Nuclear lipids in chromatin regulation: Biological roles, experimental approaches and existing challenges DOI Creative Commons
Ahmed M. Sayed, Karthik Eswara, Kaian Teles

et al.

Biology of the Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 8, 2024

Abstract Lipids are crucial for various cellular functions. Besides the storage of energy equivalents, these include forming membrane bilayers and serving as signaling molecules. While significant progress has been made in comprehension molecular biology lipids, their functions cell nucleus remain poorly understood. The main role eukaryotic is to provide an environment regulation chromatin which a complex DNA, histones, associated proteins. Recent studies suggest that nuclear lipids play epigenetics. Here, we discuss experimental methods lipid‐chromatin research, including biophysical, structural, approaches, pointing out strengths weaknesses. We take view have far more widespread impact on than currently acknowledged. This gap mostly due existing challenges study biology. Several new, interdisciplinary approaches discussed could aid elucidating roles gene expression.

Language: Английский

Recent Progress on Phase Separation of DNA‐Based System DOI
Mingyang Zhu,

Zhuang Cai,

Rui Gao

et al.

Macromolecular Rapid Communications, Journal Year: 2025, Volume and Issue: unknown

Published: April 7, 2025

Abstract Precise spatiotemporal regulation of intracellular processes has been shown to occur through phase separation. The resulting droplets and coacervates mediate critical biological functions. Although hundreds publications on this topic are generated every year, a systematic exposition DNA separation is still lacking. As highly charged polyelectrolyte, prone associative driven by the presence abundant components. DNA‐based have great potential for applications in diverse fields such as drug delivery, gene regulation, smart materials development. This perspective highlights mechanisms different substances proteins, polymers, cationic ligands, metal ions. functional characteristics corresponding products also discussed. Current challenges future directions field

Language: Английский

Citations

0
Biomolecular liquid‒liquid phase separation associated with repetitive genomic elements DOI
Sefan Asamitsu, Yuka W. Iwasaki

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

Published: April 23, 2025

Language: Английский

Citations

0
Solution AFM imaging and coarse-grained molecular modeling of yeast condensin structural variation coupled to the ATP hydrolysis cycle DOI Creative Commons
Hiroki Koide, Noriyuki Kodera, Shoji Takada

et al.

Journal of Molecular Biology, Journal Year: 2025, Volume and Issue: unknown, P. 169185 - 169185

Published: May 1, 2025

Condensin is a protein complex that regulates chromatin structural changes during mitosis. It varies the molecular conformation through ATP hydrolysis cycle and extrudes DNA loops into its ring-like structure as motor. contains Smc2 Smc4, in which coiled-coil arm tethers hinge head domains dimerizes at hinge. ATPs bind between heads, induce their engagement, are hydrolyzed to promote disengagement. Previously, we performed solution atomic force microscopy (AFM) imaging of yeast condensin holo-complex with conducted flexible fitting, obtaining open conformation. However, it has yet be clarified how opening/closing coupled cycle. In this study, AFM presence absence varying nucleotides, including AMP-PNP, ATPγS, ADP. Furthermore, dynamics simulations an Smc2/4 heterodimer selected best representing each image. Our results suggested engagement upon binding opening N-terminal region Brn1, one accessory subunits, re-associates after ADP release.

Language: Английский

Citations

0
Positive Selection Drives the Evolution of the Structural Maintenance of Chromosomes (SMC) Complexes DOI Open Access
Diego Forni, Alessandra Mozzi, Manuela Sironi

et al.

Genes, Journal Year: 2024, Volume and Issue: 15(9), P. 1159 - 1159

Published: Sept. 3, 2024

Structural Maintenance of Chromosomes (SMC) complexes are an evolutionary conserved protein family. In most eukaryotes, three SMC have been characterized, as follows: cohesin, condensin, and SMC5/6 complexes. These involved in a plethora functions, defects genes can lead to increased risk chromosomal abnormalities, infertility, cancer. To investigate the evolution complex mammals, we analyzed their selective patterns extended phylogeny. Signals positive selection were identified for condensin NCAPG, two (SMC5 NSMCE4A), all cohesin with almost exclusive meiotic expression (RAD21L1, REC8, SMC1B, STAG3). For latter, rates correlate during female meiosis, positively selected sites fall intrinsically disordered regions (IDRs). Our results support growing evidence that IDRs fast evolving, they likely contribute adaptation through modulation phase separation. We suggest natural signals may be result different pressures: host-pathogen arms race complexes, intragenomic conflict is similar described centromeres telomeres.

Language: Английский

Citations

1
PRC1 and CTCF-Mediated Transition from Poised to Active Chromatin Loops Drives Bivalent Gene Activation DOI Creative Commons
Aflah Hanafiah, Zhuangzhuang Geng, Tingting Liu

et al.

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

Published: Nov. 15, 2024

Polycomb Repressive Complex 1 (PRC1) and CCCTC-binding factor (CTCF) are critical regulators of 3D chromatin architecture that influence cellular transcriptional programs. Spatial structures comprise conserved compartments, topologically associating domains (TADs), dynamic, cell-type-specific loops. Although the role CTCF in organization is well-known, involvement PRC1 less understood. In this study, we identified an unexpected, essential for canonical Pcgf2-containing complex (cPRC1.2), a known repressor, activating bivalent genes during differentiation. Our Hi-C analysis revealed cPRC1.2 forms loops at promoters, rendering them silent yet poised activation. Using mouse embryonic stem cells (ESCs) with CRISPR/Cas9-mediated gene editing, found loss Pcgf2, though not affecting global level H2AK119ub1, disrupts these ESCs impairs induction crucial target necessary neuronal Furthermore, enrichment loop anchors group (PcG) bodies, nuclear foci concentrated its tethered domains, suggesting cooperatively shape structures. Through virtual 4C other genomic analyses, discovered establishing progenitor cell (NPC) identity involves switch from cPRC1.2-mediated to CTCF-mediated active loops, enabling expression lineage-specific factors. This study uncovers novel mechanism by which pre-formed maintain state subsequent activation, advancing our understanding controlling fate transitions.

Language: Английский

Citations

1
4D nucleome: dynamic three-dimensional genome organization over time DOI Creative Commons
Hyoung‐Pyo Kim

Experimental & Molecular Medicine, Journal Year: 2024, Volume and Issue: 56(4), P. 761 - 762

Published: April 25, 2024

Language: Английский

Citations

0
Nuclear lipids in chromatin regulation: Biological roles, experimental approaches and existing challenges DOI Creative Commons
Ahmed M. Sayed, Karthik Eswara, Kaian Teles

et al.

Biology of the Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 8, 2024

Abstract Lipids are crucial for various cellular functions. Besides the storage of energy equivalents, these include forming membrane bilayers and serving as signaling molecules. While significant progress has been made in comprehension molecular biology lipids, their functions cell nucleus remain poorly understood. The main role eukaryotic is to provide an environment regulation chromatin which a complex DNA, histones, associated proteins. Recent studies suggest that nuclear lipids play epigenetics. Here, we discuss experimental methods lipid‐chromatin research, including biophysical, structural, approaches, pointing out strengths weaknesses. We take view have far more widespread impact on than currently acknowledged. This gap mostly due existing challenges study biology. Several new, interdisciplinary approaches discussed could aid elucidating roles gene expression.

Language: Английский

Citations

0