Breaking through an epigenetic wall

Juárez-Moreno, Karla; Erices, Rafaela; Beltran, Adriana S.; Stolzenburg, Sabine; Cuello-Fredes, Mauricio; Owen, Gareth I.; Qian, Haili; Blancafort, Pilar

doi:10.4161/epi.23503

Cited by 19 publications

(11 citation statements)

References 64 publications

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“…Since, however, SK induces the same gene expressions with directions opposite to PV, our findings also emphasize the remarkable flexibility of chromatin modifications that are primarily governed by the nature of a transcription factor. This, as suggested [ 51 , 52 ], implies that the pre-assigned function for an engineered transcription factor as an activator or a repressor at a chromatin context may not be accurate and could be specific to target gene or cell type. Indeed, genome-wide studies, reviewed by Reynolds et al, [ 25 ], clearly indicate that many transcriptional repressors are also connected with actively transcribed regions; on the other hand, many activators are, in addition to active regions, associated with repressed loci that show cellular variability.…”

Section: Discussionmentioning

confidence: 99%

Modulation of Estrogen Response Element-Driven Gene Expressions and Cellular Proliferation with Polar Directions by Designer Transcription Regulators

et al. 2015

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Estrogen receptor α (ERα), as a ligand-dependent transcription factor, mediates 17β-estradiol (E2) effects. ERα is a modular protein containing a DNA binding domain (DBD) and transcription activation domains (AD) located at the amino- and carboxyl-termini. The interaction of the E2-activated ERα dimer with estrogen response elements (EREs) of genes constitutes the initial step in the ERE-dependent signaling pathway necessary for alterations of cellular features. We previously constructed monomeric transcription activators, or monotransactivators, assembled from an engineered ERE-binding module (EBM) using the ERα-DBD and constitutively active ADs from other transcription factors. Monotransactivators modulated cell proliferation by activating and repressing ERE-driven gene expressions that simulate responses observed with E2-ERα. We reasoned here that integration of potent heterologous repression domains (RDs) into EBM could generate monotransrepressors that alter ERE-bearing gene expressions and cellular proliferation in directions opposite to those observed with E2-ERα or monotransactivators. Consistent with this, monotransrepressors suppressed reporter gene expressions that emulate the ERE-dependent signaling pathway. Moreover, a model monotransrepressor regulated DNA synthesis, cell cycle progression and proliferation of recombinant adenovirus infected ER-negative cells through decreasing as well as increasing gene expressions with polar directions compared with E2-ERα or monotransactivator. Our results indicate that an ‘activator’ or a ‘repressor’ possesses both transcription activating/enhancing and repressing/decreasing abilities within a chromatin context. Offering a protein engineering platform to alter signal pathway-specific gene expressions and cell growth, our approach could also be used for the development of tools for epigenetic modifications and for clinical interventions wherein multigenic de-regulations are an issue.

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Section: Discussionmentioning

confidence: 99%

Modulation of Estrogen Response Element-Driven Gene Expressions and Cellular Proliferation with Polar Directions by Designer Transcription Regulators

et al. 2015

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“…Interestingly, the ZFPs linked to the KRAB domain resulted in transcriptional repression of some genes, whereas for other loci binding was associated with target gene activation and with promoter demethylation. In sum, the physiological capacity of ZFPs to regulate target genes appear to be highly dependent on the chromatin context of the targeted region, including the presence of co-activator or co-repressors in that particular genomic address bound by the DNA-binding domain ( 46 , 47 ).…”

Section: Dna-binding Domains and Their Specificity To Their Targetsmentioning

confidence: 99%

“…Transcriptional modulation of several tumor suppressor genes and oncogenes including MASPIN , Her2/neu , SOX2 , OCT4 , EpCAM , ICAM-I , and C13Orf18 by ZFPs linked to the VP64 or KRAB domain have been reported in breast, ovarian, and lung cancer models. In these studies, down-regulation of overexpressed oncogenes and up-regulation of silent tumor suppressor genes using ZFPs fused to KRAB and VP64, respectively, resulted in reduced growth of cancer cells both in vitro and mouse models ( 39 , 44 , 47 , 63 – 68 ). Likewise, TALEs and CRISPRs–dCas9 have demonstrated target gene modulation when linked to VP64 ( 51 , 69 ) or KRAB ( 70 , 71 ).…”

Section: Regulating the Expression Of The Cancer Genomementioning

confidence: 99%

Epigenome Engineering in Cancer: Fairytale or a Realistic Path to the Clinic?

