SCIENCE CHINA

(1)

•RESEARCH PAPER• September 2021 Vol.64 No.9: 1449–1462 https://doi.org/10.1007/s11427-020-1855-4

HDAC inhibitors improve CRISPR-mediated HDR editing efficiency in iPSCs

Jian-Ping Zhang^1†*, Zhi-Xue Yang^1†, Feng Zhang^1†, Ya-Wen Fu¹, Xin-Yue Dai¹, Wei Wen¹, Beldon Zhang², Hannah Choi³, Wanqiu Chen³, Meredith Brown³, David Baylink², Lei Zhang^1,4,7, Hongyu Qiu⁸, Charles Wang^3*, Tao Cheng^1,5,6* & Xiao-Bing Zhang^1,2*

1State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China;

2School of Medicine, Loma Linda University, Loma Linda, CA 92354, USA;

3Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA;

4CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China;

5Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China;

6Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China;

7Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China;

8Center of Molecular and Translational Medicine, Institution of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA Received August 19, 2020; accepted November 17, 2020; published online January 6, 2021

Genome-edited human induced pluripotent stem cells (iPSCs) hold great promise for therapeutic applications. However, low editing efficiency has hampered the applications of CRISPR-Cas9 technology in creating knockout and homology-directed repair (HDR)-edited iPSC lines, particularly for silent genes. This is partially due to chromatin compaction, inevitably limiting Cas9 access to the target DNA. Among the six HDAC inhibitors we examined, vorinostat, or suberoylanilide hydroxamic acid (SAHA), led to the highest HDR efficiency at both open and closed loci, with acceptable toxicity. HDAC inhibitors equally increased non-homologous end joining (NHEJ) editing efficiencies (~50%) at both open and closed loci, due to the considerable HDAC inhibitor-mediated increase in Cas9 and sgRNA expression. However, we observed more substantial HDR efficiency improvement at closed loci relative to open chromatin (2.8 vs. 1.7-fold change). These studies provide a new strategy for HDR- editing of silent genes in iPSCs.

HDAC inhibitors, CRISPR-Cas9, genome editing, iPSC

Citation: Zhang, J.P., Yang, Z.X., Zhang, F., Fu, Y.W., Dai, X.Y., Wen, W., Zhang, B., Choi, H., Chen, W., Brown, M., et al. (2021). HDAC inhibitors improve CRISPR-mediated HDR editing efficiency in iPSCs. Sci China Life Sci 64, 1449–1462.https://doi.org/10.1007/s11427-020-1855-4

INTRODUCTION

Human induced pluripotent stem cells (iPSCs) have demonstrated applications in basic research and regenerative medicine (Robinton and Daley, 2012). To achieve the full

potential of iPSCs, genetic modification of these cells are often necessary, such as correction of a diseased gene for replacement therapy, creation of a mutation for disease modeling, or precise insertion of a chimeric artificial re- ceptor (CAR) for immunotherapy (Hockemeyer and Jae- nisch, 2016). Human iPSC reporter lines have been widely used as a tool to expedite scientific discoveries. More recently, iPSC-derived universal CAR-T or CAR-NK cells have been considered the future of allogeneic im-

SCIENCE CHINA Life Sciences

†Contributed equally to this work

*Corresponding authors (Jian-Ping Zhang, email: zhangjianping@ihcams.ac.cn;

Charles Wang, email:chwang@llu.edu; Tao Cheng, email:chengtao@ihcams.ac.cn;

Xiao-Bing Zhang, email:zhangxbhk@gmail.com)

(2)

munotherapy against cancer and infectious diseases (Li et al., 2018b; Nianias and Themeli, 2019; Themeli et al., 2013).

These exciting applications rely on efficient, precise editing of human iPSCs (Avior et al., 2016; Hockemeyer and Jae- nisch, 2016;Themeli et al., 2015;Zhang, 2013).

This precision was prohibitively inefficient unless the target sequence was subject to double-strand cleavage by an artificial endonuclease. The discovery of the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats- CRISPR associated protein 9) system has changed the landscape of genome editing. CRISPR-Cas9 is a type of immune system in bacteria that can target and cut foreign DNA to protect against viruses (Lino et al., 2018). The en- gineered Cas9-sgRNA (single guide RNA) has been widely used to edit all types of mammalian cells. Several studies, however, have shown that gene editing efficiency in iPSCs is usually 3- to 20-fold lower than that of other cell types, such as 293T, K562, and LO2 cells (He et al., 2016;Hsu et al., 2013;Lin et al., 2014;Mali et al., 2013). Our interests lie in identifying strategies that improve the editing efficiency in human iPSCs. Along the same line, we found that truncated RNA is ineffective in iPSCs (Zhang et al., 2016). We recently reported that using a double-cut plasmid donor with transient BCL-XL expression considerably increases CRISPR-Cas9-mediated editing efficiency in iPSCs (Li et al., 2018a; Zhang et al., 2017). However, all these studies were conducted on highly expressed genes at open chromatin loci in iPSCs. These loci tended to have a higher editing efficiency than unexpressed genes or closed chromatin areas.

Given the clinical significance of editing closed loci of iPSCs, we attempted to further increase editing efficiency in iPSCs by screening chromatin regulators.

While CRISPR-Cas9 is a powerful technology, several studies on Streptococcus pyogenes Cas9 (SpCas9) have suggested that chromatin structures can be a major barrier to Cas9 binding and target DNA cleavage in mouse embryonic stem cells (mESCs) (Wu et al., 2014) as well as human iPSCs (Chari et al., 2015). Unlike the loosely organized DNA in prokaryotes, eukaryotic genomic DNA is tightly packed and wrapped around histones, then further compacted to form higher-order chromatin structures (Campos and Reinberg, 2009), possibly hindering the binding of Cas9 to its targets.

Thus, the gene-editing process of CRISPR-Cas9 in eu- karyotes is very different from that of prokaryotes.

Multiple methods have been reported to attempt altering local accessibility and thus improving Cas9 activity in mammalian cells. The proxy-CRISPR strategy uses an additional catalytically dead SpCas9 (dCas9) to bind to proximal locations. These rendered target sites became accessible to FnCas9, CjCas9, NcCas9, and FnCpf1, improving editing efficiency (Chen et al., 2017). Practically, however, this strategy is complicated. CRISPR-chrom, in which Cas9 or- thologs are fused with chromatin-modulating peptides

(CMPs), substantially improved Cas9 editing efficiency, particularly at refractory sites (Ding et al., 2019). CMPs are peptides derived from high mobility group (HMG) proteins HMGN and HMGB1, histone H1, and chromatin remodeling complexes. Like this approach, we attempted to test the fusion of VP64 or EP300 core protein to Cas9, since dCas9 fused to either robustly influenced epigenome editing (Hilton et al., 2015;Kwon et al., 2017).

