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Umeh-Garcia M, O’Geen H, Simion C, Gephart MH, Segal DJ, Sweeney CA. Aberrant promoter methylation contributes to LRIG1 silencing in basal/triple-negative breast cancer. Br J Cancer 2022; 127:436-448. [PMID: 35440669 PMCID: PMC9346006 DOI: 10.1038/s41416-022-01812-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND LRIG1, the founding member of the LRIG (leucine-rich repeat and immunoglobulin-like domain) family of transmembrane proteins, is a negative regulator of receptor tyrosine kinases and a tumour suppressor. Decreased LRIG1 expression is consistently observed in cancer, across diverse tumour types, and is linked to poor patient prognosis. However, mechanisms by which LRIG1 is repressed are not fully understood. Silencing of LRIG1 through promoter CpG island methylation has been reported in colorectal and cervical cancer but studies in breast cancer remain limited. METHODS In silico analysis of human breast cancer patient data were used to demonstrate a correlation between DNA methylation and LRIG1 silencing in basal/triple-negative breast cancer, and its impact on patient survival. LRIG1 gene expression, protein abundance, and methylation enrichment were examined by quantitative reverse-transcription PCR, immunoblotting, and methylation immunoprecipitation, respectively, in breast cancer cell lines in vitro. We examined the impact of global demethylation on LRIG1 expression and methylation enrichment using 5-aza-2'-deoxycytidine. We also examined the effects of targeted demethylation of the LRIG1 CpG island, and transcriptional activation of LRIG1 expression, using the RNA guided deadCas9 transactivation system. RESULTS Across breast cancer subtypes, LRIG1 expression is lowest in the basal/triple-negative subtype so we investigated whether differential methylation may contribute to this. Indeed, we find that LRIG1 CpG island methylation is most prominent in basal/triple-negative cell lines and patient samples. Use of the global demethylating agent 5-aza-2'-deoxycytidine decreases methylation leading to increased LRIG1 transcript expression in basal/triple-negative cell lines, while having no effect on LRIG1 expression in luminal/ER-positive cell lines. Using a CRISPR/deadCas9 (dCas9)-based targeting approach, we demonstrate that TET1-mediated demethylation (Tet1-dCas9) along with VP64-mediated transcriptional activation (VP64-dCas9) at the CpG island, increased endogenous LRIG1 expression in basal/triple-negative breast cancer cells, without transcriptional upregulation at predicted off-target sites. Activation of LRIG1 by the dCas9 transactivation system significantly increased LRIG1 protein abundance, reduced site-specific methylation, and reduced cancer cell viability. Our findings suggest that CRISPR-mediated targeted activation may be a feasible way to restore LRIG1 expression in cancer. CONCLUSIONS Our study contributes novel insight into mechanisms which repress LRIG1 in triple-negative breast cancer and demonstrates for the first time that targeted de-repression of LRIG1 in cancer cells is possible. Understanding the epigenetic mechanisms associated with repression of tumour suppressor genes holds potential for the advancement of therapeutic approaches.
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Affiliation(s)
- Maxine Umeh-Garcia
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, USA. .,Department Neurosurgery, Stanford University, Stanford, CA, USA.
