CRISPR-Tools in Epigenetic Research

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Methods".

Deadline for manuscript submissions: closed (15 July 2023) | Viewed by 3940

Special Issue Editor


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Guest Editor
1. Reprogramming and Regeneration, Biomedical Center (BMC), Department of Physiological Genomics, Faculty of Medicine, LMU Munich, 80539 Munich, Germany
2. German Research Center for Environmental Health, Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, 82152 Planegg-Martinsried, Germany
Interests: epigenome editing; CRISPR, dCas9; neurogenesis; neural stem cells; epigenetics; transcriptional engineering

Special Issue Information

Dear Colleagues,

Epigenetic processes regulate all aspects of life; however, it remains elusive which of the many known chromatin features are directly responsible for such processes. The question of causality has fascinated researchers in the field of epigenetics since its very beginnings. Even now, despite mapping a large number of “epigenomes” in a myriad of cell types, animals and patients, the number of individual chromatin marks known to cause a significant transcriptional or cellular change remains very low. Fortunately, new scalable experimental strategies based on CRISPR allow for a simple and efficient manipulation of chromatin, and thus promise to become a powerful tool for research and therapy alike.

This Special Issue will examine these approaches, including methods for the targeted manipulation of individual chromatin marks (epigenome editing, epigenetic engineering); the conditional manipulation of global chromatin features; targeted gene expression changes (CRISPRa, CRISPRi, transcriptional engineering); the generation of artificial transcription factors, epigenetic and epigenomic screens; and technologies allowing for the multiplexing of effectors and/or targeting sites. This Special Issue will also cover the generation of reliable systems for quantitative readouts of cellular consequences and is open to studies that convincingly demonstrate that certain chromatin features do not affect gene expression alone.

Prof. Dr. Stefan Stricker
Guest Editor

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Keywords

  • epigenome editing
  • CRISPR
  • dCas9
  • functional epigenetics
  • chromatin
  • transcriptional engineering

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Published Papers (1 paper)

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Research

17 pages, 2622 KiB  
Article
CRISPR/dCas9-KRAB-Mediated Suppression of S100b Restores p53-Mediated Apoptosis in Melanoma Cells
by Samrat Roy Choudhury, Billie Heflin, Erin Taylor, Brian Koss, Nathan L. Avaritt and Alan J. Tackett
Cells 2023, 12(5), 730; https://doi.org/10.3390/cells12050730 - 24 Feb 2023
Cited by 4 | Viewed by 3417
Abstract
Overexpression of S100B is routinely used for disease-staging and for determining prognostic outcomes in patients with malignant melanoma. Intracellular interactions between S100B and wild-type (WT)-p53 have been demonstrated to limit the availability of free WT-p53 in tumor cells, inhibiting the apoptotic signaling cascade. [...] Read more.
Overexpression of S100B is routinely used for disease-staging and for determining prognostic outcomes in patients with malignant melanoma. Intracellular interactions between S100B and wild-type (WT)-p53 have been demonstrated to limit the availability of free WT-p53 in tumor cells, inhibiting the apoptotic signaling cascade. Herein, we demonstrate that, while oncogenic overexpression of S100B is poorly correlated (R < 0.3; p > 0.05) to alterations in S100B copy number or DNA methylation in primary patient samples, the transcriptional start site and upstream promoter of the gene are epigenetically primed in melanoma cells with predicted enrichment of activating transcription factors. Considering the regulatory role of activating transcription factors in S100B upregulation in melanoma, we stably suppressed S100b (murine ortholog) by using a catalytically inactive Cas9 (dCas9) fused to a transcriptional repressor, Krüppel-associated box (KRAB). Selective combination of S100b-specific single-guide RNAs and the dCas9-KRAB fusion significantly suppressed expression of S100b in murine B16 melanoma cells without noticeable off-target effects. S100b suppression resulted in recovery of intracellular WT-p53 and p21 levels and concomitant induction of apoptotic signaling. Expression levels of apoptogenic factors (i.e., apoptosis-inducing factor, caspase-3, and poly-ADP ribose polymerase) were altered in response to S100b suppression. S100b-suppressed cells also showed reduced cell viability and increased susceptibility to the chemotherapeutic agents, cisplatin and tunicamycin. Targeted suppression of S100b therefore offers a therapeutic vulnerability to overcome drug resistance in melanoma. Full article
(This article belongs to the Special Issue CRISPR-Tools in Epigenetic Research)
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