Epigenomics of embryogenesis in turbot (Scophthalmus maximus) DOI Open Access
Óscar Aramburu, Belén G. Pardo, Ada Jiménez-González

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 17, 2024

ABSTRACT Embryogenesis is the crucial first step of ontogeny, where an organism with a complex body plan arises from single undifferentiated totipotent cell. This process orchestrated by dynamic changes in transcriptional regulation, influenced chromatin accessibility and nucleotide histone modifications constituting epigenetic signals enabling access to transcription factors. The epigenomic regulation embryogenesis has been studied model fishes, but little attention paid farmed fish - traits importance aquaculture rely on early developmental processes. study, framed within AQUA-FAANG consortium, reports comprehensive regulatory atlas for turbot ( Scophthalmus maximus ), flatfish representing order Pleuronectiformes. 14,560 genes were expressed embryonic transcriptome > 90% showing differential expression across consecutive stages. By integrating multi-histone ChIP-Seq marks ATAC-Seq, we built genome-wide state model, defining promoter enhancer activity Transcription factor binding motif (TFBM) analysis differentially active promoters enhancers revealed dynamism regulated gene functions, more than half TFBM enriched transition. Significant shifts occurred stages, most notably during transition shield segmentation, suggesting profound reorganization underpins somitogenesis organ development. Most stages did not involve regions genes, trend preceding activity. Comparative analyses zebrafish global transcriptomic correlation copy orthologs at matched species. While conserved dynamics many orthologous Hox notable cross-species differences identified before zygotic genome activation leading up hatching. multi-omics investigation provides novel non-coding elements controlling development, key applications biology enhancing sustainable aquaculture.

Language: Английский

Natural antisense transcripts as versatile regulators of gene expression DOI
Andreas Werner, Aditi Kanhere, Claes Wahlestedt

et al.

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: April 17, 2024

Language: Английский

Citations

13
The role of the dynamic epigenetic landscape in senescence: orchestrating SASP expression DOI Creative Commons
Nirmalya Dasgupta,

Rouven Arnold,

Anaïs Equey

et al.

npj Aging, Journal Year: 2024, Volume and Issue: 10(1)

Published: Oct. 24, 2024

Senescence and epigenetic alterations stand out as two well-characterized hallmarks of aging. When cells become senescent, they cease proliferation release inflammatory molecules collectively termed the Senescence-Associated Secretory Phenotype (SASP). SASP are implicated in numerous age-related diseases. Senescent cell nuclei undergo reprogramming, which intricately regulates expression. This review outlines current understanding how senescent changes these govern

Language: Английский

Citations

11
Epigenetic control of cell identities from epiblast to gastrulation DOI Creative Commons
Katrin M. Schüle, Simone Probst

FEBS Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 22, 2025

Epigenetic modifications of chromatin are essential for the establishment cell identities during embryogenesis. Between embryonic days 3.5–7.5 murine development, major lineage decisions made that discriminate extraembryonic and tissues, primary germ layers formed, thereby laying down basic body plan. In this review, we cover contribution dynamic by DNA methylation, changes accessibility, histone modifications, in combination with transcription factors control gene expression programs different types. We highlight differences regulation enhancer promoter marks discuss their requirement specification. Importantly, many cases, lineage‐specific targeting epigenetic modifiers is carried out pioneer or master factors, sum mediate landscape cell‐type‐specific thus, identities.

Language: Английский

Citations

1
HIF1A facilitates hypoxia-induced changes in H3K27ac modification to promote myometrial contractility DOI Creative Commons
Kaiyuan Ji, Bolun Wen, Xiaodi Wang

et al.

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: March 21, 2025

Language: Английский

Citations

1
Acetyltransferases CBP/p300 Control Transcriptional Switch of β-Catenin and Stat1 Promoting Osteoblast Differentiation DOI Creative Commons
Linlin Zhang, Ke-Cheng Zhu, Jing-zun Xu

et al.

Journal of Bone and Mineral Research, Journal Year: 2023, Volume and Issue: 38(12), P. 1885 - 1899

Published: Oct. 18, 2023

ABSTRACT CREB-binding protein (CBP) (CREBBP) and p300 (EP300) are multifunctional histone acetyltransferases (HATs) with extensive homology. Germline mutations of CBP or cause skeletal abnormalities in humans mice. However, the precise roles CBP/p300 bone homeostasis remain elusive. Here, we report that conditional knockout osteoblasts results reduced mass strength due to suppressed formation. The HAT activity is further confirmed be responsible for CBP/p300-mediated osteogenesis using A-485, a selective inhibitor HAT. Mechanistically, governs osteogenic gene expression part through transcriptional activation β-catenin inhibition Stat1. Furthermore, acetylation H3K27 transcription factor Foxo1 demonstrated involved HAT-regulated Stat1 transcription, respectively. Taken together, these data identify as critical regulators promote osteoblast differentiation reveal an epigenetic mechanism maintaining homeostasis. © 2023 American Society Bone Mineral Research (ASBMR). Abstract An overall illustration effects potential mechanisms on differentiation. Acetyltransferases indispensable H3K27Ac-mediated acetylated Foxo1-mediated identified novel regulatory signals HAT-governed network.