| | - Henriette O’Geen
- grid.27860.3b0000 0004 1936 9684Genome Center, University of California, Davis, CA USA
| | - Catalina Simion
- grid.27860.3b0000 0004 1936 9684Department of Biochemistry and Molecular Medicine, University of California, Davis, CA USA
| | - Melanie Hayden Gephart
- grid.168010.e0000000419368956Department Neurosurgery, Stanford University, Stanford, CA USA
| | - David J. Segal
- grid.27860.3b0000 0004 1936 9684Department of Biochemistry and Molecular Medicine, University of California, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Genome Center, University of California, Davis, CA USA
| | - Colleen A. Sweeney
- grid.27860.3b0000 0004 1936 9684Department of Biochemistry and Molecular Medicine, University of California, Davis, CA USA
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Heath NG, O’Geen H, Halmai NB, Corn JE, Segal DJ. Imaging Unique DNA Sequences in Individual Cells Using a CRISPR-Cas9-Based, Split Luciferase Biosensor. Front Genome Ed 2022; 4:867390. [PMID: 35403097 PMCID: PMC8990833 DOI: 10.3389/fgeed.2022.867390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
An extensive arsenal of biosensing tools has been developed based on the clustered regularly interspaced short palindromic repeat (CRISPR) platform, including those that detect specific DNA sequences both in vitro and in live cells. To date, DNA imaging approaches have traditionally used full fluorescent reporter-based fusion probes. Such “always-on” probes differentiate poorly between bound and unbound probe and are unable to sensitively detect unique copies of a target sequence in individual cells. Herein we describe a DNA biosensor that provides a sensitive readout for such low-copy DNA sequences through proximity-mediated reassembly of two independently optimized fragments of NanoLuc luciferase (NLuc), a small, bright luminescent reporter. Applying this “turn-on” probe in live cells, we demonstrate an application not easily achieved by fluorescent reporter-based probes, detection of individual endogenous genomic loci using standard epifluorescence microscopy. This approach could enable detection of gene edits during ex vivo editing procedures and should be a useful platform for many other live cell DNA biosensing applications.
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Affiliation(s)
- Nicholas G. Heath
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Henriette O’Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Nicole B. Halmai
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jacob E. Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- Department of Biology, ETH, Zürich, Switzerland
| | - David J. Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: David J. Segal,
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Deng P, Halmai JANM, Beitnere U, Cameron D, Martinez ML, Lee CC, Waldo JJ, Thongphanh K, Adhikari A, Copping N, Petkova SP, Lee RD, Lock S, Palomares M, O’Geen H, Carter J, Gonzalez CE, Buchanan FKB, Anderson JD, Fierro FA, Nolta JA, Tarantal AF, Silverman JL, Segal DJ, Fink KD. An in vivo Cell-Based Delivery Platform for Zinc Finger Artificial Transcription Factors in Pre-clinical Animal Models. Front Mol Neurosci 2022; 14:789913. [PMID: 35153670 PMCID: PMC8829036 DOI: 10.3389/fnmol.2021.789913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/01/2021] [Indexed: 11/28/2022] Open
Abstract
Zinc finger (ZF), transcription activator-like effectors (TALE), and CRISPR/Cas9 therapies to regulate gene expression are becoming viable strategies to treat genetic disorders, although effective in vivo delivery systems for these proteins remain a major translational hurdle. We describe the use of a mesenchymal stem/stromal cell (MSC)-based delivery system for the secretion of a ZF protein (ZF-MSC) in transgenic mouse models and young rhesus monkeys. Secreted ZF protein from mouse ZF-MSC was detectable within the hippocampus 1 week following intracranial or cisterna magna (CM) injection. Secreted ZF activated the imprinted paternal Ube3a in a transgenic reporter mouse and ameliorated motor deficits in a Ube3a deletion Angelman Syndrome (AS) mouse. Intrathecally administered autologous rhesus MSCs were well-tolerated for 3 weeks following administration and secreted ZF protein was detectable within the cerebrospinal fluid (CSF), midbrain, and spinal cord. This approach is less invasive when compared to direct intracranial injection which requires a surgical procedure.
