Nuclear Structures and Their Emerging Roles in Cell Differentiation and Development DOI Creative Commons

Hye Young Ji

BMB Reports, Journal Year: 2024, Volume and Issue: 57(9), P. 381 - 387

Published: Aug. 22, 2024

The nucleus, a highly organized and dynamic organelle, plays crucial role in regulating cellular processes. During cell differentiation, profound changes occur gene expression, chromatin organization, nuclear morphology. This review explores the intricate relationship between architecture function, focusing on roles of lamina, pore complexes (NPCs), sub-nuclear bodies, scaffold. These components collectively maintain integrity, organize chromatin, interact with key regulatory factors. remodeling its interactions structures, epigenetic modifications work concert to modulate accessibility ensure precise spatiotemporal control expression. lamina stabilizes shape is associated inactive regions, while NPCs facilitate selective transport. Sub-nuclear bodies contribute genome organization regulation, often by influencing RNA processing. scaffold provides structural support, impacting 3D which for proper expression during differentiation. underscores significance guiding Further investigation into structure will deepen our understanding mechanisms governing fate determination. [BMB Reports 2024; 57(9): 381-387].

Language: Английский

Chromatin accessibility: methods, mechanisms, and biological insights DOI Creative Commons
Andrés Mansisidor, Viviana I. Risca

Nucleus, Journal Year: 2022, Volume and Issue: 13(1), P. 238 - 278

Published: Nov. 20, 2022

Access to DNA is a prerequisite the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and repair. How proteins regulate these function in context chromatin its dynamic architectures an intensive field study. Over past decade, genome-wide assays new imaging approaches have enabled greater understanding how access genome regulated by nucleosomes associated proteins. Additional mechanisms may control accessibility vivo compaction phase separation – are beginning be understood. Here, we review ongoing development measurements, summarize different molecular structural shape landscape, detail many important biological functions linked accessibility.

Language: Английский

Citations

73
Lamins: The backbone of the nucleocytoskeleton interface DOI Creative Commons

Joan M. Sobo,

Nicholas S. Alagna,

Sean X. Sun

et al.

Current Opinion in Cell Biology, Journal Year: 2024, Volume and Issue: 86, P. 102313 - 102313

Published: Jan. 22, 2024

Language: Английский

Citations

20
Physical Nature of Chromatin in the Nucleus DOI Open Access
Kazuhiro Maeshima, Shiori Iida, Sachiko Tamura

et al.

Cold Spring Harbor Perspectives in Biology, Journal Year: 2021, Volume and Issue: 13(5), P. a040675 - a040675

Published: April 5, 2021

Kazuhiro Maeshima1,2, Shiori Iida1,2 and Sachiko Tamura1 1Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan 2Department School Life Science, Sokendai (Graduate University for Advanced Studies), Correspondence: kmaeshim{at}nig.ac.jp

Language: Английский

Citations

62
3D chromatin architecture and transcription regulation in cancer DOI Creative Commons
Siwei Deng, Yuliang Feng, Siim Pauklin

et al.

Journal of Hematology & Oncology, Journal Year: 2022, Volume and Issue: 15(1)

Published: May 4, 2022

Abstract Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role developing abnormalities diseases cancer. This review discusses chromatin (topologically associating domain, lamina-associated enhancer–promoter interactions) corresponding structural protein elements mediating interactions [CCCTC-binding factor, polycomb group protein, cohesin, Brother of the Regulator Imprinted Sites (BORIS) protein] with highlight their associations We also summarise recent development technologies bioinformatics approaches to study gene expression regulation, including crosslinking proximity ligation methods bulk population (ChIA-PET HiChIP) or single-molecule resolution (ChIA-drop), other than ligation, GAM, SPRITE, super-resolution microscopy techniques.

Language: Английский

Citations

47
An oligodendrocyte silencer element underlies the pathogenic impact of lamin B1 structural variants DOI Creative Commons
Bruce Nmezi, Guillermo Rodríguez Bey, Talia DeFrancesco Oranburg

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 5, 2025

The role of non-coding regulatory elements and how they might contribute to tissue type specificity disease phenotypes is poorly understood. Autosomal Dominant Leukodystrophy (ADLD) a fatal, adult-onset, neurological disorder that characterized by extensive CNS demyelination. Most cases ADLD are caused tandem genomic duplications involving the lamin B1 gene (LMNB1) while small subset deletions upstream gene. Utilizing data from recently identified families carry LMNB1 but do not exhibit demyelination, patient tissues, CRISPR edited cell lines mouse models, we have silencer element lost in patients specifically targets expression oligodendrocytes. This consists CTCF binding sites mediate three-dimensional chromatin looping recruitment PRC2 transcriptional repressor complex. Loss identifies for causation. An oligodendrocyte-specific determines fatal widely expressed nuclear protein (Lamin B1) suggests

Language: Английский

Citations

1
Endothelial cytoskeleton in mechanotransduction and vascular diseases DOI

Linlu Jin,

Yixue Qin,

Yili Zhao

et al.

