scholarly journals Deciphering Plant Chromatin Regulation via CRISPR/dCas9-Based Epigenome Engineering

Epigenomes ◽  
2021 ◽  
Vol 5 (3) ◽  
pp. 17
Author(s):  
Annick Dubois ◽  
François Roudier
Keyword(s):  
Recent Progress ◽  
Full Potential ◽  
Chromatin Dynamics ◽  
Epigenome Editing ◽  
Dna Accessibility ◽  
Chromatin Regulators ◽  
Genome Regulation ◽  
Transcriptional Engineering ◽  
Transcriptional State

CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss how recent progress in plants and animals provides new routes to investigate the function of chromatin regulators and address the complexity of associated regulations that are often interconnected. While efficient transcriptional engineering methodologies have been developed and can be used as tools to alter the chromatin state of a locus, examples of direct manipulation of chromatin regulators remain scarce in plants. These reports also reveal pitfalls and limitations of epigenome engineering approaches that are nevertheless informative as they are often associated with locus- and context-dependent features, which include DNA accessibility, initial chromatin and transcriptional state or cellular dynamics. Strategies implemented in different organisms to overcome and even take advantage of these limitations are highlighted, which will further improve our ability to establish the causality and hierarchy of chromatin dynamics on genome regulation.

Post-translational modifications and chromatin dynamics

2019 ◽  
Vol 63 (1) ◽  
pp. 89-96 ◽  
Author(s):  
Thomas O. Tolsma ◽  
Jeffrey C. Hansen
Keyword(s):  
Dynamic Structure ◽  
Higher Order ◽  
Post Translational Modifications ◽  
Chromatin Dynamics ◽  
Dna Accessibility ◽  
In Vivo Analysis ◽  
Nuclear Environment ◽  
Biological State

Abstract The dynamic structure of chromatin is linked to gene regulation and many other biological functions. Consequently, it is of importance to understand the factors that regulate chromatin dynamics. While the in vivo analysis of chromatin has verified that histone post-translational modifications play a role in modulating DNA accessibility, the complex nuclear environment and multiplicity of modifications prevents clear conclusions as to how individual modifications influence chromatin dynamics in the cell. For this reason, in vitro analyses of model reconstituted nucleosomal arrays has been pivotal in understanding the dynamic nature of chromatin compaction and the affects that specific post-translational modifications can have on the higher order chromatin structure. In this mini-review, we briefly describe the dynamic chromatin structures that have been observed in vitro and the environmental conditions that give rise to these various conformational states. Our focus then turns to a discussion of the specific histone post-translational modifications that have been shown to alter formation of these higher order chromatin structures in vitro and how this may relate to the biological state and accessibility of chromatin in vivo.

scholarly journals Lentiviral Vectors for Delivery of Gene-Editing Systems Based on CRISPR/Cas: Current State and Perspectives

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1288
Author(s):  
Wendy Dong ◽  
Boris Kantor
Keyword(s):  
Large Scale ◽  
Lentiviral Vector ◽  
Clinical Applications ◽  
Scale Production ◽  
Base Editing ◽  
Epigenome Editing ◽  
Vector Systems ◽  
Dividing Cells

CRISPR/Cas technology has revolutionized the fields of the genome- and epigenome-editing by supplying unparalleled control over genomic sequences and expression. Lentiviral vector (LV) systems are one of the main delivery vehicles for the CRISPR/Cas systems due to (i) its ability to carry bulky and complex transgenes and (ii) sustain robust and long-term expression in a broad range of dividing and non-dividing cells in vitro and in vivo. It is thus reasonable that substantial effort has been allocated towards the development of the improved and optimized LV systems for effective and accurate gene-to-cell transfer of CRISPR/Cas tools. The main effort on that end has been put towards the improvement and optimization of the vector’s expression, development of integrase-deficient lentiviral vector (IDLV), aiming to minimize the risk of oncogenicity, toxicity, and pathogenicity, and enhancing manufacturing protocols for clinical applications required large-scale production. In this review, we will devote attention to (i) the basic biology of lentiviruses, and (ii) recent advances in the development of safer and more efficient CRISPR/Cas vector systems towards their use in preclinical and clinical applications. In addition, we will discuss in detail the recent progress in the repurposing of CRISPR/Cas systems related to base-editing and prime-editing applications.

scholarly journals Synthesis of DOTA-pyridine chelates for 64Cu coordination and radiolabeling of αMSH peptide

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Hua Yang ◽  
Feng Gao ◽  
Brooke McNeil ◽  
Chengcheng Zhang ◽  
Zheliang Yuan ◽  
...  
Keyword(s):  
Full Potential ◽  
In Vivo Evaluation ◽  
Melanocortin 1 Receptor ◽  
Melanocyte Stimulating Hormone ◽  
Endogenous Copper ◽  
Coordination Ability ◽  
Copper Chelators ◽  
Cu Complexes ◽  
High Binding Affinity