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Affiliation(s)
- Peter Deng
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, United States,Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States,Department of Biochemistry and Molecular Medicine, Genome Center, University of California, Davis, Davis, CA, United States,Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Julian A. N. M. Halmai
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, United States,Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States,Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Ulrika Beitnere
- Department of Biochemistry and Molecular Medicine, Genome Center, University of California, Davis, Davis, CA, United States
| | - David Cameron
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, United States,Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States,Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Michele L. Martinez
- Departments of Pediatrics and Cell Biology and Human Anatomy, School of Medicine, Gene Therapy Center, and California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Charles C. Lee
- Departments of Pediatrics and Cell Biology and Human Anatomy, School of Medicine, Gene Therapy Center, and California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Jennifer J. Waldo
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, United States,Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States,Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Krista Thongphanh
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, United States,Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States
| | - Anna Adhikari
- Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Nycole Copping
- Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Stela P. Petkova
- Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Ruth D. Lee
- Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Samantha Lock
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, United States,Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States,Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Miranda Palomares
- Department of Biochemistry and Molecular Medicine, Genome Center, University of California, Davis, Davis, CA, United States
| | - Henriette O’Geen
- Department of Biochemistry and Molecular Medicine, Genome Center, University of California, Davis, Davis, CA, United States
| | - Jasmine Carter
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, United States,Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States,Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Casiana E. Gonzalez
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, United States,Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States,Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Fiona K. B. Buchanan
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, United States,Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States,Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Johnathan D. Anderson
- Department of Otolaryngology, University of California, Davis, Davis, CA, United States
| | - Fernando A. Fierro
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States
| | - Jan A. Nolta
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States
| | - Alice F. Tarantal
- Departments of Pediatrics and Cell Biology and Human Anatomy, School of Medicine, Gene Therapy Center, and California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Jill L. Silverman
- Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States
| | - David J. Segal
- Department of Biochemistry and Molecular Medicine, Genome Center, University of California, Davis, Davis, CA, United States
| | - Kyle D. Fink
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, United States,Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, United States,Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California Davis School of Medicine, Sacramento, CA, United States,*Correspondence: Kyle D. Fink,
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O’Geen H, Tomkova M, Combs JA, Tilley EK, Segal D. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3239-3253. [PMID: 35234927 PMCID: PMC8989539 DOI: 10.1093/nar/gkac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Marketa Tomkova
- Genome Center, University of California, Davis, CA 95616, USA
| | | | - Emma K Tilley
- Genome Center, University of California, Davis, CA 95616, USA
| | - David J Segal
- To whom correspondence should be addressed. Tel: +1 530 754 9134; Fax: +1 530 754 9658;
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5
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Halmai JANM, Deng P, Gonzalez CE, Coggins NB, Cameron D, Carter JL, Buchanan FKB, Waldo JJ, Lock SR, Anderson JD, O’Geen H, Segal DJ, Nolta J, Fink KD. Artificial escape from XCI by DNA methylation editing of the CDKL5 gene. Nucleic Acids Res 2020; 48:2372-2387. [PMID: 31925439 PMCID: PMC7049732 DOI: 10.1093/nar/gkz1214] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/29/2022] Open
Abstract
A significant number of X-linked genes escape from X chromosome inactivation and are associated with a distinct epigenetic signature. One epigenetic modification that strongly correlates with X-escape is reduced DNA methylation in promoter regions. Here, we created an artificial escape by editing DNA methylation on the promoter of CDKL5, a gene causative for an infantile epilepsy, from the silenced X-chromosomal allele in human neuronal-like cells. We identify that a fusion of the catalytic domain of TET1 to dCas9 targeted to the CDKL5 promoter using three guide RNAs causes significant reactivation of the inactive allele in combination with removal of methyl groups from CpG dinucleotides. Strikingly, we demonstrate that co-expression of TET1 and a VP64 transactivator have a synergistic effect on the reactivation of the inactive allele to levels >60% of the active allele. We further used a multi-omics assessment to determine potential off-targets on the transcriptome and methylome. We find that synergistic delivery of dCas9 effectors is highly selective for the target site. Our findings further elucidate a causal role for reduced DNA methylation associated with escape from X chromosome inactivation. Understanding the epigenetics associated with escape from X chromosome inactivation has potential for those suffering from X-linked disorders.
