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Epigenetic Bioengineering
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Epigenetic Bioengineering

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (15 March 2021) | Viewed by 11204

Special Issue Editors

Dr. Pernette J. Verschure

E-Mail Website
Guest Editor
Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
Interests: Dynamic epigenetic gene regulation; Genome and cell nuclear organization; Resistance development against treatment in hormone sensitive breast cancer; DNA damage and repair processing; Forensic relevance of epigenetic aging; Stochasticity and heterogeneity; Synthetic and systems biology; Advanced microscopy
Dr. Nate Hathaway

E-Mail Website
Guest Editor
The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Interests: epigenetics; chromatin biology; chemical biology; cell biology; cancer research; gene regulation; bioengineering; drug discovery

Special Issue Information

Dear Colleagues,

Epigenetic gene regulation is essential for proper mammalian development and maintains the identity of cells that make up the body. Interestingly, epigenetic regulation exhibits a dual functionality. On one hand, the epigenome is very robust, instructing gene expression patterns that persist over many cell generations. Additionally the epigenome is highly dynamic, able to respond to environmental and developmental signals. Epigenetic fluctuations can allow critical diversification of cell function. Yet, alterations to the epigenome can provide unwanted subclonality such as tumor heterogeneity. Numerous crucial questions regarding the functional output of epigenetic regulation specially in clinical context remain unanswered.

A great deal of knowledge about epigenetic regulatory networks has been gained with whole-genome mapping. Relatively less is known about the dynamics and variability of interactions, particularly in individual living cells. Technological breakthroughs to measure modify and model epigenetics at single cell, real-time and single molecule level have opened up enormous potential to measure the transient changes and determine cause-effect relationships. This special issue will be dedicated to the impact of using innovative technologies to infer design principles of epigenetic regulation and the functional output. All explorative studies which enhance the field of epigenetics and bioengineering are welcomed to contribute to this issue.

Dr. Pernette J. Verschure
Dr. Nate Hathaway
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Epigenetics
  • Bioengineering
  • Chromatin regulation
  • Nuclear organization and dynamics
  • Writing epigenetic modifications
  • Sensing epigenetic modifications
  • Single cell epigenetics
  • Emerging technologies
  • Epigenetics in human health & disease

Published Papers (4 papers)

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Research

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15 pages, 27795 KiB  
Article
Modified Histone Peptides Linked to Magnetic Beads Reduce Binding Specificity
by Jenna N. Meanor, Albert J. Keung and Balaji M. Rao
Int. J. Mol. Sci. 2022, 23(3), 1691; https://doi.org/10.3390/ijms23031691 - 1 Feb 2022
Cited by 1 | Viewed by 2341
Abstract
Histone post-translational modifications are small chemical changes to the histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such [...] Read more.
Histone post-translational modifications are small chemical changes to the histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such as antibodies, recombinant assays, and FRET-based systems. High-throughput platforms could accelerate work in this field, and also could be used to engineer de novo histone affinity reagents; yet, published studies on their use with histones have been noticeably sparse. Here, we describe specific experimental conditions that affect binding specificities of post-translationally modified histones in classic protein engineering platforms and likely explain the relative difficulty with histone targets in these platforms. We also show that manipulating avidity of binding interactions may improve specificity of binding. Full article
(This article belongs to the Special Issue Epigenetic Bioengineering)
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26 pages, 5713 KiB  
Article
Hydroxyurea and Caffeine Impact pRb-like Protein-Dependent Chromatin Architecture Profiles in Interphase Cells of Vicia faba
by Marcelina W. Musiałek, Joanna Deckert and Dorota Rybaczek
Int. J. Mol. Sci. 2021, 22(9), 4572; https://doi.org/10.3390/ijms22094572 - 27 Apr 2021
Cited by 2 | Viewed by 1793
Abstract
The survival of cells depends on their ability to replicate correctly genetic material. Cells exposed to replication stress can experience a number of problems that may lead to deregulated proliferation, the development of cancer, and/or programmed cell death. In this article, we have [...] Read more.
The survival of cells depends on their ability to replicate correctly genetic material. Cells exposed to replication stress can experience a number of problems that may lead to deregulated proliferation, the development of cancer, and/or programmed cell death. In this article, we have induced prolonged replication arrest via hydroxyurea (HU) treatment and also premature chromosome condensation (PCC) by co-treatment with HU and caffeine (CF) in the root meristem cells of Vicia faba. We have analyzed the changes in the activities of retinoblastoma-like protein (RbS807/811ph). Results obtained from the immunocytochemical detection of RbS807/811ph allowed us to distinguish five unique activity profiles of pRb. We have also performed detailed 3D modeling using Blender 2.9.1., based on the original data and some final conclusions. 3D models helped us to visualize better the events occurring within the nuclei and acted as a high-resolution aid for presenting the results. We have found that, despite the decrease in pRb activity, its activity profiles were mostly intact and clearly recognizable, with some local alterations that may correspond to the increased demand in transcriptional activity. Our findings suggest that Vicia faba’s ability to withstand harsh environments may come from its well-developed and highly effective response to replication stress. Full article
(This article belongs to the Special Issue Epigenetic Bioengineering)
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Review

