The Roles of Histone Lysine Methyltransferases in Heart Development and Disease DOI Creative Commons
Jun‐yi Zhu, Joyce van de Leemput, Zhe Han

и другие.

Journal of Cardiovascular Development and Disease, Год журнала: 2023, Номер 10(7), С. 305 - 305

Опубликована: Июль 18, 2023

Epigenetic marks regulate the transcriptomic landscape by facilitating structural packing and unwinding of genome, which is tightly folded inside nucleus. Lysine-specific histone methylation one such mark. It plays crucial roles during development, including in cell fate decisions, tissue patterning, regulating cellular metabolic processes. has also been associated with varying human developmental disorders. Heart disease linked to deregulated lysine methylation, lysine-specific methyltransferases (KMTs) are overrepresented, i.e., more numerous than expected chance, among genes variants congenital heart disease. This review outlines available evidence support a role for individual KMTs development and/or disease, genetic associations patients supporting culture animal model studies. concludes new advances field opportunities treatment.

Язык: Английский

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

Heena Satam,

Kandarp Joshi, Upasana Mangrolia

и другие.

Biology, Год журнала: 2023, Номер 12(7), С. 997 - 997

Опубликована: Июль 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.

Язык: Английский

Процитировано

473
Epigenetic regulation of early human embryo development DOI Creative Commons
Amy L. Wilkinson, Irene Zorzan, Peter J. Rugg‐Gunn

и другие.

Cell stem cell, Год журнала: 2023, Номер 30(12), С. 1569 - 1584

Опубликована: Окт. 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.

Язык: Английский

Процитировано

42
Epigenetics and individuality: from concepts to causality across timescales DOI
Amy K. Webster, Patrick C. Phillips

Nature Reviews Genetics, Год журнала: 2025, Номер unknown

Опубликована: Янв. 9, 2025

Язык: Английский

Процитировано

2
Structure and Functions of HMGB2 Protein DOI Open Access
T. Yu. Starkova, A. M. Polyanichko, Alexey Tomilin

и другие.

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(9), С. 8334 - 8334

Опубликована: Май 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.

Язык: Английский

Процитировано

31
Mind the gap: Epigenetic regulation of chromatin accessibility in plants DOI Creative Commons
Joan Candela-Ferre, Borja Diego‐Martin, Jaime Pérez-Alemany

и другие.

PLANT PHYSIOLOGY, Год журнала: 2024, Номер 194(4), С. 1998 - 2016

Опубликована: Янв. 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.

Язык: Английский

Процитировано

13
Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae DOI Creative Commons
Li E. Cheng,

Shijun Zhao,

Tianyi Li

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Янв. 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 .

Язык: Английский

Процитировано

12
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

и другие.

Computers in Biology and Medicine, Год журнала: 2025, Номер 189, С. 109962 - 109962

Опубликована: Март 6, 2025

Язык: Английский

Процитировано

1
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

и другие.

Molecular Plant Pathology, Год журнала: 2024, Номер 25(3)

Опубликована: Март 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

Язык: Английский

Процитировано

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

A Orsetti,

Daphne van Oosten,

Roxana-Geanina Vasarhelyi

и другие.

Biophysical Reviews, Год журнала: 2024, Номер 16(3), С. 365 - 382

Опубликована: Июнь 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.

Язык: Английский

Процитировано

5
Single cell spatial biology over developmental time can decipher pediatric brain pathologies DOI Creative Commons
Ruth Nussinov, Bengi Ruken Yavuz, Hyunbum Jang

и другие.

Neurobiology of Disease, Год журнала: 2024, Номер 199, С. 106597 - 106597

Опубликована: Июль 9, 2024

Pediatric low grade brain tumors and neurodevelopmental disorders share proteins, signaling pathways, networks. They also germline mutations an impaired prenatal differentiation origin. may differ in the timing of events proliferation. We suggest that their pivotal distinct, albeit partially overlapping, outcomes relate to cell states, which depend on spatial location, gene expression during development. These attributes are crucial as develops sequentially, single-cell organization influences state, thus function. Our underlying premise is root cause pediatric differentiation. Data related tumors, disorders, (sub)types, locations, developing scant. However, emerging single technologies, including transcriptomic, biology, high-resolution imaging performed over developmental time, could be transformational deciphering pathologies thereby pharmacology.

Язык: Английский

Процитировано

5