Another approach for globally opening chromatin is to increase histone acetylation levels. Histone acetylation and deacetylation control the open or closed states of chromatin structure. These reactions are typically catalyzed by two groups of enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs) (Eberharter and Becker, 2002; Seto and Yoshida, 2014). Acetylation removes the positive charge on histones, thereby decreasing the interac- tion of the N termini of histones with the negatively charged phosphate groups of DNA, and inducing chromatin relaxation (Kouzarides, 2007). This relaxation is counterbalanced by HDAC activity (Haberland et al., 2009), but the inhibition of HDAC tips the balance toward more open chromatin. As such, we hypothesized that transient global opening of chromatin with histone deacetylase (HDAC) inhibitors would provide editing factors better access to typically non- transcribed, closed chromatin regions in iPSCs, leading to high-level editing.

In this study, we compared six different HDAC inhibitors:

sodium butyrate (NaB, HDAC Class I and IIa inhibitor) (Davie, 2003), trichostatin A (TSA, HDAC Class I and II inhibitor) (Yoshida et al., 1990), vorinostat or sub- eroylanilohydroxamic acid (SAHA, pan-HDAC inhibitor) (Grant et al., 2007), valproic acid (VPA, HDAC Class I and IIa inhibitor), entinostat (MS275, HDAC Class I inhibitor) (Frys et al., 2015), and panobinostat (LBH589, pan-HDAC inhibitor) (Singh et al., 2016). We found that 24 h of treatment with HDAC inhibitors improved editing efficiency, with more pronounced improvement in closed loci HDR editing.

RESULTS

Selection of gene-editing loci

This study selected seven genes to investigate chromatin modulating agents’ effects: MESP1, GATA4, MYH6, PRDM14, GAPDH, EEF1A1, andEEF2. We divided them into two groups based on differential gene expression levels in human iPSCs, which we have previously determined by RNA-seq (Figure S1 in Supporting Information). MESP1, GATA4, andMYH6are cardiac lineage-specific genes (Bur- ridge et al., 2012), which have very low transcripts (or counts) per million reads (0.05–0.28 TPM) in iPSCs (Figure S1 in Supporting Information).GAPDH,EEF1A1, andEEF2

(3)

are internal control genes (Barber et al., 2005;Ersahin et al., 2014;Gentile et al., 2016) that have very high TPM (1,460–

9,911) in iPSCs (Figure S1 in Supporting Information).

PRDM14is one of the pluripotency marker genes in iPSCs (Chan et al., 2013), with the TPM of ~52 falling between the two (Figure S1 in Supporting Information). Thus, MESP1, GATA4, andMYH6were considered closed chromatin loci, whilePRDM14,GAPDH,EEF1A1, andEEF2were regarded as open chromatin loci.

Fusion proteins of Cas9 and VP64 or EP300 decreased gene editing efficiency

VP64 and EP300 are often fused to dCas9 for targeted transcription activation (Hilton et al., 2015;Perez-Pinera et al., 2013). VP64 is a transcription activator composed of four tandem copies of the herpes simplex virus VP16 activation domain, connected by Gly-Ser linkers. Fusing the catalytic core of the histone acetyltransferase EP300 (EP300core) to dCas9 can acetylate H3K27 (H3K27ac) at targeted proximal and distal enhancers, which can lead to transcription activation. As such, we hypothesized that the fusion of VP64 or EP300 with spCas9 might improve gene-editing efficiency in human iPSCs.

Firstly, we constructed several plasmids that express different Cas9 fusion proteins with VP64 and EP300 driven by the EF1 promoter (Figure 1A). One nuclear localization signal (NLS) is included in all vectors to promote the nuclear entry of Cas9. To quantitate these fusion proteins’ effects on gene-editing efficiency, we designed double-cut plasmid donors to insert short fragments of 6 or 15 base pairs (bp) at MESP1,GATA4, andMYH6. We then assessed non-homo- logous end joining (NHEJ) and homology-directed repair (HDR) editings by deep sequencing (Figure 1B and C).

BCL-XL was also delivered to improve iPSC survival after electroporation. Three days after transfecting the editing plasmids, we determined the HDR and NHEJ efficiencies by amplicon sequencing and CRISPResso2 analysis (Clement et al., 2019).

To our surprise, the Cas9 fusion proteins SpCas9-VP64, SpCas9-EP300, and EP300-SpCas9 did not improve the HDR or NHEJ editing efficiencies at any of the three closed loci (Figure 1E; Figure S2 in Supporting Information). Next, we tested these Cas9 fusion proteins’ effects on gene editing at four open loci (GAPDH,PRDM14,EEF1A1, andEEF2) (Figure 1B–D). Again, Cas9 fusion proteins decreased HDR and NHEJ efficiencies at all these loci (Figure 1F; Figure S3 in Supporting Information). We noticed that the nimble SpCas9-VP64 fusion gene only moderately reduced HDR efficiencies. In contrast, SpCas9 and EP300 fusion protein significantly reduced HDR efficiencies, suggesting that this cumbersome fusion has considerably decreased cleavage efficacy on both genome target sites and the double-cut

donor.

Taken together, using a fusion protein of Cas9 and a transactivation or histone acetyltransferase domain to improve iPSC editing is counterproductive. We then turned our focus to HDAC inhibitors.

Histone deacetylase inhibitors promote gene editing at open chromatin loci

We firstly investigated the effects of different HDAC inhibitors (Figure S4 in Supporting Information;Figure 2B) on CRISPR-Cas9-mediated gene knockin and knockout efficiencies at open loci (Figure 2A). To test their cellular toxicity, we examined cell number change after the treatment of HDAC inhibitors in iPSCs (Figure S5 in Supporting In- formation). We found that cell number was not affected on days 1 and 2 (Figure S5A in Supporting Information).

However, all of the HDAC inhibitor-treated cells showed reduced cell numbers compared to the control group on day 3 (Figure S5A in Supporting Information). We also tested each inhibitor’s dose and found that the cell number decreased in a dose-dependent manner (Figure S5B in Supporting In- formation). We decided to use the moderate amounts in all subsequent experiments for HDAC inhibitors: NaB (1 mmol L^–1), SAHA (5 μmol L^–1), TSA (0.1 μmol L^–1), VPA (1 mmol L^–1), entinostat (5 μmol L^–1), and panobinostat (100 nmol L^–1) (Figure S5B in Supporting Information). To assess whether treatment with these inhibitors affects cell stemness, we conducted RT-qPCR three days after treatment.

