Human Endogenous Retroviruses as Novel Therapeutic Targets in Neurodegenerative Disorders DOI Creative Commons
Elena Rita Simula, Seyedesomaye Jasemi, Davide Cossu

et al.

Vaccines, Journal Year: 2025, Volume and Issue: 13(4), P. 415 - 415

Published: April 15, 2025

Human Endogenous Retroviruses comprise approximately 8% of the human genome, serving as fragments ancient retroviral infections. Although they are generally maintained in a silenced state by robust epigenetic mechanisms, specific HERV groups, particularly HERV-W and HERV-K, can become derepressed under pathological conditions, thereby contributing to initiation progression neuroinflammatory neurodegenerative processes. Preclinical studies clinical trials, such those investigating monoclonal antibodies, indicate that directly targeting these elements may offer novel therapeutic strategy. In this review, we provide an overview HERVs′ biology, examine their role diseases amyotrophic lateral sclerosis, multiple Alzheimer′s disease, Parkinson′s explore prospects, highlighting both challenges potential future research directions needed translate approaches into interventions.

Language: Английский

Next-Generation Sequencing Technology: Current Trends and Advancements DOI Creative Commons

Heena Satam,

Kandarp Joshi, Upasana Mangrolia

et al.

Biology, Journal Year: 2023, Volume and Issue: 12(7), P. 997 - 997

Published: July 13, 2023

The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules high-throughput cost-effective manner. This transformative technology swiftly propelled advancements across diverse domains. NGS allows the rapid millions fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, epigenetic modifications. versatility platforms expanded scope facilitating studies on rare diseases, cancer genomics, microbiome analysis, infectious population genetics. Moreover, enabled development targeted therapies, precision medicine approaches, improved diagnostic methods. review provides an insightful overview current trends recent technology, highlighting its potential impact areas genomic research. delves challenges encountered future directions including endeavors to enhance accuracy sensitivity data, novel algorithms data pursuit more efficient, scalable, solutions that lie ahead.

Language: Английский

Citations

550
Epigenetic regulation of early human embryo development DOI Creative Commons
Amy L. Wilkinson, Irene Zorzan, Peter J. Rugg‐Gunn

et al.

Cell stem cell, Journal Year: 2023, Volume and Issue: 30(12), P. 1569 - 1584

Published: Oct. 18, 2023

Studies of mammalian development have advanced our understanding the genetic, epigenetic, and cellular processes that orchestrate embryogenesis uncovered new insights into unique aspects human embryogenesis. Recent studies now produced first epigenetic maps early embryogenesis, stimulating ideas about reprogramming, cell fate control, potential mechanisms underpinning developmental plasticity in embryos. In this review, we discuss these regulation importance for safeguarding development. We also highlight unanswered questions key challenges remain to be addressed.

Language: Английский

Citations

45
Epigenetics and individuality: from concepts to causality across timescales DOI
Amy K. Webster, Patrick C. Phillips

Nature Reviews Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 9, 2025

Language: Английский

Citations

4
Structure and Functions of HMGB2 Protein DOI Open Access
T. Yu. Starkova, A. M. Polyanichko, Alexey Tomilin

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(9), P. 8334 - 8334

Published: May 5, 2023

High-Mobility Group (HMG) chromosomal proteins are the most numerous nuclear non-histone proteins. HMGB domain abundant and well-studied HMG They involved in variety of biological processes. HMGB1 HMGB2 were first members HMGB-family to be discovered found all studied eukaryotes. Despite high degree homology, differ from each other both structure functions. In contrast HMGB2, there is a large pool works devoted protein whose structure–function properties have been described detail our previous review 2020. this review, we attempted bring together diverse data about functions protein. The also describes post-translational modifications its role development number diseases. Particular attention paid interaction with various targets, including DNA partners. influence level expression on processes associated cell differentiation aging ability mediate embryonic adult stem cells discussed.

Language: Английский

Citations

33
Mind the gap: Epigenetic regulation of chromatin accessibility in plants DOI Creative Commons
Joan Candela-Ferre, Borja Diego‐Martin, Jaime Pérez-Alemany

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 194(4), P. 1998 - 2016

Published: Jan. 17, 2024

Abstract Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central these processes, determining chromatin accessibility by limiting access to DNA various proteins acting as important signaling hubs. The association histones with nucleosomes folding into higher-order structures strongly influenced variety epigenetic marks, including methylation, histone variants, post-translational modifications. Additionally, wide array chaperones ATP-dependent remodelers regulate aspects nucleosome biology, assembly, deposition, positioning. This review provides an overview recent advances our mechanistic understanding how organization regulated marks plants. Furthermore, we present current technologies profiling organization.

