Cotranslational mechanisms of protein biogenesis and complex assembly in eukaryotes

F Morales-Polanco, JH Lee… - Annual review of …, 2022 - annualreviews.org
The formation of protein complexes is crucial to most biological functions. The cellular
mechanisms governing protein complex biogenesis are not yet well understood, but some …

[HTML][HTML] Regulation of gene expression via translational buffering

EP Kusnadi, C Timpone, I Topisirovic, O Larsson… - … et Biophysica Acta (BBA …, 2022 - Elsevier
Translation of an mRNA represents a critical step during the expression of protein-coding
genes. As mechanisms governing post-transcriptional regulation of gene expression are …

Cohesin prevents cross-domain gene coactivation

P Dong, S Zhang, V Gandin, L Xie, L Wang… - Nature Genetics, 2024 - nature.com
The contrast between the disruption of genome topology after cohesin loss and the lack of
downstream gene expression changes instigates intense debates regarding the structure …

Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts

D Ramsköld, GJ Hendriks, AJM Larsson, JV Mayr… - Nature Cell …, 2024 - nature.com
Analyses of transcriptional bursting from single-cell RNA-sequencing data have revealed
patterns of variation and regulation in the kinetic parameters that could be inferred. Here we …

3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network

P Trzaskoma, SK Jung, A Pękowska, CH Bohrer… - Science …, 2024 - science.org
Discontinuous transcription is evolutionarily conserved and a fundamental feature of gene
regulation; yet, the exact mechanisms underlying transcriptional bursting are unresolved …

Synthetic analysis of chromatin tracing and live-cell imaging indicates pervasive spatial coupling between genes

CH Bohrer, DR Larson - Elife, 2023 - elifesciences.org
The role of the spatial organization of chromosomes in directing transcription remains an
outstanding question in gene regulation. Here, we analyze two recent single-cell imaging …

Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome

Y He, Y Xue, J Wang, Y Huang, L Liu, Y Huang… - Genome …, 2023 - genome.cshlp.org
The interactome networks at the DNA, RNA, and protein levels are crucial for cellular
functions, and the diverse variations of these networks are heavily involved in the …

Regulatory mechanisms ensuring coordinated expression of functionally related genes

OQH Zinani, K Keseroğlu, EM Özbudak - Trends in Genetics, 2022 - cell.com
Coordinated spatiotemporal expression of large sets of genes is required for the
development and homeostasis of organisms. To achieve this goal, organisms use myriad …

Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis

D M. Ribeiro, C Ziyani, O Delaneau - Communications biology, 2022 - nature.com
Most human genes are co-expressed with a nearby gene. Previous studies have revealed
this local gene co-expression to be widespread across chromosomes and across dozens of …

Genes enriched in A/T-ending codons are co-regulated and conserved across mammals

H Benisty, X Hernandez-Alias, M Weber… - Cell Systems, 2023 - cell.com
Codon usage influences gene expression distinctly depending on the cell context. Yet, the
importance of codon bias in the simultaneous turnover of specific groups of protein-coding …