We found that HDAC inhibitor treatment did not decrease the expression of pluripotency markers, such as OCT4, NANOG, and SOX2 (Figure S5C in Supporting Informa- tion). Besides, we observed no changes in iPSC morphology during long-term culture of the edited cells. Therefore, iPSCs tolerate transient HDAC inhibition.

Similar to our previous design (Li et al., 2018a), we used a promoterless double-cut HDR donor pD-mNeonGreen-sg to guide HDR insertion (Figure 2A). Only HDR editing of the target locus leads to green fluorescent protein expression;

thus, the percentage of mNeonGreen⁺cells directly reflected the HDR efficiency. We electroporated hiPSCs with pDonor- sg (double-cut HDR donor), pU6-sgDocut (targets the double-cut donor to release the HDR template from the plasmid), pU6-sgRNA (guides to the target gene), and pEF1-Cas9 (expresses Cas9 under EF1 promoter). We then cultured cells with four different HDAC inhibitors (NaB, SAHA, TSA, and VPA) on day 0. The culture medium was replaced with fresh medium without HDAC inhibitors on day 1, and cells were analyzed on day 3. Half the cells were assessed by flow cytometry to test mNeonGreen⁺HDR efficiency (Figure 2C).

The remaining cells’ genomic DNA underwent PCR for high-throughput amplicon sequencing, and NHEJ efficiency was analyzed using CRISPResso2 (Figure 2D). The effects

(4)

of HDAC inhibitors on relative induction fold of HDR efficiency, NHEJ efficiency, total indels (HDR+NHEJ), and relative HDR (HDR/(HDR+NHEJ)) at four open chromatin loci (GAPDH,PRDM14,EEF1A1, andEEF2) are shown in

Figure 2E and Figure S6 in Supporting Information. NaB, TSA, and VPA slightly increased HDR and NHEJ frequencies by 20%, whereas there was no change in relative HDR (Figure 2E). These data suggest that increased HDR

Figure 1 Fusion proteins of Cas9 and VP64 or EP300 decrease gene editing efficiency at both open and closed loci. A, Schematic of Cas9 fusion protein expression constructs driven by the EF1 promoter. SpCas9 (Cas9 only), Cas9-VP64 (Cas9 fused with VP64), Cas9-EP300 (EP300 fused with Cas9 at the 3′

end), EP300-Cas9 (EP300 fused with Cas9 at 5′ end). NLS, nuclear localization signal. B, Schematic of gene editing at three closed loci (MESP1,MYH6, and GATA4) and four open loci (GAPDH,EEF1A1,PRDM14, andEEF2). We electroporated human iPSCs with pDonor-sg (double-cut HDR donor), pU6- sgDocut (cut the donor), pU6-sgRNA (cut the gene), and pEF1-Cas9fu (different Cas9 fusion proteins). The HDR and NHEJ efficiencies were determined by FACS and Illumina sequencing. C, Representative HDR and NHEJ data. Substitutions are shown in bold font. Red rectangles highlight inserted sequences.

Horizontal dashed lines indicate deleted sequences. Vertical dashed lines indicate the predicted cleavage site. Asterisks indicate an unedited allele. D, HDR knockin efficiencies at open loci were determined by FACS analysis of mNeonGreen⁺cells. Representative FACS diagrams are shown. E, Summary of the effect of Cas9 fusion proteins on relative induction fold of HDR efficiency (KI), NHEJ efficiency (KO), and HDR percentage in all edited cells at three closed loci (MESP1,MYH6, andGATA4). HDR and NHEJ efficiencies were determined three days after transfection;n=15. F, Summary of the effect of Cas9 fusion proteins on relative induction fold of HDR efficiency (KI), NHEJ efficiency (KO), and HDR percentage in all edited cells at four open loci (GAPDH, PRDM14,EEF1A1, andEEF2). Three days after transfection, HDR efficiency was determined by FACS and NHEJ efficiency by high-throughput se- quencing. n=12. An unpaired t-test with Welch’s correction was used for statistical analysis; ns, not significant; *P<0.05, **P<0.01, ***P<0.001,

****P<0.0001.

(5)

Figure2HDACinhibitorsimproveHDRandNHEJefficienciesatopenloci.A,Schematicofgeneeditingatfouropenloci(GAPDH,PRDM14,EEF1A1,orEEF2).WeelectroporatediPSCswithpDonor-sg (double-cutHDRdonor),pU6-sgDocut(cutthedonor),pU6-sgRNA(cutthegene),andpEF1-Cas9(Cas9expressionunderEF1promoter).WethenculturedcellswithfourdifferentHDACinhibitors(NaB, SAHA,TSA,VPA)onday0andthenchangedtofreshmediumwithoutHDACinhibitorsonday1.Weharvestedcellsthreedayslaterforflowcytometryandhigh-throughputsequencing.NHEJefficiencywas analyzedusingCRISPResso2.B,MolecularstructuresoftheHDACinhibitors.C,KnockinefficienciesweredeterminedbyFACSanalysisofmNeonGreen+ cells,withrepresentativeFACSdiagramsshown.D, Representativeresultsofhigh-throughputsequencingdataafterCRISPResso2analysis.Substitutionsareshowninboldfont.Redrectangleshighlightinsertedsequences.Horizontaldashedlinesindicatedeleted sequences.Verticaldashedlinesindicatethepredictedcleavagesite.Asterisksindicateanuneditedallele.E,SummaryoftheeffectofHDACinhibitorsonrelativeinductionfoldofHDRefficiency(KI),NHEJ efficiency(KO),indels(HDR+NHEJ),andHDRpercentageinalleditedcellsatfourloci(GAPDH,PRDM14,EEF1A1,EEF2).Threedaysaftertransfection,HDRefficiencywasdeterminedbyFACSand NHEJefficiencybyhigh-throughputsequencing.n=5.Anunpairedt-testwithWelch’scorrectionwasusedforstatisticalanalysis;ns,notsignificant;*P<0.05,**P<0.01,***P<0.001,****P<0.0001.

(6)

editing efficacy at open loci is mainly due to increased DNA cleavage or NHEJ editing.

In the above studies, we designed donor templates to insert a fluorescent protein expression cassette (1–2 kb) by HDR, followed by quantitation of HDR efficiency by flow cytometry (FACS) and NHEJ efficiency by amplicon sequencing.