Abstract Background 64Cu is one of the few radioisotopes that can be used for both imaging and therapy, enabling theranostics with identical chemical composition. Development of stable chelators is essential to harness the potential of this isotope, challenged by the presence of endogenous copper chelators. Pyridyl type chelators show good coordination ability with copper, prompting the present study of a series of chelates DOTA-xPy (x = 1–4) that sequentially substitute carboxyl moieties with pyridyl moieties on a DOTA backbone. Results We found that the presence of pyridyl groups significantly increases 64Cu labeling conversion yield, with DOTA-2Py, −3Py and -4Py quantitatively complexing 64Cu at room temperature within 5 min (1 × 10− 4 M). [64Cu]Cu-DOTA-xPy (x = 2–4) exhibited good stability in human serum up to 24 h. When challenged with 1000 eq. of NOTA, no transmetallation was observed for all three 64Cu complexes. DOTA-xPy (x = 1–3) were conjugated to a cyclized α-melanocyte-stimulating hormone (αMSH) peptide by using one of the pendant carboxyl groups as a bifunctional handle. [64Cu]Cu-DOTA-xPy-αMSH retained good serum stability (> 96% in 24 h) and showed high binding affinity (Ki = 2.1–3.7 nM) towards the melanocortin 1 receptor. Conclusion DOTA-xPy (x = 1–3) are promising chelators for 64Cu. Further in vivo evaluation is necessary to assess the full potential of these chelators as a tool to enable further theranostic radiopharmaceutical development.

scholarly journals Single-cell mapping of focused ultrasound-transfected brain

Gene Therapy ◽  
2021 ◽  
Author(s):  
A. S. Mathew ◽  
C. M. Gorick ◽  
R. J. Price
Keyword(s):  
Single Cell ◽  
Focused Ultrasound ◽  
Cell Types ◽  
Brain Cell ◽  
Therapeutic Modality ◽  
Full Potential ◽  
Stress Genes ◽  
Multiple Cell ◽  
Differential Gene

AbstractGene delivery via focused ultrasound (FUS) mediated blood-brain barrier (BBB) opening is a disruptive therapeutic modality. Unlocking its full potential will require an understanding of how FUS parameters (e.g., peak-negative pressure (PNP)) affect transfected cell populations. Following plasmid (mRuby) delivery across the BBB with 1 MHz FUS, we used single-cell RNA-sequencing to ascertain that distributions of transfected cell types were highly dependent on PNP. Cells of the BBB (i.e., endothelial cells, pericytes, and astrocytes) were enriched at 0.2 MPa PNP, while transfection of cells distal to the BBB (i.e., neurons, oligodendrocytes, and microglia) was augmented at 0.4 MPa PNP. PNP-dependent differential gene expression was observed for multiple cell types. Cell stress genes were upregulated proportional to PNP, independent of cell type. Our results underscore how FUS may be tuned to bias transfection toward specific brain cell types in vivo and predict how those cells will respond to transfection.

Recent progress in the development of sensing systems for in vivo detection of biological hydrogen sulfide

2021 ◽  
pp. 109451
Author(s):  
Jie Li ◽  
Zhe Su ◽  
Changmin Yu ◽  
Yan Yuan ◽  
Qiong Wu ◽  
...  
Keyword(s):  
Hydrogen Sulfide ◽  
Recent Progress ◽  
Sensing Systems ◽  
In Vivo Detection

183 CHROMATIN DYNAMICS IN VIVO REVEAL EARLY MESENCHYMAL REPROGRAMMING AND LIMITED LINEAGE REVERSION IN PANCREATIC INJURY AND TUMORIGENESIS

2021 ◽  
Vol 160 (6) ◽  
pp. S-45
Author(s):  
David Falvo ◽  
Jason Pitarresi ◽  
Alexa Osterhoudt ◽  
Adrien Grimont ◽  
Anil Rustgi ◽  
...  
Keyword(s):  
Pancreatic Injury ◽  
Chromatin Dynamics

scholarly journals Recent progress in single-molecule studies of mRNA localization in vivo

RNA Biology ◽  
2018 ◽  
Vol 16 (9) ◽  
pp. 1108-1118 ◽  
Author(s):  
Songhee H. Kim ◽  
Melissa Vieira ◽  
Jae Youn Shim ◽  
Hongyoung Choi ◽  
Hye Yoon Park
Keyword(s):  
Single Molecule ◽  
Recent Progress ◽  
Mrna Localization ◽  
Single Molecule Studies

scholarly journals A CDK-regulated chromatin segregase promoting chromosome replication

2020 ◽  
Author(s):  
Erika Chacin ◽  
Priyanka Bansal ◽  
Karl-Uwe Reusswig ◽  
Luis M. Diaz-Santin ◽  
Pedro Ortega ◽  
...  
Keyword(s):  
Atp Hydrolysis ◽  
Genome Instability ◽  
Chromosome Replication ◽  
S Phase ◽  
Chromatin Dynamics ◽  
Replicative Stress ◽  
Cdk Phosphorylation ◽  
Nucleosome Disassembly

The replication of chromosomes during S phase is critical for cellular and organismal function. Replicative stress can result in genome instability, which is a major driver of cancer. Yet how chromatin is made accessible during eukaryotic DNA synthesis is poorly understood.Here, we report the identification of a novel class of chromatin remodeling enzyme, entirely distinct from classical SNF2-ATPase family remodelers. Yta7 is a AAA+-ATPase that assembles into ~ 1 MDa hexameric complexes capable of segregating histones from DNA. Yta7 chromatin segregase promotes chromosome replication both in vivo and in vitro. Biochemical reconstitution experiments using purified proteins revealed that Yta7’s enzymatic activity is regulated by S phase-forms of Cyclin-Dependent Kinase (S-CDK). S-CDK phosphorylation stimulates ATP hydrolysis by Yta7, promoting nucleosome disassembly and chromatin replication.Our results present a novel mechanism of how cells orchestrate chromatin dynamics in co-ordination with the cell cycle machinery to promote genome duplication during S phase.

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