Biology subjects

Ide, S.

Publications and source records attributed to Ide, S..

8 recordsLinked to original sources

bioRxiv2025

Liquid-like transcription condensates locally constrain chromatin in living human cells

The organization and dynamics of chromatin play important roles in transcriptional regulation. The transcription machinery is known to constrain chromatin dynamics. Recently, transcription condensates formed via liquid-liquid phase separation (LLPS) or other mechanisms have emerged as key regulators of gene expression. What is the physical nature of such condensates in the cell? Do they interact with and constrain chromatin? To address these questions, we focused on BRD4-NUT, a fusion oncoprotein found in NUT carcinoma. Using single-molecule dual-color imaging, we found that individual BRD4-NUT molecules diffuse within condensates like a viscous liquid in live human cells. Single-nucleosome imaging specific to euchromatin shows that these liquid-like condensates restrict the movement of chromatin through BRD4 bromodomain-dependent crosslinking of neighboring acetylated nucleosomes. Our findings uncover a previously unrecognized mechanism by which LLPS-based condensates modulate chromatin dynamics, suggesting that condensates contribute to genome regulation through physical, and not only biochemical, control.

cell biology↗

bioRxiv2025

Linker histone H1 functions as a liquid-like glue to organize chromatin in living human cells

Linker histone H1, the most abundant chromatin protein, condenses chromatin, modulates DNA transactions such as transcription and DNA replication/repair, and participates in differentiation, development and tumorigenesis. While recent studies indicate that nucleosomes are clustered as condensed chromatin domains in higher eukaryotic cells, how histone H1 mechanically condenses chromatin remains unclear. Here, using a combination of direct visualization of single-H1 molecules in living human cells and multiscale molecular dynamics simulations, we demonstrate that the majority of H1 behaves like a liquid inside chromatin domains, rather than binding stably to nucleosomes as suggested by the traditional model. H1 functions as a liquid-like "glue", mediating dynamic multivalent electrostatic interactions between nucleosomes within chromatin domains. Consistently, rapid-depletion of H1.2 leads to decondensed chromatin domains both in cells and in silico. Our findings suggest that the H1 "glue" condenses chromatin domains while keeping them fluid and accessible, thereby supporting essential DNA transactions.

cell biology↗

bioRxiv2024

Replication-dependent histone (Repli-Histo) labeling dissects the physical properties of euchromatin/heterochromatin in living human cells.

A string of nucleosomes, where genomic DNA is wrapped around histones, is organized in the cell as chromatin. Chromatin in the cell varies greatly, from euchromatin to heterochromatin, in its genome functions. It is important to understand how heterochromatin is physically different from euchromatin. However, their specific labeling methods in living cells are limited. To address this, we have developed replication-dependent histone labeling (Repli-Histo labeling) to label nucleosomes in euchromatin and heterochromatin based on DNA replication timing. We investigated local nucleosome motion in the four chromatin classes from euchromatin to heterochromatin of living human and mouse cells. We found that more euchromatic regions (earlier replicated regions) show greater nucleosome motion. Notably, the motion profile in each chromatin class persists throughout interphase. Genome chromatin is essentially replicated from regions with greater nucleosome motions, even though the replication timing program is perturbed. Our findings, combined with computational modeling, suggest that earlier replicated regions have more accessibility and local chromatin motion can be a major determinant of genome-wide replication timing.

cell biology↗

bioRxiv2024

PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing

BackgroundTracking of Insertions and DEletions (TIDE) analysis, which computationally deconvolves capillary sequencing data derived from the DNA of bulk or clonal cell populations to estimate the efficiency of targeted mutagenesis by programmable nucleases, has played a significant role in the field of genome editing. However, the detection range covered by conventional TIDE analysis is limited. Range extension for deconvolution is required to detect larger deletions and insertions (indels) derived from genome editing in TIDE analysis. However, extending the deconvolution range introduces uncertainty into the deconvolution process. Moreover, the accuracy and sensitivity of TIDE analysis tools for large deletions (>50 bp) remain poorly understood. ResultsIn this study, we introduced a new software called PtWAVE that can detect a wide range of indel sizes, up to 200 bp. PtWAVE also offers options for variable selection and fitting algorithms to prevent uncertainties in the model. We evaluated the performance of PtWAVE by using in vitro capillary sequencing data that mimicked DNA sequencing, including large deletions. Furthermore, we confirmed that PtWAVE can stably analyze trace sequencing data derived from actual genome-edited samples. ConclusionsPtWAVE demonstrated superior accuracy and sensitivity compared to the existing TIDE analysis tools for DNA samples, including large deletions. PtWAVE can accelerate genome editing applications in organisms and cell types in which large deletions often occur when programmable nucleases are applied.

molecular biology↗

bioRxiv2023

Orientation-Independent-DIC imaging reveals that a transient rise in macromolecular crowding contributes to mitotic chromosome condensation