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22 pages, 2534 KiB  
Review
Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease
by Laura Leo and Nunzia Colonna Romano
Int. J. Mol. Sci. 2021, 22(16), 8809; https://doi.org/10.3390/ijms22168809 - 16 Aug 2021
Cited by 6 | Viewed by 4360
Abstract
Epigenetic regulators play a crucial role in establishing and maintaining gene expression states. To date, the main efforts to study cellular heterogeneity have focused on elucidating the variable nature of the chromatin landscape. Specific chromatin organisation is fundamental for normal organogenesis and developmental [...] Read more.
Epigenetic regulators play a crucial role in establishing and maintaining gene expression states. To date, the main efforts to study cellular heterogeneity have focused on elucidating the variable nature of the chromatin landscape. Specific chromatin organisation is fundamental for normal organogenesis and developmental homeostasis and can be affected by different environmental factors. The latter can lead to detrimental alterations in gene transcription, as well as pathological conditions such as cancer. Epigenetic marks regulate the transcriptional output of cells. Centromeres are chromosome structures that are epigenetically regulated and are crucial for accurate segregation. The advent of single-cell epigenetic profiling has provided finer analytical resolution, exposing the intrinsic peculiarities of different cells within an apparently homogenous population. In this review, we discuss recent advances in methodologies applied to epigenetics, such as CUT&RUN and CUT&TAG. Then, we compare standard and emerging single-cell techniques and their relevance for investigating human diseases. Finally, we describe emerging methodologies that investigate centromeric chromatin specification and neocentromere formation. Full article
(This article belongs to the Special Issue Epigenetic Bioengineering)
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11 pages, 754 KiB  
Review
Combinatorial Use of Both Epigenetic and Non-Epigenetic Mechanisms to Efficiently Reactivate HIV Latency
by Joseph Hokello, Adhikarimayum Lakhikumar Sharma and Mudit Tyagi
Int. J. Mol. Sci. 2021, 22(7), 3697; https://doi.org/10.3390/ijms22073697 - 2 Apr 2021
Cited by 6 | Viewed by 2045
Abstract
The persistence of latent HIV provirus pools in different resting CD4+ cell subsets remains the greatest obstacle in the current efforts to treat and cure HIV infection. Recent efforts to purge out latently infected memory CD4+ T-cells using latency-reversing agents have failed in [...] Read more.
The persistence of latent HIV provirus pools in different resting CD4+ cell subsets remains the greatest obstacle in the current efforts to treat and cure HIV infection. Recent efforts to purge out latently infected memory CD4+ T-cells using latency-reversing agents have failed in clinical trials. This review discusses the epigenetic and non-epigenetic mechanisms of HIV latency control, major limitations of the current approaches of using latency-reversing agents to reactivate HIV latency in resting CD4+ T-cells, and potential solutions to these limitations. Full article
(This article belongs to the Special Issue Epigenetic Bioengineering)
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