RNA-like structure
- Can Cas13a fight RNA viruses in plants?
- FLI1 circRNA FECR1 drives metastasis
- How open is the Listeria pan-genome?
Study Role Design N Population Outcome CRISPR repeats conserve RNA-like structure Supports Computational / modellingGenome-wide CRISPR array detection and repeat secondary-structure scoring N=439 · 439 bacterial/archaeal genomes; 561 arrays in 195 genomes Bacterial and archaeal sequenced genomes Conserved CRISPR repeat sequence/structure features across clusters Can Cas13a fight RNA viruses in plants? Supports Animal / in-vitroProgrammed Cas13a targeting TuMV genomic regions in plants Plant molecular interference assays — no single primary analytic N in stored text Plants infected with Turnip mosaic virus (TuMV) Cas13a-mediated reduction of viral GFP and accumulation FLI1 circRNA FECR1 drives metastasis Supports Animal / in-vitrodCas9 CasIP and functional assays of FECR1 circRNA in MDA-MB231 cells Cell-line mechanistic study; no single primary analytic N in stored text MDA-MB231 breast cancer cells (with tumor vs adjacent FLI1 context) FECR1 activation of FLI1 and invasive phenotypes How open is the Listeria pan-genome? Supports Computational / modellingExtended L. monocytogenes complete-genome set covering all serotypes for pan-genome analysis N=16 · 16 completely sequenced chromosomes (extended by 11 strains in this work) Listeria monocytogenes genomes across serotypes Pan-genome stability and accessory-gene hotspot dynamics Even among tool papers, the enzyme is not always Cas9 cutting DNA. Cas13a targets RNA viruses; dCas9 in CasIP binds without requiring a cut. Calling every experiment a 'CRISPR knockout' is false for this set.
Study Role Design N Population Outcome Can Cas13a fight RNA viruses in plants? Supports Animal / in-vitroProgrammed Cas13a targeting TuMV genomic regions in plants Plant molecular interference assays — no single primary analytic N in stored text Plants infected with Turnip mosaic virus (TuMV) Cas13a-mediated reduction of viral GFP and accumulation FLI1 circRNA FECR1 drives metastasis Supports Animal / in-vitrodCas9 CasIP and functional assays of FECR1 circRNA in MDA-MB231 cells Cell-line mechanistic study; no single primary analytic N in stored text MDA-MB231 breast cancer cells (with tumor vs adjacent FLI1 context) FECR1 activation of FLI1 and invasive phenotypes
Common misconceptions
CRISPR in a paper always means the authors knocked out a gene with Cas9.
In this library CRISPR often means a bacterial repeat-spacer array (439 genomes, 561 arrays) or a non-cutting tool (dCas9 CasIP, Cas13a RNA interference). Gene knockout and knockdown is a separate method page when loss-of-function is actually what was done.
If Cas13a reduces viral GFP in plants, CRISPR is ready as a field antiviral for any RNA virus.
Interference depended on which TuMV region was targeted; the paper does not demonstrate deployment across viruses or environments.
Computational folding of CRISPR repeats proves those RNAs exist and function in the cell.
The 2007 paper reports folding-potential scores across clusters as support for RNA intermediates, and explicitly is not direct RNA-structure proof for every array.
Exam-style questions
Short-answer questions that ask you to explain or compare, not recall.
A methods section says 'we analysed CRISPR.' List two experiments in this library that sentence could honestly describe, and one it should not.
It could mean scanning genomes for repeat-spacer arrays and scoring RNA-like folding, or programming Cas13a against TuMV, or pulling promoter-associated RNAs with dCas9. It should not be taken to mean an APEX2 mitochondrial-ER proteomic map or an scRNA-seq oxygen titration merely because those papers mention CRISPR in the text.
Compare Cas13a interference with dCas9 CasIP: what molecule is targeted, and is a double-strand DNA break required?
Cas13a is aimed at RNA virus genomes and reduces viral accumulation without being a DNA-cutting knockout. dCas9 in CasIP is used as a DNA-binding hook to recover RNAs at the FLI1 promoter; catalysis of a cut is not the point of that assay.
Why does finding 561 CRISPR arrays in 195 genomes not tell you what happens if you knock out FLI1 in a breast-cancer line?
That scan catalogues native prokaryotic arrays and predicted repeat structure. FLI1/FECR1 work uses dCas9 in human cells to study a circular RNA at a eukaryotic promoter. The shared acronym does not transfer the result.
How should a student use the gene-knockout-and-knockdown page together with this one?
Use this page when the paper's claim is about CRISPR arrays or Cas targeting. Use knockout/knockdown when the actual perturbation is loss of a gene product (shRNA, siRNA, a true knockout), which several papers in this index never do despite matching the CRISPR lexicon.
The studies
9 studies in this library bear on CRISPR-Cas9 Genome Editing, ordered by citations. The first 8 are shown.
- Can Cas13a fight RNA viruses in plants?
CRISPR/Cas13a interferes with TuMV in plants, cutting viral RNA and reducing reporter/virus accumulation.
- What marks definitive endoderm progenitors in hESCs?
Single-cell RNA-seq separates definitive endoderm progenitors and links metabolism/hypoxia to DE differentiation.
- FLI1 circRNA FECR1 drives metastasis
Exonic circular RNA FECR1 binds the FLI1 promoter and epigenetically activates FLI1 in breast cancer.
- Mapping the faces of mitochondria and ER
APEX2 proximity biotinylation yields high-quality proteomic maps of cytosol-facing outer mitochondrial and ER membranes in living human cells.
- CRISPR repeats conserve RNA-like structure
CRISPR repeats across microbes form clusters with conserved sequence and predicted RNA secondary structure.
- How open is the Listeria pan-genome?
Eleven new genomes spanning serotypes show a stable but open pan-genome with nine hypervariable hotspots dominated by mobile elements.
- Histone acylations respond to plant stress
Rice histone butyrylation and crotonylation mark active chromatin and shift under starvation/submergence.
- How does ZFP36 reshape metabolism after growth signals?
Growth factors induce ZFP36, which binds and decays metabolic enzyme/transporter mRNAs—especially Eno2—tuning glycolytic metabolism.
Show 1 more studiesShow fewer studies
- Folliculin tunes mTORC1 toward TFE3
FLCN–RagC signaling makes mTORC1 substrate-selective for TFE3 phosphorylation under amino-acid cues.
Learn alongside