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Genome editing, specifically CRISPR/Cas9 technology, has revolutionized biomedical research and offers potential cures for genetic diseases. Despite rapid progress, low efficiency of targeted DNA integration and generation of unintended mutations represent major limitations for genome editing applications caused by the interplay with DNA double-strand break repair pathways. To address this, we conduct a large-scale compound library screen to identify targets for enhancing targeted genome insertions. Our study reveals DNA-dependent protein kinase (DNA-PK) as the most effective target to improve CRISPR/Cas9-mediated insertions, confirming previous findings. We extensively characterize AZD7648, a selective DNA-PK inhibitor, and find it to significantly enhance precise gene editing. We further improve integration efficiency and precision by inhibiting DNA polymerase theta (Polϴ). The combined treatment, named 2iHDR, boosts templated insertions to 80% efficiency with minimal unintended insertions and deletions. Notably, 2iHDR also reduces off-target effects of Cas9, greatly enhancing the fidelity and performance of CRISPR/Cas9 gene editing. Low efficiency of target DNA integration remains a challenge in genome engineering. Here the authors perform large-scale compound library and genetic screens to identify targets that enhance gene editing: they see that combined DNA-PK and Polϴ inhibition with potent compounds increases editing efficiency and precision.

TET proteins convert 5‐methylcytosine to 5‐hydroxymethylcytosine, an emerging dynamic epigenetic state of DNA that can influence transcription. Evidence has linked TET1 function to epigenetic repression complexes, yet mechanistic information, especially for the TET2 and TET3 proteins, remains limited. Here, we show a direct interaction of TET2 and TET3 with O ‐GlcNAc transferase (OGT). OGT does not appear to influence hmC activity, rather TET2 and TET3 promote OGT activity. TET2/3–OGT co‐localize on chromatin at active promoters enriched for H3K4me3 and reduction of either TET2/3 or OGT activity results in a direct decrease in H3K4me3 and concomitant decreased transcription. Further, we show that Host Cell Factor 1 (HCF1), a component of the H3K4 methyltransferase SET1/COMPASS complex, is a specific GlcNAcylation target of TET2/3–OGT, and modification of HCF1 is important for the integrity of SET1/COMPASS. Additionally, we find both TET proteins and OGT activity promote binding of the SET1/COMPASS H3K4 methyltransferase, SETD1A, to chromatin. Finally, studies in Tet2 knockout mouse bone marrow tissue extend and support the data as decreases are observed of global GlcNAcylation and also of H3K4me3, notably at several key regulators of haematopoiesis. Together, our results unveil a step‐wise model, involving TET–OGT interactions, promotion of GlcNAcylation, and influence on H3K4me3 via SET1/COMPASS, highlighting a novel means by which TETs may induce transcriptional activation. This paper identifies the N‐acetylglucosamine transferase OGT as binding partner for TET2/3 proteins. Their genome‐wide chromatin binding and the characterization of the Set1/COMPASS complex as OGT target implies coordinated gene regulation.

Concerted multidisciplinary efforts have led to the development of Cyclin-Dependent Kinase inhibitors (CDKi’s) as small molecule drugs and chemical probes of intracellular CDK function. However, conflicting data has been reported on the inhibitory potency of CDKi’s and a systematic characterization of affinity and selectivity against intracellular CDKs is lacking. We have developed a panel of cell-permeable energy transfer probes to quantify target occupancy for all 21 human CDKs in live cells, and present a comprehensive evaluation of intracellular isozyme potency and selectivity for a collection of 46 clinically-advanced CDKi’s and tool molecules. We observed unexpected intracellular activity profiles for a number of CDKi’s, offering avenues for repurposing of highly potent molecules as probes for previously unreported targets. Overall, we provide a broadly applicable method for evaluating the selectivity of CDK inhibitors in living cells, and present a refined set of tool molecules to study CDK function. Cyclin-dependent kinase (CDK) inhibitors are widely used both in the clinic and for basic research aimed at dissecting the specific cellular functions of specific CDKs. Here, the authors report the development of a panel of fluorescent reporter probes and provide a comprehensive profile of the inhibitory activity of several CDK inhibitors towards all 21 CDKs in living cells.

The ability to analyze protein function in a native context is central to understanding cellular physiology. This study explores whether tagging endogenous proteins with a reporter is a scalable strategy for generating cell models that accurately quantitate protein dynamics. Specifically, it investigates whether CRISPR-mediated integration of the HiBiT luminescent peptide tag can easily be accomplished on a large-scale and whether integrated reporter faithfully represents target biology. For this purpose, a large set of proteins representing diverse structures and functions, some of which are known or potential drug targets, were targeted for tagging with HiBiT in multiple cell lines. Successful insertion was detected for 86% of the targets, as determined by luminescence-based plate assays, blotting, and imaging. In order to determine whether endogenously tagged proteins yield more representative models, cells expressing HiBiT protein fusions either from endogenous loci or plasmids were directly compared in functional assays. In the tested cases, only the edited lines were capable of accurately reproducing the anticipated biology. This study provides evidence that cell lines expressing HiBiT fusions from endogenous loci can be rapidly generated for many different proteins and that these cellular models provide insight into protein function that may be unobtainable using overexpression-based approaches.

