The epigenetic basis of cellular heterogeneity

B Carter, K Zhao - Nature Reviews Genetics, 2021 - nature.com
Single-cell sequencing-based methods for profiling gene transcript levels have revealed
substantial heterogeneity in expression levels among morphologically indistinguishable …

Intratumoral heterogeneity: more than just mutations

K Hinohara, K Polyak - Trends in cell biology, 2019 - cell.com
Most human tumors are composed of genetically and phenotypically heterogeneous cancer
cell populations, which poses a major challenge for the clinical management of cancer …

RNA velocity unraveled

G Gorin, M Fang, T Chari, L Pachter - PLOS Computational …, 2022 - journals.plos.org
We perform a thorough analysis of RNA velocity methods, with a view towards
understanding the suitability of the various assumptions underlying popular …

Genomic encoding of transcriptional burst kinetics

AJM Larsson, P Johnsson, M Hagemann-Jensen… - Nature, 2019 - nature.com
Mammalian gene expression is inherently stochastic,, and results in discrete bursts of RNA
molecules that are synthesized from each allele,,,–. Although transcription is known to be …

The missing link between genetic association and regulatory function

NJ Connally, S Nazeen, D Lee, H Shi… - Elife, 2022 - elifesciences.org
The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is
widely assumed that such alleles exert small regulatory effects on the expression of cis …

A growing toolbox to image gene expression in single cells: sensitive approaches for demanding challenges

X Pichon, M Lagha, F Mueller, E Bertrand - Molecular cell, 2018 - cell.com
The spatiotemporal regulation of gene expression is key to many biological processes.
Recent imaging approaches opened exciting perspectives for understanding the intricate …

Modulation of transcriptional burst frequency by histone acetylation

D Nicolas, B Zoller, DM Suter… - Proceedings of the …, 2018 - National Acad Sciences
Many mammalian genes are transcribed during short bursts of variable frequencies and
sizes that substantially contribute to cell-to-cell variability. However, which molecular …

An optogenetic platform for real-time, single-cell interrogation of stochastic transcriptional regulation

M Rullan, D Benzinger, GW Schmidt, A Milias-Argeitis… - Molecular cell, 2018 - cell.com
Transcription is a highly regulated and inherently stochastic process. The complexity of
signal transduction and gene regulation makes it challenging to analyze how the dynamic …

Spatial organization of transcribed eukaryotic genes

S Leidescher, J Ribisel, S Ullrich, Y Feodorova… - Nature cell …, 2022 - nature.com
Despite the well-established role of nuclear organization in the regulation of gene
expression, little is known about the reverse: how transcription shapes the spatial …

BurstDECONV: a signal deconvolution method to uncover mechanisms of transcriptional bursting in live cells

M Douaihy, R Topno, M Lagha, E Bertrand… - Nucleic Acids …, 2023 - academic.oup.com
Monitoring transcription in living cells gives access to the dynamics of this complex
fundamental process. It reveals that transcription is discontinuous, whereby active periods …