2015

Self Cite

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Epigenetic modifications such as histone post-transcriptional modifications, DNA methylation, and non-protein-coding RNAs organize the DNA in the nucleus of eukaryotic cells and are critical for the spatio-temporal regulation of gene expression. These epigenetic modifications are reversible and precisely regulated by epigenetic enzymes. In addition to genetic mutations, epigenetic modifications are highly disrupted in cancer relative to normal tissues. Many epigenetic alterations (epi-mutations) are associated with aberrations in the expression and/or activity of epigenetic enzymes. Thus, epigenetic regulators have emerged as prime targets for cancer therapy. Currently, several inhibitors of epigenetic enzymes (epi-drugs) have been approved for use in the clinic to treat cancer patients with hematological malignancies. However, one potential disadvantage of epi-drugs is their lack of locus-selective specificity, which may result in the over-expression of undesirable parts of the genome. The emerging and rapidly growing field of epigenome engineering has opened new grounds for improving epigenetic therapy in view of reducing the genome-wide “off-target” effects of the treatment. In the current review, we will first describe the language of epigenetic modifications and their involvement in cancer. Next, we will overview the current strategies for engineering of artificial DNA-binding domains in order to manipulate and ultimately normalize the aberrant landscape of the cancer epigenome (epigenome engineering). Lastly, the potential clinical applications of these emerging genome-engineering approaches will be discussed.

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“… 117 In another attempt, the fusion of a KRAB domain fused to a designer ZFP could activate endogenous Oct4 protein in series of cell lines. 118 This was a surprising observation because the KRAB conventionally acts as transcriptional repressor. dTALE-VP16 fusions designed to bind proximal promoter sequences of SOX2, Klf4, c-MYC and Oct4 could activate reporter constructs, but only dTALEs targeting Klf4 and SOX2 could also activate the endogenous genes in 293FT cells.…”

Section: Engineering Synthetic Reprogramming Factorsmentioning

confidence: 99%

Reprogramming cells with synthetic proteins

Yang¹,

Malik²,

Jauch³

2015

Asian J Androl

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Conversion of one cell type into another cell type by forcibly expressing specific cocktails of transcription factors (TFs) has demonstrated that cell fates are not fixed and that cellular differentiation can be a two-way street with many intersections. These experiments also illustrated the sweeping potential of TFs to “read” genetically hardwired regulatory information even in cells where they are not normally expressed and to access and open up tightly packed chromatin to execute gene expression programs. Cellular reprogramming enables the modeling of diseases in a dish, to test the efficacy and toxicity of drugs in patient-derived cells and ultimately, could enable cell-based therapies to cure degenerative diseases. Yet, producing terminally differentiated cells that fully resemble their in vivo counterparts in sufficient quantities is still an unmet clinical need. While efforts are being made to reprogram cells nongenetically by using drug-like molecules, defined TF cocktails still dominate reprogramming protocols. Therefore, the optimization of TFs by protein engineering has emerged as a strategy to enhance reprogramming to produce functional, stable and safe cells for regenerative biomedicine. Engineering approaches focused on Oct4, MyoD, Sox17, Nanog and Mef2c and range from chimeric TFs with added transactivation domains, designer transcription activator-like effectors to activate endogenous TFs to reprogramming TFs with rationally engineered DNA recognition principles. Possibly, applying the complete toolkit of protein design to cellular reprogramming can help to remove the hurdles that, thus far, impeded the clinical use of cells derived from reprogramming technologies.

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Breaking through an epigenetic wall

Cited by 19 publications

References 64 publications

Modulation of Estrogen Response Element-Driven Gene Expressions and Cellular Proliferation with Polar Directions by Designer Transcription Regulators

Modulation of Estrogen Response Element-Driven Gene Expressions and Cellular Proliferation with Polar Directions by Designer Transcription Regulators

Epigenome Engineering in Cancer: Fairytale or a Realistic Path to the Clinic?

Reprogramming cells with synthetic proteins

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