Genome editing tools, especially CRISPR/Cas9-based strategies, have transformed biomedical research and opened opportunities for developing curative treatments for genetic diseases. Despite rapid progress, low efficiency of targeted DNA integration and generation of undesired mutations represent major limitations for genome editing applications. Both issues arise from the interplay between the main DNA Double-Strand Break (DSB) repair pathways, Homology-Directed Repair (HDR), Non-Homologous End Joining (NHEJ), and Microhomology-Mediated End Joining (MMEJ). To improve efficiencies of targeted CRISPR-Cas9 genome editing, we screened a large compound library. This led to the discovery of AZD7648, a DNA-dependent protein kinase (DNA-PK) inhibitor and potent enhancer of CRISPR-Cas9-mediated integration. We demonstrated that AZD7648 increased HDR and decreased mutagenic NHEJ repair, thus resulting in improved performance of precise gene editing. Furthermore, we observed additional improvement of integration efficiency by impairing MMEJ repair through DNA polymerase ϴ (Polϴ) inhibition. Combined treatment with AZD7648 and Polϴ inhibitors (which we named 2iHDR) substantially increased precision of templated insertions, with efficiencies of up to 80%, and nearly no formation of undesired Insertion-Deletions (InDels). Importantly, 2iHDR also decreased Cas9-associated off-target activity, dramatically improving the performance and fidelity of CRISPR-Cas9 gene editing.Competing Interest StatementS.W., N.A., M.F., J.B., S.E., A.L., P.H., S.L., S.C., J.S., B.B., B.S., B.M., S.DC., P.I., M.B., T.M., S.R., O.E., E.C., J.V.F., S.S., P.A., A.T.G. and M.M. are presently or were previously employed by AstraZeneca and may be AstraZeneca shareholders. M.K.S., M.R.S., and TM are presently employed by Promega Corporation.

Flavonoids, in particular the anthocyanins,are responsible for flower colour in manyspecies. The dihydroflavonols represent abranch point in flavonoid biosynthesis,being the intermediates for production ofboth the coloured anthocyanins, through theaction of the enzyme dihydroflavonol4-reductase (DFR), and the colourlessflavonols, produced by flavonol synthase(FLS). In this study the white-flowered,flavonol accumulating Mitchell line ofpetunia was used as a model to examine theinteraction between DFR and FLS enzymeactivities and possibilities forredirecting flavonoid biosynthesis awayfrom production of flavonols and towardsanthocyanins. Introduction of a 35SCaMV-DFR sense transgene construct causedthe production of anthocyanins, resultingin a pink-flowered phenotype. Furthermore,inhibition of FLS production throughintroduction of an FLS antisense RNAconstruct also led to anthocyaninproduction and a pink-flowered phenotype. A combination of both transgenes gave thehighest level of anthocyanin formation. Anthocyanins were produced in the DFR-senseand FLS-antisense transgenic lines in spiteof the greatly reduced levels of geneexpression in the Mitchell line for threeenzymes late in anthocyanin biosynthesis,anthocyanindin synthase, UDP-glucose:flavonoid 3-O-glucosyltransferase andUDP-rhamnose: anthocyanidin-3-glucosiderhamnosyltransferase. Thus, the level ofgene activity required for visibleanthocyanin formation is much lower thanthe high levels normally induced duringpetal development. Altering the balancebetween the DFR and FLS enzyme activities,using genetic modification, may be a usefulstrategy for introducing or increasinganthocyanin production in target ornamentalspecies.[PUBLICATION ABSTRACT]

Three cultivars of lisianthus (Eustoma grandiflorum (Grise.)) were transformed with a homologous antisense CHS cDNA via Agrobacterium-mediated transformation. Over 50% of the transgenics derived from the purple flowering lines exhibited an altered flower colour pattern ranging from small streaks of white on the wild-type purple background through to completely white flowers. A significant portion of the transgenic lines showed unstable phenotypes. Northern and biochemical analysis showed that the altered flower patterns were associated with a loss of CHS gene transcript and a corresponding loss of CHS enzyme activity. In the white flowering line the level of total flavonoids was reduced to ca. 2.0% of the wild-type level. Some of the transgenic plants also exhibited alterations in flower form such as the formation of frilled petal tips and reduced flower opening. Several of the new patterned lines are being evaluated for stability and possible commercial release.