Genomic information must be faithfully transmitted into two daughter cells during mitosis. To ensure the transmission process, interphase chromatin is further condensed into mitotic chromosomes. Although protein factors like condensins and topoisomerase II are involved in the assembly of mitotic chromosomes, the physical bases of the condensation process remain unclear. Depletion force/macromolecular crowding, an effective attractive force that arises between large structures in crowded environments around chromosomes, may contribute to the condensation process. To approach this issue, we investigated the "chromosome milieu" during mitosis of living human cells using orientation-independent-differential interference contrast (OI-DIC) module combined with a confocal laser scanning microscope, which is capable of precisely mapping optical path differences and estimating molecular densities. We found that the molecular density surrounding chromosomes increased with the progression from prometaphase to anaphase, concurring with chromosome condensation. However, the molecular density went down in telophase, when chromosome decondensation began. Changes in the molecular density around chromosomes by hypotonic or hypertonic treatment consistently altered the condensation levels of chromosomes. In vitro, native chromatin was converted into liquid droplets of chromatin in the presence of cations and a macromolecular crowder. Additional crowder made the chromatin droplets stiffer and more solid-like, with further condensation. These results suggest that a transient rise in depletion force, likely triggered by the relocation of macromolecules (proteins, RNAs and others) via nuclear envelope breakdown and also by a subsequent decrease in cell-volumes, contributes to mitotic chromosome condensation, shedding light on a new aspect of the condensation mechanism in living human cells. Significance StatementMitotic chromosome condensation is an essential process to transmit replicated chromosomes into two daughter cells during cell division. To study the underlying physical principles of this process, we focused on depletion force/macromolecular crowding, which is a force that attracts large structures in crowded cell environments. Using newly developed special light microscopy, which can image the molecular density of cellular environments, we found that crowding around chromosomes increases during cell division. In vitro, higher concentrations of macromolecules condense chromatin and make it stiffer and more solid-like. Our results suggest that the rise in depletion force renders chromosomes more rigid, ensuring accurate chromosome transmission during cell division.

cell biology↗

bioRxiv2022

A bug's tale: revealing the history, biogeography and ecological patterns of 500 years of insect introductions

The arrival of Europeans to the Americas triggered a massive exchange of organisms on a continental scale. This exchange was accelerated by the amazing increase in the movement of people and goods during the 20th century. In Chile, scientific and technical literature contains hundreds of records of exotic insect species in different parts of the territory, from the hyperarid Atacama Desert to the Magallanes Region. Here, we analyze the biological patterns obtained from the database of introductions of exotic insects to Chile from the European arrival to the present. Our task includes a review of old records in museums, libraries, collections, expedition records and catalogs. Almost 600 species of exotic insects have been reported in Chile. Introductions started at the very arrival of Europeans to the central valley of Chile and underwent a huge acceleration in the second half of the 20th century. The order Hemiptera was the most prevalent among introduced insects. Most species are linked to agriculture and forestry. Species are of Palearctic origin in more than 50% of the records. In terms of temporal trends, the rate of introduced species shows an abrupt increase at the beginning of the 1950s. This change may be associated with the strong development in agriculture and forestry in Chile after World War II and the increase in intercontinental air traffic. We believe that the understanding of past patterns of introductions is an important component in the design of current policies to minimize the impact of invasive insects.

ecology↗

bioRxiv2021

Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair

Overwhelming lipid peroxidation induces ferroptotic stress and ferroptosis, a non-apoptotic form of regulated cell death that has been implicated in maladaptive renal repair in mice and humans. Using single-cell transcriptomic and mouse genetic approaches, we show that proximal tubular (PT) cells develop a molecularly distinct, pro-inflammatory state following injury. While these inflammatory PT cells transiently appear after mild injury and return to their original state without inducing fibrosis, they accumulate and contribute to persistent inflammation after severe injury. This transient inflammatory PT state significantly downregulates glutathione metabolism genes, making them vulnerable to ferroptotic stress. Genetic induction of high ferroptotic stress in these cells after mild injury leads to the accumulation of the inflammatory PT cells, enhancing inflammation and fibrosis. Our study broadens the roles of ferroptotic stress from being a trigger of regulated cell death to include the promotion and accumulation of proinflammatory cells that underlie maladaptive repair.

cell biology↗

bioRxiv2019

Yolk-Sac-Derived Macrophages Progressively Expand in the Mouse Kidney with Age

Renal macrophages represent a highly heterogeneous and specialized population of myeloid cells with mixed developmental origins from the yolk-sac and hematopoietic stem cells (HSC). They promote both injury and repair by regulating inflammation, angiogenesis, and tissue remodeling. Recent reports highlight differential roles for ontogenically distinct renal macrophage populations in disease. However, little is known about how these populations change over time in normal, uninjured kidneys. Prior reports demonstrated a high proportion of HSC-derived macrophages in the young adult kidney. Unexpectedly, using genetic fate-mapping and parabiosis studies, we find that yolk-sac-derived macrophages progressively expand in number with age and become a major contributor to the renal macrophage population in older mice. This chronological shift in macrophage composition involves cellular proliferation and recruitment from circulating progenitors and may contribute to the distinct immune responses, limited reparative capacity, and increased disease susceptibility of kidneys in the elderly population.

immunology↗