Mechanisms of cellular mRNA transcript homeostasis

S Berry, L Pelkmans - Trends in Cell Biology, 2022 - cell.com
For most genes, mRNA transcript abundance scales with cell size to ensure a constant
concentration. Scaling of mRNA synthesis rates with cell size plays an important role, with …

Multiplex protein imaging in tumour biology

N de Souza, S Zhao, B Bodenmiller - Nature Reviews Cancer, 2024 - nature.com
Tissue imaging has become much more colourful in the past decade. Advances in both
experimental and analytical methods now make it possible to image protein markers in …

Pooled multicolour tagging for visualizing subcellular protein dynamics

A Reicher, J Reiniš, M Ciobanu, P Růžička… - Nature Cell …, 2024 - nature.com
Imaging-based methods are widely used for studying the subcellular localization of proteins
in living cells. While routine for individual proteins, global monitoring of protein dynamics …

Dynamic label-free analysis of SARS-CoV-2 infection reveals virus-induced subcellular remodeling

N Saunders, B Monel, N Cayet, L Archetti… - Nature …, 2024 - nature.com
Assessing the impact of SARS-CoV-2 on organelle dynamics allows a better understanding
of the mechanisms of viral replication. We combine label-free holotomographic microscopy …

Graph Fourier transform for spatial omics representation and analyses of complex organs

Y Chang, J Liu, Y Jiang, A Ma, YY Yeo, Q Guo… - Nature …, 2024 - nature.com
Spatial omics technologies decipher functional components of complex organs at cellular
and subcellular resolutions. We introduce Spatial Graph Fourier Transform (SpaGFT) and …

Bento: a toolkit for subcellular analysis of spatial transcriptomics data

CK Mah, N Ahmed, NA Lopez, DC Lam, A Pong… - Genome Biology, 2024 - Springer
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 spatial …

[HTML][HTML] Global control of RNA polymerase II

A Gillis, S Berry - Biochimica et Biophysica Acta (BBA)-Gene Regulatory …, 2024 - Elsevier
Abstract RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing
all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on …

Recent advancements in subcellular proteomics: growing impact of organellar protein niches on the understanding of cell biology

V Bhushan, A Nita-Lazar - Journal of Proteome Research, 2024 - ACS Publications
The mammalian cell is a complex entity, with membrane-bound and membrane-less
organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches …

Differential labelling of human sub-cellular compartments with fluorescent dye esters and expansion microscopy

TMD Sheard, TB Shakespeare, RS Seehra… - Nanoscale, 2023 - pubs.rsc.org
Amine-reactive esters of aromatic fluorescent dyes are emerging as imaging probes for
nondescript staining of cellular and tissue architectures. We characterised the staining …

MIM-CyCIF: masked imaging modeling for enhancing cyclic immunofluorescence (CyCIF) with panel reduction and imputation

Z Sims, GB Mills, YH Chang - Communications Biology, 2024 - nature.com
Abstract Cyclic Immunofluorescence (CyCIF) can quantify multiple biomarkers, but panel
capacity is limited by technical challenges. We propose a computational panel reduction …