To further validate these results, we designed plasmid donors to insert a short fragment of 6–15 bp atGAPDH,PRDM14, EEF1A1, orEEF2, allowing assessment of both NHEJ and HDR editing by deep sequencing (Figure 3). In the process of preparing our manuscript, two additional HDAC inhibitors, entinostat and panobinostat, were reported to improve gene editing efficiency in somatic cells (Liu et al., 2020). As such, we also investigated their effects on HDR and NHEJ efficiency in our system (Figure 3A). Among these compounds, NaB, TSA, and VPA showed less pronounced effects on both NHEJ and HDR editing improvement (9%–24% vs. 28%–

43%) (Figure 3D, Figure S7 in Supporting Information). In contrast, SAHA, entinostat, and panobinostat more pro- nouncedly increased both NHEJ and HDR editing efficiencies (38%–54% vs. 54%–84%) (Figure 3D; Figure S7 in Supporting Information). However, we observed no significant differences in relative HDR editing efficiency (Figure 3D; Figure S7 in Supporting Information), suggesting that HDAC inhibitors improve gene editing efficiency by increasing cleavage efficiency at open chromatin loci in iPSCs.

Histone deacetylase inhibitors considerably promote gene editing efficiency at closed chromatin loci

Having demonstrated that HDAC inhibitors mediated increased gene editing efficiency at open chromatin loci, we examined their effects on HDR editing efficiency at closed chromatin loci. We decided to target MESP1, MYH6, and GATA4 genes, highly expressed in cardiomyocytes, but not iPSCs (Figure 4A–C). We observed greater HDR and NHEJ editing efficiencies at these closed loci compared to editing at closed loci (Figure 4D; Figure S8 in Supporting In- formation). Similar to editing at open loci (Figure 3), SAHA, entinostat, and panobinostat tended to have more significant effects relative to NaB, TSA, and VPA (98% vs. 46% increase in total indels) (Figure 4D). Our results showed that SAHA, entinostat, and panobinostat significantly increased HDR frequencies in hiPSCs by ~2.8-fold (Figure 4D), whereas NHEJ frequencies increased by 1.5-fold. Conse- quently, relative HDR also rose considerably in closed loci (a 28%–35% increase) (Figure 4D). These data suggest that HDAC inhibitors not only increase cleavage efficiency but may also increase the accessibility of HDR templates to compact chromatin regions, guiding HDR editing.

To increase the statistical power, we combined data from the three potent HDAC inhibitors, SAHA, entinostat, and

panobinostat, for further analysis, comparing their differential effects on editing efficiency at both open and closed loci (Figure 5). They all increased NHEJ editing to the same extent, but profoundly enhanced HDR efficiency was at closed loci relative to open chromatin (277% vs. 169%).

These data demonstrate that HDAC inhibitors significantly increase HDR editing efficiency in human iPSCs at both open and closed chromatin regions, with more pronounced effects occurring in closed loci.

HDAC inhibitors improve editing efficiency partly by increasing Cas9 and sgRNA expression

Initially, we hypothesized that HDAC inhibitors might increase the CRISPR-Cas9-mediated gene editing by expand- ing the target loci’s accessibility. If so, we would not expect increased indels at open loci. However, we observed increased total indels in every single experiment, which cannot be explained by merely the opening of chromatin. Because indel levels are usually associated with the amount of Cas9 protein and sgRNA in each cell, we further hypothesized that HDAC inhibitor treatment might increase Cas9 protein and sgRNA expression levels. Therefore, we performed additional experiments to determine the influence of HDAC inhibitors on transgene expression.

To explore their impact on Cas9 protein expression, we constructed a Cas9-GS-mNeonGreen (GS is a flexible linker composed of glycine and serine) fusion protein. The green fluorescent intensity directly reflected the Cas9 protein expression levels. We transfected human iPSCs with Cas9-GS- mNeonGreen and sgRNA plasmids and measured mNeon- Green expression and intensity 1 and 2 days later using flow cytometry (Figure 6A). We observed an ~50% increase in mNeonGreen⁺cells at both time points and a 2- to 3-fold increase in mNeonGreen expression levels (Figure 6B;

Figure S9A and B in Supporting Information). In compar- ison, RT-qPCR showed a 3- to 5-fold increase in Cas9 mRNA. Since the Cas9 transcript is fused with mNeon- Green, we also assessed mNeonGreen mRNA expression.

We found that Cas9 and mNeonGreen expressions are ex- cellently correlated (R²=0.96), indicating the reproducibility of the RT-qPCR data (Figure S9C in Supporting Informa- tion).

We also determined the effects of HDAC inhibitors on sgRNA expression by RT-qPCR (Figure 6D). Of interest, VPA did not increase sgRNA expression, which may explain the observation that it was the least effective HDAC inhibitor. After NaB and TSA treatments, we observed ~2-fold increase in sgRNA on both days 1 and 2. In contrast, SAHA, entinostat, and panobinostat were most potent at stimulating sgRNA expression, with a ~2-fold and a ~5-fold increase on day 1 and day 2, respectively (Figure 6D). These results coincide with their impressive effects on enhancing editing,

(7)

Figure3HDACinhibitorsimproveHDRandNHEJefficienciesatopenlociwiththesmallfragmentknockin.A,Schematicofgeneeditingatfouropenloci(GAPDH,PRDM14,EEF1A1,orEEF2).We electroporatediPSCswitheditingplasmidsandculturedwithsixdifferentHDACinhibitors(NaB,SAHA,TSA,VPA,entinostat,andpanobinostat)onday0.Cultureswerechangedwithfreshmediumwithout HDACinhibitorsonday1.Cellswereharvestedcellsonday3forhigh-throughputsequencing.HDRandNHEJefficiencieswereanalyzedusingCRISPResso2.B,VisualizationofrepresentativeHDRand NHEJhigh-throughputsequencingdata.Substitutionsareshowninboldfont.Redrectangleshighlightinsertedsequences.Horizontaldashedlinesindicatedeletedsequences.Verticaldashedlinesindicatethe predictedcleavagesite.TheredasteriskindicatesanHDR-editedallele.Theblackasteriskindicatesanuneditedallele.C,SchematicofHDReditingatfouropenloci(GAPDH,PRDM14,EEF1A1,orEEF2). sgGAPDHtargetsintron7ofGAPDH.sgPRDM14targetsthestopcodonofPRDM14.sgEEF1A1targetsintron7ofEEF1A1.sgEEF2targetsthestopcodonofEEF2.Adouble-cutHDRdonor(pD-sg)was usedtoguideHDRinsertionofa12-bpfragment.WeusedsgDocuttocutthedonor.Leftandrighthomologyarms(HA)arelightblues(600bp);theredlightningmarkindicatestheCas9-sgRNAcleavagesite. D,TheeffectofHDACinhibitorsonrelativeinductionfoldofHDRefficiency(KI),NHEJefficiency(KO),Indels(HDR+NHEJ),andHDRpercentageinalleditedcellsatfourloci(GAPDH,PRDM14, EEF1A1,orEEF2).HDRpercentageistheratioofHDRtoHDR+NHEJ.HDRandNHEJefficienciesweredeterminedthreedaysaftertransfectionbyhigh-throughputsequencing.n=12.Apairedt-testwasused forstatisticalanalysis;ns,notsignificant;*P<0.05,**P<0.01,***P<0.001,****P<0.0001.