Language: Английский

Citations

11
Long non-coding RNAs and their role in muscle regeneration DOI
Beatrice Biferali, Emanuele Mocciaro, Valeria Runfola

et al.

Current topics in developmental biology/Current Topics in Developmental Biology, Journal Year: 2024, Volume and Issue: unknown, P. 433 - 465

Published: Jan. 1, 2024

Language: Английский

Citations

4
From Environment to Gene Expression: Epigenetic Methylations and One-Carbon Metabolism in Amyotrophic Lateral Sclerosis DOI Creative Commons

Marina Hernán-Godoy,

Caroline Rouaux

Cells, Journal Year: 2024, Volume and Issue: 13(11), P. 967 - 967

Published: June 3, 2024

The etiology of the neurodegenerative disease amyotrophic lateral sclerosis (ALS) is complex and considered multifactorial. majority ALS cases are sporadic, but familial also exist. Estimates heritability range from 8% to 61%, indicating that additional factors beyond genetics likely contribute ALS. Numerous environmental considered, which may add up synergize throughout an individual's lifetime building its unique exposome. One level integration between genetic epigenetics, results in alterations gene expression without modification genome sequence. Methylation reactions, targeting DNA or histones, represent a large proportion epigenetic regulations strongly depend on availability methyl donors provided by ubiquitous one-carbon (1C) metabolism. Thus, understanding interplay exposome, 1C metabolism, modifications will elucidating mechanisms underlying altered related developing targeted therapeutic interventions. Here, we review evidence for metabolism methylation dysregulations ALS, with focus impairments reported neural tissues, discuss these environmentally driven as consequences cumulative exposome late hits, possible result early developmental defects.

Language: Английский

Citations

4
Decoding the Epigenome of Breast Cancer DOI Open Access

Elisa Cortellesi,

Isabella Savini,

M Veneziano

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(6), P. 2605 - 2605

Published: March 13, 2025

Breast cancer (BC) is the most prevalent malignancy among women, characterized by extensive heterogeneity stemming from molecular and genetic alterations. This review explores intricate epigenetic landscape of BC, highlighting significant role modifications—particularly DNA methylation, histone modifications, influence non-coding RNAs—in initiation, progression, prognosis disease. Epigenetic alterations drive crucial processes, including gene expression regulation, cell differentiation, tumor microenvironment interactions, contributing to tumorigenesis metastatic potential. Notably, aberrations in methylation patterns, global hypomethylation hypermethylation CpG islands, have been associated with distinct BC subtypes, implications for early detection risk assessment. Furthermore, such as acetylation affect plasticity aggressiveness profoundly influencing chromatin dynamics transcription. Finally, RNAs contribute modulating machinery expression. Despite advances our knowledge, clinical application therapies still challenging, often yielding limited efficacy when used alone. However, combining epi-drugs established treatments shows promise enhancing therapeutic outcomes. underscores importance integrating insights into personalized treatment strategies, emphasizing potential biomarkers improving diagnosis, prognosis, response affected patients.

Language: Английский

Citations

0
Revolutionizing Implantation Studies: Uterine-Specific Models and Advanced Technologies DOI Creative Commons

Shuyun Li,

Francesco J. DeMayo

Biomolecules, Journal Year: 2025, Volume and Issue: 15(3), P. 450 - 450

Published: March 20, 2025

Implantation is a complex and tightly regulated process essential for the establishment of pregnancy. It involves dynamic interactions between receptive uterus competent embryo, orchestrated by ovarian hormones such as estrogen progesterone. These regulate proliferation, differentiation, gene expression within three primary uterine tissue types: myometrium, stroma, epithelium. Advances in genetic manipulation, particularly Cre/loxP system, have enabled vivo investigation role genes compartmental cell type-specific manner, providing valuable insights into biology during pregnancy disease. The development endometrial organoids has further revolutionized implantation research. They mimic native structure function, offering powerful platform studying hormonal responses, implantation, maternal-fetal interactions. Combined with omics technologies, these models uncovered molecular mechanisms signaling pathways that implantation. This review provides comprehensive overview uterine-specific tools, organoids, omics. We explore how advancements enhance our understanding biology, receptivity, decidualization reproductive

Language: Английский

Citations

0
20 years of histone lysine demethylases: From discovery to the clinic and beyond DOI

Zach H. Gray,

M. Honer, Pooja Ghatalia

et al.

Cell, Journal Year: 2025, Volume and Issue: 188(7), P. 1747 - 1783

Published: April 1, 2025

Language: Английский

Citations

0