Timeless noncoding DNA contains cell-type preferential enhancers important for proper Drosophila circadian regulation DOI Creative Commons
Dingbang Ma,

Pranav Ojha,

Albert D. Yu

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(15)

Published: April 3, 2024

To address the contribution of transcriptional regulation to Drosophila clock gene expression and behavior, we generated a series CRISPR-mediated deletions within two regions circadian timeless ( tim ), an intronic E-box region upstream that are both recognized by key transcription factor Clock (Clk) its heterodimeric partner Cycle. The but not deletion dramatically impact in fly heads; biggest reduces peak RNA levels cycling amplitude about 15% normal, there similar effects on protein (TIM). other genes is also strongly reduced, these cases due increases trough levels. These data underscore important enhancer TIM repression heads. Surprisingly, neurons only modestly affected similarly region. This distinction between glia paralleled enhanced accessibility neurons. distinctive feature chromatin was revealed ATAC-seq (assay for transposase-accessible with sequencing) assays purified as well cell type–specific explains resilience neuron behavior otherwise more prominent

Language: Английский

Computational solutions for spatial transcriptomics DOI Creative Commons
Iivari Kleino,

Paulina Frolovaitė,

Tomi Suomi

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2022, Volume and Issue: 20, P. 4870 - 4884

Published: Jan. 1, 2022

Transcriptome level expression data connected to the spatial organization of cells and molecules would allow a comprehensive understanding how gene is structure function in biological systems. The transcriptomics platforms may soon provide such information. However, current still lack resolution, capture only fraction transcriptome heterogeneity, or throughput for large scale studies. strengths weaknesses ST computational solutions need be taken into account when planning basis analysis developed single-cell RNA-sequencing data, with advancements taking connectedness transcriptomes. scRNA-seq tools are modified new like deep learning-based joint expression, spatial, image extract information spatially resolved can reveal remarkable insights patterns cell signaling, type variations connection type-specific signaling complex tissues. This review covers topics that help choosing platform research. We focus on currently available methods their limitations. Of solutions, we an overview steps used analysis. compatibility types provided by frameworks summarized.

Language: Английский

Citations

86
Engineering RNA export for measurement and manipulation of living cells DOI Creative Commons
Felix Horns,

Joe A. Martinez,

Chengcheng Fan

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(17), P. 3642 - 3658.e32

Published: July 11, 2023

A system for programmable export of RNA molecules from living cells would enable both non-destructive monitoring cell dynamics and engineering capable delivering executable programs to other cells. We developed genetically encoded cellular exporters, inspired by viruses, that efficiently package secrete cargo mammalian within protective nanoparticles. Exporting sequencing barcodes enabled population with clonal resolution. Further, incorporating fusogens into the nanoparticles, we demonstrated delivery, expression, functional activity exported mRNA in recipient term these systems COURIER (controlled output uptake interrogation, regulation). enables measurement establishes a foundation hybrid gene therapies based on cell-to-cell delivery RNA.

Language: Английский

Citations

47
Bento: a toolkit for subcellular analysis of spatial transcriptomics data DOI Creative Commons
Clarence K. Mah, Noorsher Ahmed, Nicole A. Lopez

et al.

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: April 2, 2024

Abstract The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell–cell interactions, and expression patterns, they are limited to the multicellular scale. We present Bento, Python toolkit that takes advantage single-molecule information enable analysis at subcellular Bento ingests molecular coordinates segmentation boundaries perform three analyses: defining domains, annotating localization quantifying gene–gene colocalization. demonstrate MERFISH, seqFISH + , Molecular Cartography, Xenium datasets. part open-source Scverse ecosystem, enabling integration with other single-cell tools.

Language: Английский

Citations

25
RS-FISH: precise, interactive, fast, and scalable FISH spot detection DOI Creative Commons
Ella Bahry, Laura Breimann, Marwan Zouinkhi

et al.

Nature Methods, Journal Year: 2022, Volume and Issue: 19(12), P. 1563 - 1567

Published: Nov. 17, 2022

Fluorescent in-situ hybridization (FISH)-based methods extract spatially resolved genetic and epigenetic information from biological samples by detecting fluorescent spots in microscopy images, an often challenging task. We present Radial Symmetry-FISH (RS-FISH), accurate, fast, user-friendly software for spot detection two- three-dimensional images. RS-FISH offers interactive parameter tuning readily scales to large datasets image volumes of cleared or expanded using distributed processing on workstations, clusters, the cloud. maintains high accuracy low localization error across a wide range signal-to-noise ratios, key feature single-molecule FISH, spatial transcriptomics, genomics applications.

