Phase separation in genome organization across evolution

M Feric, T Misteli - Trends in cell biology, 2021 - cell.com
Phase separation is emerging as a paradigm to explain the self-assembly and organization
of membraneless bodies in the cell. Recent advances show that this principle also extends …

Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom

HM Amemiya, J Schroeder, L Freddolino - Transcription, 2021 - Taylor & Francis
Genome architecture has proven to be critical in determining gene regulation across almost
all domains of life. While many of the key components and mechanisms of eukaryotic …

WHIRLIES are multifunctional DNA-binding proteins with impact on plant development and stress resistance

K Krupinska, C Desel, S Frank, G Hensel - Frontiers in Plant Science, 2022 - frontiersin.org
WHIRLIES are plant-specific proteins binding to DNA in plastids, mitochondria, and nucleus.
They have been identified as significant components of nucleoids in the organelles where …

The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in …

V Norris, C Kayser, G Muskhelishvili… - FEMS Microbiology …, 2023 - academic.oup.com
How to adapt to a changing environment is a fundamental, recurrent problem confronting
cells. One solution is for cells to organize their constituents into a limited number of spatially …

Spatial features and functional implications of plant 3D genome organization

K Domb, N Wang, G Hummel… - Annual Review of Plant …, 2022 - annualreviews.org
The advent of high-throughput sequencing-based methods for chromatin conformation,
accessibility, and immunoprecipitation assays has been a turning point in 3D genomics …

Soft X‐ray tomograms provide a structural basis for whole‐cell modeling

V Loconte, JH Chen, B Vanslembrouck… - The FASEB …, 2023 - Wiley Online Library
Develo** in silico models that accurately reflect a whole, functional cell is an ongoing
challenge in biology. Current efforts bring together mathematical models, probabilistic …

Self‐assembly of multi‐component mitochondrial nucleoids via phase separation

M Feric, TG Demarest, J Tian, DL Croteau… - The EMBO …, 2021 - embopress.org
Mitochondria contain an autonomous and spatially segregated genome. The organizational
unit of their genome is the nucleoid, which consists of mitochondrial DNA (mtDNA) and …

Spatial rearrangement of the Streptomyces venezuelae linear chromosome during sporogenic development

MJ Szafran, T Małecki, A Strzałka… - Nature …, 2021 - nature.com
Bacteria of the genus Streptomyces have a linear chromosome, with a core region and two
'arms'. During their complex life cycle, these bacteria develop multi-genomic hyphae that …

Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity

SB Yoshua, GD Watson, JAL Howard… - Nucleic Acids …, 2021 - academic.oup.com
Nucleoid-associated proteins (NAPs) are crucial in organizing prokaryotic DNA and
regulating genes. Vital to these activities are complex nucleoprotein structures, however …

Non‐specific and specific DNA binding modes of bacterial histone, HU, separately regulate distinct physiological processes through different mechanisms

SC Verma, A Harned, K Narayan… - Molecular …, 2023 - Wiley Online Library
The histone‐like protein HU plays a diverse role in bacterial physiology from the
maintenance of chromosome structure to the regulation of gene transcription. HU binds DNA …