Journal of Biomechanics, Journal Year: 2025, Volume and Issue: 182, P. 112579 - 112579

Published: Feb. 9, 2025

Language: Английский

Citations

1
Choreography of lamina‐associated domains: structure meets dynamics DOI Open Access

Nicholas S. Alagna,

Tiera I. Thomas,

Katherine L. Wilson

et al.

FEBS Letters, Journal Year: 2023, Volume and Issue: 597(22), P. 2806 - 2822

Published: Nov. 1, 2023

Lamina‐associated domains are large regions of heterochromatin positioned at the nuclear periphery. These have been implicated in gene repression, especially context development. In mammals, LAD organization is dependent on lamins, inner membrane proteins, and chromatin state. addition, readers modifier proteins this organization, potentially serving as molecular tethers that interact with both envelope chromatin. More recent studies focused teasing apart rules govern dynamic how turn, relates to regulation overall 3D genome organization. This review highlights mammalian cells uncovering factors instruct choreography re‐organization, dynamics lamina, including interphase through mitotic exit, when re‐established, well intra‐LAD subdomain variations.

Language: Английский

Citations

15
Parallel Proteomic and Transcriptomic Microenvironment Mapping (μMap) of Nuclear Condensates in Living Cells DOI
Steve D. Knutson, Chenmengxiao Pan, Niels Bisballe

et al.

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 21, 2024

Cellular activity is spatially organized across different organelles. While several structures are well-characterized, many organelles have unknown roles. Profiling biomolecular composition key to understanding function but difficult achieve in the context of small, dynamic structures. Photoproximity labeling has emerged as a powerful tool for mapping these interaction networks, yet maximizing catalyst localization and reducing toxicity remains challenging live cell applications. Here, we disclose new intracellular photocatalyst with minimal cytotoxicity off-target binding, utilize this HaloTag-based microenvironment-mapping (μMap) catalog subnuclear condensates living cells. We also specifically develop novel RNA-focused workflow (μMap-seq) enable parallel transcriptomic proteomic profiling After validating accuracy our approach, generate spatial map nucleolus, nuclear lamina, Cajal bodies, paraspeckles, PML bodies. These results provide potential insights into RNA metabolism gene regulation while significantly expanding μMap platform improved live-cell proximity biological systems.

Language: Английский

Citations

5
Nuclear envelope budding and its cellular functions DOI Creative Commons
Katharina Keuenhof, Verena Kohler, Filomena Broeskamp

et al.

Nucleus, Journal Year: 2023, Volume and Issue: 14(1)

Published: Feb. 22, 2023

The nuclear pore complex (NPC) has long been assumed to be the sole route across envelope, and under normal homeostatic conditions it is indeed main mechanism of nucleo-cytoplasmic transport. However, also known that e.g. herpesviruses cross envelope utilizing a pathway entitled egress or envelopment/de-envelopment. Despite this, thread observations suggests mechanisms similar viral may transiently used in healthy cells. It since proposed like budding (NEB) can facilitate transport RNA granules, aggregated proteins, inner membrane mis-assembled NPCs. Herein, we will summarize roles NEB as physiological intrinsic cellular feature highlight many unanswered questions surrounding these intriguing events.

Language: Английский

Citations

12
SMAP3-ID for Identification of Endogenous Protein–Protein Interactions Reveals Regulation of Mitochondrial Activity by Lamins DOI Creative Commons
Julia T. Warren, Jian Wang,

Francis Dhoro

et al.

JACS Au, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 14, 2025

Proteins regulate biological functions through the formation of distinct protein complexes. Identification and characterization these protein–protein interactions are critical to deciphering their mechanism action. Different antibody-based or cross-linking-based methods have been developed identify interactions. However, require genetic engineering other means disrupt native environments. To circumvent this limitation, we introduce here SMAP3-ID (small-molecule-assisted identification proximity) method in cellular environment. This combines a selective ligand for binding interest photo-cross-linking, live-cell-compatible bioorthogonal click reaction with trifunctional chemical probe, final photo-cross-linking covalently capture interacting proteins. Using nuclear lamins as an example, identified numerous lamin interactors cells. Significantly, number mitochondrial enzymes novel A (LA) interactors. The between LA were further validated, which provides mechanistic insights underlying metabolic alterations caused by mutations LA. Furthermore, our previously described small-molecule LA, LBL1, also induced changes activity bioenergetic organization. We conclude that is potentially powerful generalizable

Language: Английский

Citations

0