(8)

Figure4HDACinhibitorsconsiderablyimproveHDReditingatclosedchromatinregions.A,Schematicofgeneeditingatthreeclosedchromatinloci(MESP1,MYH6,andGATA4).WeelectroporatediPSCs witheditingplasmidsandculturedwithsixdifferentHDACinhibitors(NaB,SAHA,TSA,VPA,entinostat,andpanobinostat)for24h.Cellswereharvestedonday3forhigh-throughputsequencing.HDRand NHEJefficiencieswereanalyzedusingCRISPResso2.B,VisualizationofrepresentativeHDRandNHEJeditedsequencingdata.Substitutionsareshowninboldfont.Redrectangleshighlightinserted sequences.Horizontaldashedlinesindicatedeletedsequences.Averticaldashedlineindicatesthepredictedcleavagesite.C,Editingatthreeclosedchromatinloci(MESP1,MYH6,andGATA4).AfterHDR editing,a6-to12-bpfragmentwillbeinsertedatthreedifferentloci.WedesignedsgMESP1,sgMYH6,andsgGATA4totargetthestopcodonofspecifiedgenes.WeusedsgDocuttocutthedonor.Leftandright HAsarelightblues(600bp);aredlightningmarkindicatestheCas9-sgRNAcleavagesite.D,TheeffectofHDACinhibitorsonrelativeinductionfoldofHDRefficiency(KI),NHEJefficiency(KO),Indels (HDR+NHEJ),andHDRpercentageinalleditedcellsatthreeloci(MESP1,MYH6,andGATA4).HDRandNHEJefficiencywasdeterminedbyhigh-throughputsequencing.n=9.Apairedt-testwasusedfor statisticalanalysis;ns,notsignificant;*P<0.05,**P<0.01,***P<0.001,****P<0.0001.

(9)

in particular HDR editing in closed loci. These data demonstrate that HDAC inhibitors increase editing efficiency in human iPSCs mainly by increasing the expression of Cas9 and sgRNA.

DISCUSSION

In this study, we comprehensively investigated the effects of six HDAC inhibitors—NaB (butyrate), TSA, SAHA, VPA, entinostat, and panobinostat—on CRISPR-Cas9 gene-editing efficiency in human iPSCs at both open and closed chromatin loci. Our experiments demonstrate that these compounds can improve HDR and NHEJ efficiencies in both chromatin forms, but more profoundly at closed loci. Among the six inhibitors, SAHA, entinostat, and panobinostat showed the most significant improvement in iPSC editing, particularly HDR editing. Entinostat and panobinostat, however, are more toxic than SAHA (Figure S5 in Sup- porting Information). As such, our data suggest the use of SAHA in iPSC HDR editing experiments. The Cas9 protein and sgRNA expression data indicate that increased HDR efficiency is mainly due to increased Cas9 expression and sgRNA levels. In closed loci, HDAC inhibitor-mediated

loosening of the closed chromatin also plays a role, leading to more considerable improvements in HDR efficiency than effects in open chromatin.

Human iPSCs hold great potential for future therapeutic applications, most of which would benefit significantly from HDR editing. The salient feature of iPSCs is that they are derived from patient-specific cells, carrying all mutations that cause a particular disease (Robinton and Daley, 2012).

Correcting these mutations in iPSCs or re-creation of identified mutations in isogenic cells is instrumental in unveiling the specific disorder’s fundamental mechanisms. These stem cells are also immortalized, allowing unlimited expansion in cell numbers. This creates a unique platform for generating iPSC-derived CAR-T or CAR-NK cells for immunotherapy (Nianias and Themeli, 2019). Recent reports have demonstrated that multiple forms of editing, including knockout and HDR insertion, are essential to establish hypoimmuno- genic cells for allogeneic cell therapy (Ashmore-Harris and Fruhwirth, 2020). Our improved strategy, which increases the HDR editing efficiency of unexpressed genes by 2–3- fold, will undoubtedly benefit these applications.

Previously, we have reported two strategies to strikingly increase HDR efficiency in human iPSCs: the use of a double-cut donor plasmid, which is a conventional targeting vector flanked on either side by a Cas9-sgRNA recognition sequence (Zhang et al., 2019;Zhang et al., 2017); and co- transfection of BCL-XL expressing plasmids (Li et al., 2018a). Building upon our previous studies, we found that HDAC inhibitors further improve the HDR knockin efficiencies in iPSCs, particularly at closed loci.

Earlier studies have demonstrated that chromatin accessibility affects CRISPR editing. Genome-wide mapping of the binding sites of dCas9 revealed its enrichment in open chromatin regions (Kuscu et al., 2014; Wu et al., 2014).

Moreover, the production of CRISPR-Cas9-induced indels in human cells is higher in open chromatin regions (Chari et al., 2015). Cas9-mediated genome editing is also more efficient in euchromatic than in heterochromatic areas in mammalian cells (Jensen et al., 2017). In contrast, chromatin accessibility does not affect CRISPR-Cas9 activity in zebrafish (Moreno-Mateos et al., 2015). How chromatin accessibility affects Cas9 editing in human iPSCs has not been previously reported. Here we compared the effects of HDAC inhibitors, which transiently open chromatin to some extent, on indel and HDR editing of highly expressed genes vs. unexpressed genes. Our results demonstrate that HDAC inhibitors increase indels and HDR efficiency at every locus we investigated, whether open or closed. However, the effects on closed loci were more pronounced, with a ~2–3-fold increase in HDR efficiency.

Eighteen identified HDACs are classified into four classes, including Zn²⁺-dependent classes (class I, II, and IV) and NAD-dependent classes (class III). HDAC inhibitors typi-

Figure 5 HDAC inhibitors preferentially enhance HDR editing efficiency at closed loci. We summarized the effects of three potent HDAC inhibitors (SAHA, entinostat, or panobinostat) on the relative induction fold of HDR efficiency (KI), NHEJ efficiency (KO), Indels (HDR+NHEJ), and HDR percentage in all edited cells at four open loci (GAPDH, PRDM14, EEF1A1, andEEF2) and three closed loci (MESP1,MYH6, andGATA4).

HDR and NHEJ efficiency was determined three days after transfection by high-throughput sequencing. For three closed locin=9, for four open loci n=12. An unpaired t-test was used for statistical analysis; ns, not sig- nificant; *P<0.05, ***P<0.001, ****P<0.0001.

(10)

cally target the “classical” classes I, II, and IV, which com- prise of 11 family members in humans (Witt et al., 2009).

