The emerging landscape of spatial profiling technologies

JR Moffitt, E Lundberg, H Heyn - Nature Reviews Genetics, 2022 - nature.com
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein
profiling methods as a major pillar for cellular atlas building of complex samples, from …

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 …

PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency

P Dobrinić, AT Szczurek, RJ Klose - Nature structural & molecular …, 2021 - nature.com
The Polycomb repressive system plays a fundamental role in controlling gene expression
during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 …

[HTML][HTML] A guidebook of spatial transcriptomic technologies, data resources and analysis approaches

L Yue, F Liu, J Hu, P Yang, Y Wang, J Dong… - Computational and …, 2023 - Elsevier
Advances in transcriptomic technologies have deepened our understanding of the cellular
gene expression programs of multicellular organisms and provided a theoretical basis for …

Making use of noise in biological systems

Y Ilan - Progress in biophysics and molecular biology, 2023 - Elsevier
Disorder and noise are inherent in biological systems. They are required to provide systems
with the advantages required for proper functioning. Noise is a part of the flexibility and …

Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions

X Fu, HP Patel, S Coppola, L Xu, Z Cao, TL Lenstra… - Elife, 2022 - elifesciences.org
Transcriptional rates are often estimated by fitting the distribution of mature mRNA numbers
measured using smFISH (single molecule fluorescence in situ hybridization) with the …

Reduction in gene expression noise by targeted increase in accessibility at gene loci

LTCR Fraser, RJ Dikdan, S Dey… - Proceedings of the …, 2021 - National Acad Sciences
Many eukaryotic genes are expressed in randomly initiated bursts that are punctuated by
periods of quiescence. Here, we show that the intermittent access of the promoters to …

[HTML][HTML] A guide to ERK dynamics, part 2: downstream decoding

A Ram, D Murphy, N DeCuzzi, M Patankar… - Biochemical …, 2023 - portlandpress.com
Signaling by the extracellular signal-regulated kinase (ERK) pathway controls many cellular
processes, including cell division, death, and differentiation. In this second installment of a …

Accurate cell tracking and lineage construction in live-cell imaging experiments with deep learning

E Moen, E Borba, G Miller, M Schwartz, D Bannon… - Biorxiv, 2019 - biorxiv.org
Live-cell imaging experiments have opened an exciting window into the behavior of living
systems. While these experiments can produce rich data, the computational analysis of …

[HTML][HTML] Coupling gene expression dynamics to cell size dynamics and cell cycle events: Exact and approximate solutions of the extended telegraph model

C Jia, R Grima - Iscience, 2023 - cell.com
The standard model describing the fluctuations of mRNA numbers in single cells is the
telegraph model which includes synthesis and degradation of mRNA, and switching of the …