Language: Английский

Citations

15
Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae DOI Creative Commons
Li E. Cheng,

Shijun Zhao,

Tianyi Li

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 26, 2024

Abstract Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. However, the potential of SCRaMbLE rearrangements currently hindered, because strain containing all 16 synthetic chromosomes not yet available. Here, we construct SparLox83R, yeast 83 loxPsym sites distributed across chromosomes. SparLox83R produces versatile genome-wide rearrangements, including inter-chromosomal events. Moreover, when combined with chromosomes, hetero-diploids leads increased diversity relatively faster evolution traits compared only wild-type Analysis SCRaMbLEd tolerance nocodazole demonstrates that can perturb transcriptome 3D genome structure consequently impact phenotypes. In summary, sparsely serve as powerful for studying consequence accelerating engineering in Saccharomyces cerevisiae .

Language: Английский

Citations

13
An extensive review on infectious disease diagnosis using machine learning techniques and next generation sequencing: State-of-the-art and perspectives DOI

Javed Aalam,

Syed Naseer Ahmad Shah,

Rafat Parveen

et al.

Computers in Biology and Medicine, Journal Year: 2025, Volume and Issue: 189, P. 109962 - 109962

Published: March 6, 2025

Language: Английский

Citations

1
Molecular dynamics simulations of nucleosomes are coming of age DOI

Anastasiia S. Fedulova,

Grigoriy A. Armeev,

Tatiana A. Romanova

et al.

Wiley Interdisciplinary Reviews Computational Molecular Science, Journal Year: 2024, Volume and Issue: 14(4)

Published: July 1, 2024

Abstract Understanding the function of eukaryotic genomes, including human genome, is undoubtedly one major scientific challenges 21st century. The cornerstone genome organization nucleosomes—elementary building blocks chromatin about 10 nm in size that wrap DNA around an octamer histone proteins. Nucleosomes are integral players all genomic processes, transcription, replication and repair. They mediate regulation at epigenetic level, bridging discrete nature genetic information encoded with analog physical intermolecular interactions required to access information. Due their relatively large dynamic nature, nucleosomes difficult objects for experimental characterization. Molecular dynamics (MD) simulations have emerged over years as a useful tool complement studies. Particularly recent years, advances computing power, refinement MD force fields codes opened up new frontiers terms simulation timescales quality related systems. It has become possible elucidate atomistic detail functional modes such unwrapping sliding, characterize effects modifications, protein sequence variation on nucleosome structure stability, describe mechanisms governing chromatin‐associated proteins formation supranucleosome structures. In this review, we systematically analyzed all‐atom studies structures published since 2018 discussed relevance context older studies, data, coarse‐grained multiscale This article categorized under: Software > Modeling Statistical Mechanics Dynamics Monte‐Carlo Methods Structure Mechanism Computational Biochemistry Biophysics

Language: Английский

Citations

7
Integrated ATAC‐seq and RNA‐seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa DOI Creative Commons
Miaomiao Li, Jing Li, Yan Zhang

et al.

Molecular Plant Pathology, Journal Year: 2024, Volume and Issue: 25(3)

Published: March 1, 2024

Abstract Animal studies have shown that virus infection causes changes in host chromatin accessibility, but little is known about accessibility of plants infected by viruses and its potential impact. Here, rice stripe (RSV) was used to investigate virus‐induced accessibility. Our analysis identified a total 6462 open‐ 3587 closed‐differentially accessible regions (DACRs) under RSV ATAC‐seq. Additionally, integrating ATAC‐seq RNA‐seq, 349 up‐regulated genes open‐DACRs 126 down‐regulated closed‐DACRs were identified, which 34 transcription factors (TFs) further search upstream motifs. Transcription levels eight these TFs validated reverse transcription‐PCR. Importantly, four (OsWRKY77, OsWRKY28, OsZFP12 OsERF91) interacted with proteins are therefore predicted play important roles infection. This the first application RNA‐seq techniques analyse caused Integrating provides new approach select candidate response

Language: Английский

Citations

5
Structural dynamics in chromatin unraveling by pioneer transcription factors DOI Creative Commons

A Orsetti,

Daphne van Oosten,

Roxana-Geanina Vasarhelyi

et al.

Biophysical Reviews, Journal Year: 2024, Volume and Issue: 16(3), P. 365 - 382

Published: June 1, 2024

Pioneer transcription factors are proteins with a dual function. First, they regulate by binding to nucleosome-free DNA regulatory elements. Second, bind while wrapped around histone in the chromatin and mediate opening. The molecular mechanisms that connect two functions yet be discovered. In recent years, pioneer received increased attention mainly because of their crucial role promoting cell fate transitions could used for regenerative therapies. For example, three required induce pluripotency somatic cells, Oct4, Sox2, Klf4 were classified as studied extensively. With this attention, several structures complexes between structural units (nucleosomes) have been resolved experimentally. Furthermore, experimental computational approaches designed study unresolved, key scientific questions: do directly local opening nucleosomes fibers upon binding? And second, how unstructured tails histones impact dynamics involved such conformational transitions? Here we review current knowledge about factor-induced nucleosome process. We discuss what is needed bridge gap static views obtained from dynamic events Finally, propose integrating nuclear magnetic resonance spectroscopy simulations powerful approach studying factor-mediated perhaps small using native sequences.

Language: Английский

Citations

5