The FDA has approved multiple HDAC inhibitors as antic- ancer agents (Yoon and Eom, 2016): SAHA has been used for the treatment of cutaneous T-cell lymphoma; entinostat is the first amino-benzamide-based HDAC inhibitor to treat multiple solid tumors (Ryan et al., 2005); panobinostat, a hydroxamic acid-based HDAC inhibitor, has been approved as adjunctive therapy in relapsed/refractory multiple mye- loma (McClure et al., 2018). These three inhibitors were more potent in enhancing HDR editing when compared to NaB, VPA, and TSA. The primary mechanism of HDAC inhibitor-mediated effects is believed to be chromatin de- condensation. Here we found that another tool for increased editing, particularly HDR editing at closed loci, is the increased expression of Cas9 and sgRNAs. We observed a 2–3- fold increase in Cas9 protein and a 2–5-fold increase in sgRNA 24–48 h after transfection, which led to higher cleavage efficiency. The significant effect at closed loci is most likely due to the decondensed chromatin, increasing the

HDR template’s mobility and local availability, translating into higher relative HDR efficiency.

Previous studies in H27 (derived from HeLa) and HT29 (human colon adenocarcinoma) cells showed that 5 μmol L^–1 entinostat or 0.1 μmol L^–1panobinostat do not affect viabi- lity (Liu et al., 2020). Using the same concentrations, however, we found that both compounds considerably reduced human iPSC cell numbers on day 3. Like our results, TSA reduced cell expansion dramatically in K562 (ery- throleukemia cell line) cells (Joglekar et al., 2014). The cells survived best after VPA treatment, but the beneficial effect was also modest. Suppose the iPSC line under investigation is sensitive to HDAC inhibitors. In that case, we recommend using butyrate due to its low toxicity, although one may also expect a less pronounced improvement in HDR editing.

Balancing HDR efficiency and toxicity, SAHA is the best choice for editing human iPSCs.

Recently, dCas9-VP64 and dCas9-EP300 have been suc- cessfully used to activate gene expression (Hilton et al., 2015;Perez-Pinera et al., 2013). As such, we hypothesized

Figure 6 HDAC inhibitors increase the expression of Cas9 and sgRNA levels. A, Experimental design for assessing changes of Cas9 and sgRNA expression after HDAC inhibitor treatment. B, The intensity of mNeonGreen was assessed by flow cytometry 24 and 48 h after electroporation of Cas9- mNeonGreen plasmid.n=5. C and D, Relative expression of Cas9 mRNA (C) and sgRNA by RT-qPCR.n=4. We conducted RT-qPCR analysis 24 and 48 h after the transfection of CRISPR plasmids. At-test was used for statistical analysis; ns, not significant; *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001.

(11)

that a fusion of the transcription activation domain VP64 or histone acetyltransferase domain EP300 with wildtype Cas9 might play a role in opening chromatin and thus increase HDR efficiency in closed loci. To our surprise, Cas9-VP64 had no positive effects on indel and HDR editing, while Cas9-EP300 considerably decreased indel and HDR editing, by up to 90%. We speculate that the negative charge of VP64 and the bulky size of Cas9-EP300 might have reduced the mobility of the ribonucleoprotein (RNP) editing complex, or their expression levels or protein stability decreased.

We also found that HDAC inhibitor treatment could increase Cas9 protein and sgRNA expression levels. Con- sistent with our results, previous studies also showed that HDAC inhibitors, such as VPA, NaB, TSA, and SAHA, could increase transgene expression from IDLVs (integrase- defective lentiviral vectors) (Joglekar et al., 2014;Pelascini et al., 2013). Panobinostat could also enhance Cas9 protein expression (Liu et al., 2020). The principal mechanism for the effects of HDAC inhibitors on improving gene expression was their modulation of the cell cycle and the influence of heterochromatinization.

In conclusion, our study provides a practical option for improving HDR editing efficiency through chromatin de- condensation and increased Cas9-sgRNA expression using HDAC inhibitors. This finding is significant since, in basic research and clinical applications such as creating reporter lines, iPSCs do not express the genes of interest in most scenarios.

MATERIALS AND METHODS

Human iPSC culture

The human iPSCs used in this study were detailed previously (Li et al., 2018a). In brief, human iPSCs were cultured in Matrigel-coated (Corning, USA) tissue-culture treated 6-well plates (BD, USA) in mTeSR™ Plus medium (STEMCELL Technologies, Canada) according to the manufacturer’s manual. For routine passaging, iPSCs were propagated as small aggregates with 0.5 mmol L^–1 EDTA/PBS solution (Thermo Fisher Scientific, USA) and recovered in mTeSR™

Plus medium. Cells were cultured at 37°C with 5% CO2and changed with fresh medium every day.

sgRNA plasmid design

The sgRNA vectors were constructed as detailed previously (Li et al., 2018a). In brief, we used the CHOPCHOP website (https://chopchop.rc.fas.harvard.edu/) (Labun et al., 2016) to design sgRNAs targeting GFP (sgDocut), humanPRDM14, GAPDH,EEF1A1,EEF2,MESP1,MYH6, andGATA4. If the first nucleotide of sgRNA was not a guanine (G), we added one in front since U6 promoter-mediated transcription starts

at G. The sgRNAs were cloned into a pU6-sgRNA backbone vector using a NEBuilder® HiFi DNA Assembly Cloning Kit (New England Biolabs, USA). The vectors were verified by Sanger sequencing (MCLAB, USA). The sgRNAs used in this paper are listed in Table S1 in Supporting Information.

Donor plasmid construction

The double-cut donor (pDonor-sg) vectors were constructed as detailed previously (Li et al., 2018a). In short, the left and right homology arms (HA) and the desired knock-in fragment, overlapping by ~20 bp, were amplified by PCR using KAPA HiFi polymerase (KAPA Biosystems, Swiss). They were purified using the Zymoclean Gel DNA Recovery Kit (ZYMO Research, USA). The fragments were then as- sembled with plasmid backbone using the NEBuilder® HiFi DNA Assembly Cloning Kit (New England Biolabs, USA) to generate the pDonor-sg vectors. Left and right HAs (~600 bp) were amplified from human genomic DNA, and sgDocut (donor cut) recognition sequences were added up- stream of the left HA and downstream of the right HA. All vectors were verified by Sanger sequencing (MCLAB, USA).

Plasmid construction

All Cas9 fusion vectors were constructed in the same vector backbone using the same EF1 promoter, which was constructed with the NEBuilder HiFi DNA Assembly Kit (New England Biolabs, USA). First, we used the digestion method to obtain the plasmid backbone. The Cas9 and fusion protein fragments were produced using KAPA HiFi polymerase (KAPA Biosystems, Swiss) and purified using the Zymo- clean Gel DNA Recovery Kit (ZYMO Research, USA). The linear PCR products overlapping by ~20 bp were then as- sembled into the plasmid backbone. The correct clones were identified by Sanger sequencing (MCLAB, USA).

