Transcription activator WCC recruits deacetylase HDA3 to control transcription dynamics and bursting in Neurospora

M Oehler, L Geisser, ACR Diernfellner, M Brunner - Science Advances, 2023 - science.org
RNA polymerase II initiates transcription either randomly or in bursts. We examined the light-
dependent transcriptional activator White Collar Complex (WCC) of Neurospora to …

Living in a noisy world—origins of gene expression noise and its impact on cellular decision‐making

S Pal, R Dhar - FEBS letters, 2024 - Wiley Online Library
The expression level of a gene can vary between genetically identical cells under the same
environmental condition—a phenomenon referred to as gene expression noise. Several …

Cis-regulatory control of transcriptional timing and noise in response to estrogen

M Ginley-Hidinger, H Abewe, K Osborne, A Richey… - Cell Genomics, 2024 - cell.com
Cis-regulatory elements control transcription levels, temporal dynamics, and cell-cell
variation or transcriptional noise. However, the combination of regulatory features that …

[HTML][HTML] Evaluating single-cell variability in proteasomal decay.

S Das, A Singh, P Shah - bioRxiv, 2023 - ncbi.nlm.nih.gov
Gene expression is a stochastic process that leads to variability in mRNA and protein
abundances even within an isogenic population of cells grown in the same environment …

NetREm Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation

S Khullar, X Huang, R Ramesh, J Svaren, D Wang - bioRxiv, 2023 - biorxiv.org
Transcription factor (TF) coordination plays a key role in target gene (TG) regulation via
protein-protein interactions (PPIs) and DNA co-binding to regulatory elements. Single-cell …

Capturing statistical fluctuations in gene expression activity using discrete stochastic systems

Z Vahdat, S Rezaee, A Singh - IFAC-PapersOnLine, 2024 - Elsevier
We present a discrete-event system formalism to capture experimentally observed activity of
genes in single cells, where a gene can stochastically switch between an active state …

[HTML][HTML] Reverse tracking from drug-induced transcriptomes through multilayer molecular networks reveals hidden drug targets

G Kim, D Lee - Computers in Biology and Medicine, 2023 - Elsevier
Identifying molecular targets of a drug is an essential process for drug discovery and
development. The recent in-silico approaches are usually based on the structure information …

Molecular Sequestration Enhances Precision in Timing of Intracellular Events

K Biswas, S Dey, A Singh - bioRxiv, 2024 - biorxiv.org
Expressed gene products often interact ubiquitously with binding sites at nucleic acids and
macromolecular complexes, known as decoys. Binding of transcription factors (TFs) to …

Multimodal screen reveals noise regulatory proteins

O Garcia-Blay, X Hu, CL Wassermann, T van Bokhoven… - bioRxiv, 2024 - biorxiv.org
Gene-expression noise can influence cell-fate choices across pathology and physiology.
However, a crucial question persists: do regulatory proteins or pathways exist that control …

Ribosome demand links transcriptional bursts to protein expression noise

S Pal, U Ray, R Dhar - bioRxiv, 2023 - biorxiv.org
Stochastic variation in protein expression generates phenotypic heterogeneity in a cell
population, and has important role in antibiotic persistence, mutation penetrance, cancer …