Cited by Nuclear speckle biology: At the cross-roads of discovery and functional analysis

Liquid–Liquid Phase Separation in Chromatin DOI

Karsten Rippe

Cold Spring Harbor Perspectives in Biology, Journal Year: 2021, Volume and Issue: 14(2), P. a040683 - a040683

Published: June 14, 2021

Karsten Rippe Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120 Heidelberg, Germany Correspondence: Karsten.Rippe{at}dkfz.de

Language: Английский

Citations

110

Genome organization around nuclear speckles drives mRNA splicing efficiency DOI

Prashant Bhat,

Amy Chow,

Benjamin Emert

et al.

Nature, Journal Year: 2024, Volume and Issue: 629(8014), P. 1165 - 1173

Published: May 8, 2024

Language: Английский

Citations

Transcriptional condensates: a blessing or a curse for gene regulation? DOI

Martín Stortz,

Diego M. Presman, Valeria Levi

et al.

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: Feb. 16, 2024

Whether phase-separation is involved in the organization of transcriptional machinery and if it aids or inhibits process a matter intense debate. In this Mini Review, we will cover current knowledge regarding role condensates on gene expression regulation. We summarize latest discoveries relationship between condensate formation, genome organization, activity, focusing strengths weaknesses experimental approaches used to interrogate these aspects transcription living cells. Finally, discuss challenges for future research.

Language: Английский

Citations

Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus DOI

Léa Meneu, Christophe Chapard, Jacques Serizay

et al.

Science, Journal Year: 2025, Volume and Issue: 387(6734)

Published: Feb. 6, 2025

In eukaryotes, DNA-associated protein complexes coevolve with genomic sequences to orchestrate chromatin folding. We investigate the relationship between DNA sequence and spontaneous loading activity of components in absence coevolution. Using bacterial genomes integrated into Saccharomyces cerevisiae , which diverged from yeast more than 2 billion years ago, we show that nucleosomes, cohesins, associated transcriptional machinery can lead formation two different archetypes, one transcribed other silent, independently heterochromatin formation. These archetypes also form on eukaryotic exogenous sequences, depend composition, be predicted using neural networks trained native genome. They do not mix nucleus, leading a bipartite nuclear compartmentalization, reminiscent organization vertebrate nuclei.

Language: Английский

Citations

Nuclear speckles – a driving force in gene expression DOI

Gabriel P. Faber,

Shani Nadav-Eliyahu,

Yaron Shav‐Tal

et al.

Journal of Cell Science, Journal Year: 2022, Volume and Issue: 135(13)

Published: July 1, 2022

Nuclear speckles are dynamic membraneless bodies located in the cell nucleus. They harbor RNAs and proteins, many of which splicing factors, that together display complex biophysical properties dictating nuclear speckle formation maintenance. Although these were discovered decades ago, only recently has in-depth genomic analysis begun to unravel their essential functions modulation gene activity. Major advancements mapping techniques combined with microscopy approaches have enabled insights into roles may play enhancing expression, how positioning specific landmarks can regulate expression RNA processing. Some studies drawn a link between disease. Certain maladies either involve directly or dictate localization reorganization factors. This is most striking during viral infection, as viruses alter entire architecture highjack host machinery. As discussed this Review, represent fascinating target study not reveal links positioning, genome subcompartments activity, but also potential for therapeutics.

Language: Английский

Citations

High-resolution spatial multi-omics reveals cell-type specific nuclear compartments DOI

Yodai Takei, Yujing Yang, Jonathan A. White

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 9, 2023

The mammalian nucleus is compartmentalized by diverse subnuclear structures. These structures, marked nuclear bodies and histone modifications, are often cell-type specific affect gene regulation 3D genome organization

Language: Английский

Citations

True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin DOI

Márton Gelléri,

Shih‐Ya Chen,

Barbara Hübner

et al.

Cell Reports, Journal Year: 2023, Volume and Issue: 42(6), P. 112567 - 112567

Published: May 26, 2023

Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based fluorescence microscopy with conventional resolution, however, suggest only modest (∼2-10×) between the active nuclear compartment (ANC) inactive (INC). Here, we present maps landscapes true-to-scale densities, ranging from <5 >300 Mbp/μm3. Maps are generated human mouse cell nuclei single-molecule localization at ∼20 nm lateral ∼100 axial optical resolution supplemented by electron spectroscopic imaging. Microinjection fluorescent nanobeads sizes corresponding for transcription into living cells demonstrates movements within ANC exclusion INC.

Language: Английский

Citations

From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization DOI

Shuming Liu, Advait Athreya,

Zhuohan Lao

et al.

Annual Review of Biophysics, Journal Year: 2024, Volume and Issue: 53(1), P. 221 - 245

Published: Feb. 12, 2024

Chromatin organization plays a critical role in cellular function by regulating access to genetic information. However, understanding chromatin folding is challenging due its complex, multiscale nature. Significant progress has been made studying vitro systems, uncovering the structure of individual nucleosomes and their arrays, elucidating physicochemical forces stabilizing these structures. Additionally, remarkable advancements have achieved characterizing vivo, particularly at whole-chromosome level, revealing important features such as loops, topologically associating domains, nuclear compartments. bridging gap between vivo studies remains challenging. The resemblance conformations relevance internucleosomal interactions for are subjects debate. This article reviews experimental computational conducted various length scales, highlighting significance intrinsic roles vivo.

Language: Английский

Citations

Evolution and regulation of animal sex chromosomes DOI

Zexian Zhu, Lubna Younas, Qi Zhou

et al.

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

Published: July 18, 2024

Language: Английский

Citations

Nanometer condensate organization in live cells derived from partitioning measurements DOI

Christina M. Dollinger, Evdokiia Potolitsyna, Aaron J. Martin

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 27, 2025

Biomolecules associate, forming condensates that house essential biochemical processes, including ribosome biogenesis. Unraveling how shape macromolecular assembly and transport requires cellular measurements of nanoscale structure. Here, we determine the organization around between specific proteins at nanometer resolution within condensates, deploying thermodynamic principles to interpret partitioning designed protein probes. When applied nucleolus as a proof principle, data reveals considerable inhomogeneity, deviating from expected liquid-like phase. The inhomogeneity can be attributed biogenesis, with local meshwork weakening biogenesis progresses, facilitating transport. Beyond introducing an innovative modality for biophysical interrogation, our results suggest are far uniform, simple liquids, property conjecture enables regulation proofreading.

Language: Английский

Citations