Nucleofection of human iPSCs

The nucleofection of human iPSCs was described previously (Li et al., 2018a). Briefly, before nucleofection, cells were dissociated with Accutase (STEMCELL Technologies, Ca- nada) to achieve a single-cell suspension. Then 0.8–1.5×10⁶ cells were electroporated with 1 μg Cas9, 0.5 μg sgRNA (cut genome), 0.5 μg sgDocut (cut pDonor), 1 μg pDonor, and 0.5 μg BCL-XL plasmids using the Amaxa Human Stem Cell Nucleofector® Kit 2 (Lonza, program B-016, Swiss) on a Nucleofector^TM2b device (Lonza, Swiss) according to the manufacturer’s protocol. Cells were recovered in mTeSR™

Plus medium, supplemented with 10 μmol L^–1 Rho-associated kinase (ROCK) inhibitor Y-27632 (Millipore, USA) on Matrigel-coated plates. One day later, the cells were fed

(12)

with fresh mTeSR™ Plus medium without the ROCK inhibitor.

HDAC inhibitors

To test the effects of the small molecules on gene editing efficiency, we equally split human iPSCs into several wells after nucleofection with editing plasmids. Sodium butyrate (NaB, Sigma, Germany), vorinostat or suberoylanilohy- droxamic acid (SAHA, Selleckchem, USA), trichostatin A (TSA, Selleckchem, USA), valproic acid (VPA, Sell- eckchem, USA), entinostat (MS275, Selleckchem, USA), and panobinostat (LBH589, Selleckchem, USA) were first diluted in 50 μL of culture medium to make a master mix.

Then 50 μL of the diluted small molecules were added evenly into each well with the desired working concentra- tion. We refreshed the culture medium 24 h later. A parallel well only added with DMSO (0.1%) was carried out as a control. Three days after nucleofection, the cells were harvested for FACS analysis or PCR and deep sequencing to determine editing efficiency.

Flow cytometry

The mNeonGreen⁺ human iPSCs were analyzed by flow cytometry 3 days post-nucleofection. Human iPSCs were dissociated with Accutase to obtain a single-cell suspension, then analyzed on a BD FACSAria III flow cytometer. For HDR-mediated knockin of mNeonGreen reporter into a target gene (PRDM14, GAPDH, EEF1A1, and EEF2), the mNeonGreen-positive cell population was considered as HDR edited cells 72 h post-nucleofection. Nucleofection without relevant sgRNAs was carried out as negative con- trols, showing 0% fluorescence. For Cas9-GS-mNeonGreen expression 24, 48, or 72 h post-nucleofection, frequencies of mNeonGreen-positive cells, and mean fluorescence intensity (MFI) values were determined by flow cytometry. GS linker consists of GGGGS, where G is glycine, and S is serine.

Toxicity of HDAC inhibitors

To assess the toxicity of HDAC inhibitors, we determined human iPSC survival by counting cell numbers on days 1, 2, and 3 after nucleofection. We cultured cells with different concentrations of the HDAC inhibitors for 24 h. The next day, we fed cells with fresh medium without HDAC inhibitors. Experiments were performed in triplicate and re- peated at least three times.

Detecting Cas9 expression at mRNA and protein levels after nucleofection

To quickly detect the expression levels of Cas9 at both the

mRNA and the protein levels, the pEF1-Cas9-GS-mNeon- Green vector was constructed according to the protocol in the

“Plasmid construction” section. After transfection, the EF1 promoter drives expression of the Cas9-mNeonGreen fusion gene, and the fluorescence intensity detected by FACS ac- curately reflects the Cas9 protein expression level. Human iPSCs were electroporated with 1 μg of pEF1-Cas9-GS- mNeonGreen, and cells were harvested at 24, 48, and 72 h after nucleofection for flow cytometry and RT-qPCR analysis. These methods are detailed in the “Flow cytometry”

and “RT-qPCR analysis” sections, respectively.

RNA extraction and RT-qPCR

Human iPSCs were washed with PBS and harvested with Accutase. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Germany) following the protocol for purification of total RNA containing miRNA. Briefly, cells were disrupted and homogenized in Buffer RLT Plus and centrifuged through the gDNA Eliminator Spin column.

Then 1.5 volumes of 100% ethanol were added and applied to the RNeasy mini spin column. The spin-column mem- brane was washed with RNase-free water, and the total RNA containing miRNA was finally eluted. The RNA was quan- tified using the NanoDrop 2000 (Thermo Scientific, USA) and diluted to the same concentrations. We conducted reverse transcription using the Easy Script Plus cDNA Synthesis Kit (Applied Biological Materials), following the manufacturer’s instructions. Quantitative real-time RT-PCR (RT-qPCR) was performed as previously described (Meng et al., 2012;Meng et al., 2013). Expression of Cas9, mNeon- Green, sgRNA, OCT4, SOX2, and NANOG was normalized to that ofACTB(primers are listed in Table S2 in Supporting Information). KAPA SYBR Fast qPCR Kits (Kapa Biosys- tems, Swiss) were used for real-time PCR. qPCR cycling condition was 98°C for 1 min, followed by 40 cycles of 98°C for 5 s and 60°C for 30 s.

Analysis of NHEJ/HDR editing by deep sequencing

Human iPSCs treated in different conditions were harvested three days after nucleofection for genomic DNA extraction using proteinase K (PK) digestion buffer: 100 mmol L^–1 NaCl, 10 mmol L^–1 Tris pH 8, 5 mmol L^–1 EDTA, pH 8, 0.5% Tween 20, and 1% proteinase K (Qiagen or ABM,

~10 mg mL^–1). Cells released gDNA after running the following program: 56°C for 60 min and 95°C for 10 min. After a short spindown, 0.5–1 μL of the supernatant was used for PCR amplification. To prevent artifacts from amplification of the donor plasmid templates, the primary (first) PCR was conducted using primers targeting genomic sequences flanking the homology arms of the donor. PCR was conducted with KAPA HiFi DNA polymerase (Kapa Biosys-

(13)

tems, Swiss). The first PCR cycling condition was as follows: 98°C hold for 2 min, followed by 30 cycles of 98°C for 5 s, 64°C for 15 s, and 72°C for 30 s. We conducted the second PCR with primers containing sample-specific bar- codes to amplify DNA for deep sequencing using 1% of the PCR product from the first PCR. The second PCR cycling conditions were as follows: 98°C hold for 1 min, followed by 25 cycles of 98°C for 5 s, 64°C for 10 s, 68°C for 5 s, and 72°

C for 10 s. The primers used for both PCR cycles are listed in Table S3 in Supporting Information. The PCR products were confirmed by electrophoresis on 1% agarose gels. Approxi- mately 50 ng of PCR products from each reaction was mixed. All the amplicons from the same sample were mixed for 150 bp paired-end sequencing on the Illumina HiSeq X Ten sequencer (Novogene Co., Ltd, Tianjin, China).