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MESH Headings
- Alleles
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- Catalytic Domain
- Cell Line, Tumor
- Chromosomes, Human, X/chemistry
- Chromosomes, Human, X/metabolism
- CpG Islands
- Epigenesis, Genetic
- Gene Editing
- Gene Silencing
- Humans
- Mixed Function Oxygenases/genetics
- Mixed Function Oxygenases/metabolism
- Neurons/cytology
- Neurons/metabolism
- Promoter Regions, Genetic
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Trans-Activators/genetics
- Trans-Activators/metabolism
- X Chromosome Inactivation
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Julian A N M Halmai
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Peter Deng
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Casiana E Gonzalez
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Nicole B Coggins
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - David Cameron
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Jasmine L Carter
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Fiona K B Buchanan
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Jennifer J Waldo
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Samantha R Lock
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | | | - Henriette O’Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Jan Nolta
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
| | - Kyle D Fink
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
- Stem Cell Program and Gene Therapy Center, University of California, Davis, Sacramento, CA, USA
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O’Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ. Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner. Epigenetics Chromatin 2019; 12:26. [PMID: 31053162 PMCID: PMC6498470 DOI: 10.1186/s13072-019-0275-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/23/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Rewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems. RESULTS Here, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). We demonstrate that the histone methyltransferase requirement can be locus specific. Co-targeting Ezh2-dCas9, but not KRAB-dCas9, with DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2-dCas9 with KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2-dCas9 required full-length DNMT3L for maximal activity and that co-targeting DNMT3L was sufficient for persistent repression by Ezh2-dCas9 or KRAB-dCas9. CONCLUSIONS These data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine-tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type.
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Affiliation(s)
- Henriette O’Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
| | - Sofie L. Bates
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
| | - Sakereh S. Carter
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
| | - Karly A. Nisson
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Julian Halmai
- Department of Neurology and Stem Cell Program, University of California, Sacramento, CA 95817 USA
| | - Kyle D. Fink
- Department of Neurology and Stem Cell Program, University of California, Sacramento, CA 95817 USA
| | - Suhn K. Rhie
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - David J. Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616 USA
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O’Geen H, Ren C, Coggins NB, Bates SL, Segal DJ. Unexpected binding behaviors of bacterial Argonautes in human cells cast doubts on their use as targetable gene regulators. PLoS One 2018; 13:e0193818. [PMID: 29584750 PMCID: PMC5870970 DOI: 10.1371/journal.pone.0193818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/20/2018] [Indexed: 11/18/2022] Open
Abstract
Prokaryotic Argonaute proteins (pAgos) have been proposed as an alternative to the CRISPR/Cas9 platform for gene editing. Although Argonaute from Natronobacterium gregoryi (NgAgo) was recently shown unable to cleave genomic DNA in mammalian cells, the utility of NgAgo or other pAgos as a targetable DNA-binding platform for epigenetic editing has not been explored. In this report, we evaluated the utility of two prokaryotic Argonautes (NgAgo and TtAgo) as DNA-guided DNA-binding proteins. NgAgo showed no meaningful binding to chromosomal targets, while TtAgo displayed seemingly non-specific binding to chromosomal DNA even in the absence of guide DNA. The observed lack of DNA-guided targeting and unexpected guide-independent genome sampling under the conditions in this study provide evidence that these pAgos might be suitable for neither gene nor epigenome editing in mammalian cells.
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Affiliation(s)
- Henriette O’Geen
- Genome Center, University of California, Davis, California, United States of America
| | - Chonghua Ren
- Genome Center, University of California, Davis, California, United States of America
| | - Nicole B. Coggins
- Genome Center, University of California, Davis, California, United States of America
| | - Sofie L. Bates
- Genome Center, University of California, Davis, California, United States of America
| | - David J. Segal
- Genome Center, University of California, Davis, California, United States of America
- Department of Biochemistry and Molecular Medicine, University of California, Davis, California, United States of America
- * E-mail:
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8
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Abstract
The specificity of RNA-guided nucleases has gathered considerable interest as they become broadly applied to basic research and therapeutic development. Reports of the simple generation of animal models and genome engineering of cells raised questions about targeting precision. Conflicting early reports led the field to believe that CRISPR/Cas9 system was promiscuous, leading to a variety of strategies for improving specificity and increasingly sensitive methods to detect off-target events. However, other studies have suggested that CRISPR/Cas9 is a highly specific genome-editing tool. This review will focus on deciphering and interpreting these seemingly opposing claims.
