Unravelling the role of epigenetics in reproductive adaptations to early-life environment

B Bar-Sadeh, S Rudnizky, L Pnueli… - Nature Reviews …, 2020 - nature.com
Reproductive function adjusts in response to environmental conditions in order to optimize
success. In humans, this plasticity includes age of pubertal onset, hormone levels and age at …

Structural dynamics in chromatin unraveling by pioneer transcription factors

A Orsetti, D van Oosten, RG Vasarhelyi… - Biophysical …, 2024 - Springer
Pioneer transcription factors are proteins with a dual function. First, they regulate
transcription by binding to nucleosome-free DNA regulatory elements. Second, they bind to …

Model-driven generation of artificial yeast promoters

BJ Kotopka, CD Smolke - Nature communications, 2020 - nature.com
Promoters play a central role in controlling gene regulation; however, a small set of
promoters is used for most genetic construct design in the yeast Saccharomyces cerevisiae …

The complex architecture of p53 binding sites

A Senitzki, J Safieh, V Sharma… - Nucleic Acids …, 2021 - academic.oup.com
Sequence-specific protein-DNA interactions are at the heart of the response of the tumor-
suppressor p53 to numerous physiological and stress-related signals. Large variability has …

The development of single molecule force spectroscopy: from polymer biophysics to molecular machines

C Bustamante, S Yan - Quarterly Reviews of Biophysics, 2022 - cambridge.org
The advent of single-molecule force spectroscopy represents the introduction of forces,
torques, and displacements as controlled variables in biochemistry. These methods afford …

The base pair-scale diffusion of nucleosomes modulates binding of transcription factors

S Rudnizky, H Khamis, O Malik… - Proceedings of the …, 2019 - National Acad Sciences
The structure of promoter chromatin determines the ability of transcription factors (TFs) to
bind to DNA and therefore has a profound effect on the expression levels of genes …

Extended and dynamic linker histone-DNA Interactions control chromatosome compaction

S Rudnizky, H Khamis, Y Ginosar, E Goren, P Melamed… - Molecular Cell, 2021 - cell.com
Chromatosomes play a fundamental role in chromatin regulation, but a detailed
understanding of their structure is lacking, partially due to their complex dynamics. Using …

An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context

T Refael, M Sudman, G Golan, L Pnueli, S Naik… - Cellular and Molecular …, 2024 - Springer
Genome-wide studies have demonstrated regulatory roles for diverse non-coding elements,
but their precise and interrelated functions have often remained enigmatic. Addressing the …

Investigation of metal ion binding biomolecules one molecule at a time

M de la Torre, A Pomorski - Frontiers in Chemistry, 2024 - frontiersin.org
Metal ions can perform multiple roles ranging from regulatory to structural and are crucial for
cell function. While some metal ions like Na+ are ubiquitously present at high …

Dynamics and inhibition of MLL1 CXXC domain on DNA revealed by single-molecule quantification

L Liang, K Ma, Z Wang, R Janissen, Z Yu - Biophysical Journal, 2021 - cell.com
CpG islands recruit MLL1 via the CXXC domain to modulate chromatin structure and
regulate gene expression. The amino acid motif of CXXC also plays a pivotal role in MLL1's …