High-quality reads (Qscore>30) were analyzed for indels using the Galaxy platform (Blankenberg et al., 2010;Goecks et al., 2010). First, the overlapping paired reads were joined together using the FLASH program. Then all the merged reads were reverse-complemented and concatenated before extracting data for each amplicon using Barcode Splitter. The pre-processed sequencing data were then analyzed using the CRISPResso2 program to determine indel patterns (Clement et al., 2019).

Statistical analysis

Prism 7.0 (Graphpad Software, USA) was used to prepare figures and statistical analysis. The mean±SEM was determined for each group in the individual experiments. We used two-tailed Welch’s paired t-test or Welch’s unpaired t-test to determine significance between the treatment and control groups.P-values <0.05 were considered significant:

*P<0.05, **P<0.01, ***P<0.001, ****P<0.0001.

Compliance and ethics The author(s) declare that they have no conflict of interest.

Acknowledgements This work was supported by the National Natural Science Foundation of China (81870149, 82070115, 81770198, 81700184, 81570164, 81861148029, 81700183, 81421002, 81890990, 81730006), National Key Research and Development Program of China (2019YFA0110803, 2019YFA0110204, 2016YFA0100600, 2017YFA0103400), CAMS Innovation Fund for Medical Sciences (CIFMS ) (2017-I2M-B&R-04, 2019-I2M-1-006, 2017-I2M-1-015, 2016-I2M-1-017, 2017-I2M-2-001), Ministry of Science and Technology of China (2015CB964902, 2015CB964400), Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences (2018PT31004), CAMS Key Laboratory of Gene Therapy for Blood Diseases (2017PT31047, 2018PT31038), and American Heart Association (18IPA34170301).

References

Ashmore-Harris, C., and Fruhwirth, G.O. (2020). The clinical potential of gene editing as a tool to engineer cell-based therapeutics.Clin Transl Med9, 15.

Avior, Y., Sagi, I., and Benvenisty, N. (2016). Pluripotent stem cells in

disease modelling and drug discovery.Nat Rev Mol Cell Biol17, 170–

182.

Barber, R.D., Harmer, D.W., Coleman, R.A., and Clark, B.J. (2005).

GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues. Physiol Genomics 21, 389–395.

Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., and Taylor, J. (2010). Galaxy: a web- based genome analysis tool for experimentalists. Current protocols in molecular biology, Chapter 19, Unit 19 10 11–21.

Burridge, P.W., Keller, G., Gold, J.D., and Wu, J.C. (2012). Production of de novocardiomyocytes: human pluripotent stem cell differentiation and direct reprogramming.Cell Stem Cell10, 16–28.

Campos, E.I., and Reinberg, D. (2009). Histones: annotating chromatin.

Annu Rev Genet43, 559–599.

Chan, Y.S., Göke, J., Lu, X., Venkatesan, N., Feng, B., Su, I.H., and Ng, H.

H. (2013). A PRC2-dependent repressive role of PRDM14 in human embryonic stem cells and induced pluripotent stem cell reprogramming.

Stem Cells31, 682–692.

Chari, R., Mali, P., Moosburner, M., and Church, G.M. (2015). Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach.Nat Methods12, 823–826.

Chen, F., Ding, X., Feng, Y., Seebeck, T., Jiang, Y., and Davis, G.D. (2017).

Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting.Nat Commun8, 14958.

Clement, K., Rees, H., Canver, M.C., Gehrke, J.M., Farouni, R., Hsu, J.Y., Cole, M.A., Liu, D.R., Joung, J.K., Bauer, D.E., et al. (2019).

CRISPResso2 provides accurate and rapid genome editing sequence analysis.Nat Biotechnol37, 224–226.

Davie, J.R. (2003). Inhibition of histone deacetylase activity by butyrate.J Nutr133, 2485S–2493S.

Ding, X., Seebeck, T., Feng, Y., Jiang, Y., Davis, G.D., and Chen, F. (2019).

Improving CRISPR-Cas9 genome editing efficiency by fusion with chromatin-modulating peptides.CRISPR J2, 51–63.

Eberharter, A., and Becker, P.B. (2002). Histone acetylation: a switch between repressive and permissive chromatin.EMBO Rep3, 224–229.

Ersahin, T., Carkacioglu, L., Can, T., Konu, O., Atalay, V., and Cetin- Atalay, R. (2014). Identification of novel reference genes based on MeSH categories.PLoS ONE9, e93341.

Frys, S., Simons, Z., Hu, Q., Barth, M.J., Gu, J.J., Mavis, C., Skitzki, J., Song, L., Czuczman, M.S., and Hernandez-Ilizaliturri, F.J. (2015).

Entinostat, a novel histone deacetylase inhibitor is active in B-cell lymphoma and enhances the anti-tumour activity of rituximab and chemotherapy agents.Br J Haematol169, 506–519.

Gentile, A.M., Lhamyani, S., Coín-Aragüez, L., Oliva-Olivera, W., Zayed, H., Vega-Rioja, A., Monteseirin, J., Romero-Zerbo, S.Y., Tinahones, F.

J., Bermúdez-Silva, F.J., et al. (2016). RPL13A and EEF1A1 are suitable reference genes for qPCR during adipocyte differentiation of vascular stromal cells from patients with different BMI and HOMA-IR.

PLoS ONE11, e0157002.

Goecks, J., Nekrutenko, A., Taylor, J., and Galaxy Team, T. (2010).

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.Genome Biol11, R86.

Grant, S., Easley, C., and Kirkpatrick, P. (2007). Vorinostat.Nat Rev Drug Discov6, 21–22.

Haberland, M., Montgomery, R.L., and Olson, E.N. (2009). The many roles of histone deacetylases in development and physiology: implications for disease and therapy.Nat Rev Genet10, 32–42.

He, X., Tan, C., Wang, F., Wang, Y., Zhou, R., Cui, D., You, W., Zhao, H., Ren, J., and Feng, B. (2016). Knock-in of large reporter genes in human cells via CRISPR/Cas9-induced homology-dependent and independent DNA repair.Nucleic Acids Res44, e85.

Hilton, I.B., D'Ippolito, A.M., Vockley, C.M., Thakore, P.I., Crawford, G.

E., Reddy, T.E., and Gersbach, C.A. (2015). Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.Nat Biotechnol33, 510–517.