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Affiliation(s)
- Henriette O’Geen
- Genome Center, Department of Biochemistry and Molecular Medicine, and MIND Institute, University of California, Davis, CA 95616, USA
| | - Abigail S. Yu
- Genome Center, Department of Biochemistry and Molecular Medicine, and MIND Institute, University of California, Davis, CA 95616, USA
| | - David J. Segal
- Genome Center, Department of Biochemistry and Molecular Medicine, and MIND Institute, University of California, Davis, CA 95616, USA
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9
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Jin VX, O’Geen H, Iyengar S, Green R, Farnham PJ. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res 2007; 17:807-17. [PMID: 17567999 PMCID: PMC1891340 DOI: 10.1101/gr.6006107] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ChIP-chip studies have revealed that many in vivo binding sites have a weak match to the consensus sequence for the transcription factor being analyzed. Possible explanations for these observations include (1) the in vitro-derived consensus site does not represent the in vivo binding site and/or (2) the factor is recruited to a weak binding site via interaction with another protein. To address these possibilities, we developed an approach (ChIPMotifs) that incorporates a bootstrap resampling method to statistically infer the optimal cutoff threshold for a position weight matrix (PWM) of a motif identified from ChIP-chip data by ab initio motif discovery programs. Using OCT4 ChIP-chip data and the ChIPMotifs approach, we first developed a refined OCT4 PWM. We then used the refined PWM and a ChIPModules approach to identify transcription factors colocalizing with OCT4 in Ntera2 testicular embryonal carcinoma cells. We found that the consensus binding site for SRY, a transcription factor critical for testis development, colocalizes with the OCT4 PWM. To further characterize the relationship between OCT4 and SRY, we performed ChIP-chip experiments with human promoter microarrays, and found that 49% of the top approximately 1000 OCT4 target promoters were also bound by SRY. This analysis represents the first identification of SRY target promoters. Interestingly, we determined that promoters bound by OCT4 and SRY, but not those bound by SRY alone, were also bound by the transcriptional repressor KAP1. Our studies not only validate the ChIPMotifs and ChIPModules combinatorial approach but also identify a possible new regulatory partner of OCT4.
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Affiliation(s)
- Victor X. Jin
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Henriette O’Geen
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Sushma Iyengar
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Roland Green
- NimbleGen Systems, Inc., Madison, Wisconsin 53711, USA
| | - Peggy J. Farnham
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
- Corresponding author.E-mail ; fax (530) 754-9658
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Squazzo SL, O’Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, Margueron R, Reinberg D, Green R, Farnham PJ. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res 2006; 16:890-900. [PMID: 16751344 PMCID: PMC1484456 DOI: 10.1101/gr.5306606] [Citation(s) in RCA: 257] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Suz12 is a component of the Polycomb group complexes 2, 3, and 4 (PRC 2/3/4). These complexes are critical for proper embryonic development, but very few target genes have been identified in either mouse or human cells. Using a variety of ChIP-chip approaches, we have identified a large set of Suz12 target genes in five different human and mouse cell lines. Interestingly, we found that Suz12 target promoters are cell type specific, with transcription factors and homeobox proteins predominating in embryonal cells and glycoproteins and immunoglobulin-related proteins predominating in adult tumors. We have also characterized the localization of other components of the PRC complex with Suz12 and investigated the overall relationship between Suz12 binding and markers of active versus inactive chromatin, using both promoter arrays and custom tiling arrays. Surprisingly, we find that the PRC complexes can be localized to discrete binding sites or spread through large regions of the mouse and human genomes. Finally, we have shown that some Suz12 target genes are bound by OCT4 in embryonal cells and suggest that OCT4 maintains stem cell self-renewal, in part, by recruiting PRC complexes to certain genes that promote differentiation.
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Affiliation(s)
- Sharon L. Squazzo
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Henriette O’Geen
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Vitalina M. Komashko
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Sheryl R. Krig
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Victor X. Jin
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
| | - Sung-wook Jang
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Raphael Margueron
- Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
| | - Roland Green
- NimbleGen Systems Inc., Madison, Wisconsin 53711, USA
| | - Peggy J. Farnham
- Department of Pharmacology and the Genome Center, University of California–Davis, Davis, California 95616, USA
- Corresponding author.E-mail ; fax (530) 754-9658
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