Language: Английский

Citations

52
RNA at the surface of phase-separated condensates impacts their size and number DOI Creative Commons
Audrey Cochard,

Marina Garcia-Jove Navarro,

Leonard Piroska

et al.

Biophysical Journal, Journal Year: 2022, Volume and Issue: 121(9), P. 1675 - 1690

Published: March 29, 2022

Language: Английский

Citations

42
An interactive murine single-cell atlas of the lung responses to radiation injury DOI Creative Commons
Sandra Curras-Alonso, Juliette Soulier, Thomas Defard

et al.

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

Published: April 28, 2023

Abstract Radiation Induced Lung Injury (RILI) is one of the main limiting factors thorax irradiation, which can induce acute pneumonitis as well pulmonary fibrosis, latter being a life-threatening condition. The order cellular and molecular events in progression towards fibrosis key to physiopathogenesis disease, yet their coordination space time remains largely unexplored. Here, we present an interactive murine single cell atlas lung response generated from C57BL6/J female mice. This tool opens door for exploration spatio-temporal dynamics mechanisms that lead radiation-induced fibrosis. It depicts with unprecedented detail type-specific responses associated either regeneration or failure thereof. A better understanding leading will help finding new therapeutic options could improve patients’ quality life.

Language: Английский

Citations

38
Dynamical control enables the formation of demixed biomolecular condensates DOI Creative Commons
Andrew Z. Lin, Kiersten M. Ruff, Furqan Dar

et al.

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

Published: Nov. 24, 2023

Abstract Cellular matter can be organized into compositionally distinct biomolecular condensates. For example, in Ashbya gossypii , the RNA-binding protein Whi3 forms condensates with different RNA molecules. Using criteria derived from a physical framework for explaining how form spontaneously via thermodynamic considerations, we find that vitro mainly heterotypic interactions binary mixtures of and RNA. However, within these condensates, molecules become dynamically arrested. As result, ternary systems, simultaneous additions pairs lead to well-mixed whereas delayed addition an component results compositional distinctness. Therefore, identities achieved dynamical control, being driven, at least partially, by arrest Finally, show synchronizing production RNAs leads more well-mixed, as opposed vivo.

Language: Английский

Citations

35
SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9 DOI Creative Commons
Nora Schmidt, Sabina Ganskih, Yuanjie Wei

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(22), P. 4834 - 4850.e23

Published: Oct. 1, 2023

Regulation of viral RNA biogenesis is fundamental to productive SARS-CoV-2 infection. To characterize host RNA-binding proteins (RBPs) involved in this process, we biochemically identified bound genomic and subgenomic RNAs. We find that the protein SND1 binds 5' end negative-sense required for synthesis. SND1-depleted cells form smaller replication organelles display diminished virus growth kinetics. discover NSP9, a RBP direct interaction partner, covalently linked ends positive- RNAs produced during These linkages occur at replication-transcription initiation sites, consistent with NSP9 priming Mechanistically, remodels occupancy alters covalent linkage initiating nucleotides RNA. Our findings implicate synthesis unravel an unsuspected role cellular orchestrating production.

Language: Английский

Citations

29
In vivo interaction screening reveals liver-derived constraints to metastasis DOI Creative Commons
Costanza Borrelli, Morgan Roberts, Davide Eletto

et al.

Nature, Journal Year: 2024, Volume and Issue: 632(8024), P. 411 - 418

Published: July 24, 2024

It is estimated that only 0.02% of disseminated tumour cells are able to seed overt metastases

Language: Английский

Citations

15
An iron rheostat controls hematopoietic stem cell fate DOI Creative Commons

Yun-Ruei Kao,

Jiahao Chen, Rajni Kumari

et al.

Cell stem cell, Journal Year: 2024, Volume and Issue: 31(3), P. 378 - 397.e12

Published: Feb. 22, 2024

Mechanisms governing the maintenance of blood-producing hematopoietic stem and multipotent progenitor cells (HSPCs) are incompletely understood, particularly those regulating fate, ensuring long-term maintenance, preventing aging-associated cell dysfunction. We uncovered a role for transitory free cytoplasmic iron as rheostat adult fate control. found that HSPCs harbor comparatively small amounts show activation conserved molecular response to limited iron-particularly during mitosis. To study functional consequences restriction, we developed models allowing transient bioavailability limitation combined single-molecule RNA quantification, metabolomics, single-cell transcriptomic analyses with studies. Our data reveal triggers coordinated metabolic epigenetic events, establishing stemness-conferring gene regulation. Notably, find loading reversibly attenuates iron-dependent control, explicating intervention strategies dysfunctional aged cells.

Language: Английский

Citations

12