Structures and consequences of pioneer factor binding to nucleosomes
E Luzete-Monteiro, KS Zaret - Current opinion in structural biology, 2022 - Elsevier
Pioneer transcription factors are able to bind a partially exposed motif on the surface of a
nucleosome, enabling the proteins to target sites in silent regions of chromatin that have …
nucleosome, enabling the proteins to target sites in silent regions of chromatin that have …
Genome modeling: from chromatin fibers to genes
The intricacies of the 3D hierarchical organization of the genome have been approached by
many creative modeling studies. The specific model/simulation technique combination …
many creative modeling studies. The specific model/simulation technique combination …
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
Residue-level coarse-grained (CG) models have become one of the most popular tools in
biomolecular simulations in the trade-off between modeling accuracy and computational …
biomolecular simulations in the trade-off between modeling accuracy and computational …
[HTML][HTML] Multiscale modeling of genome organization with maximum entropy optimization
ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …
role in all DNA-templated processes, including gene transcription, gene regulation, and …
Structural mechanism of LIN28B nucleosome targeting by OCT4
Pioneer transcription factors are essential for cell fate changes by targeting closed
chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However …
chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However …
Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails
Little is known about the roles of histone tails in modulating nucleosomal DNA accessibility
and its recognition by other macromolecules. Here we generate extensive atomic level …
and its recognition by other macromolecules. Here we generate extensive atomic level …
From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization
Chromatin organization plays a critical role in cellular function by regulating access to
genetic information. However, understanding chromatin folding is challenging due to its …
genetic information. However, understanding chromatin folding is challenging due to its …
FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells
Background The FACT complex is a conserved histone chaperone with critical roles in
transcription and histone deposition. FACT is essential in pluripotent and cancer cells, but …
transcription and histone deposition. FACT is essential in pluripotent and cancer cells, but …
Epigenetic landscape of small cell lung cancer: small image of a giant recalcitrant disease
Small cell lung cancer (SCLC) is a particular subtype of lung cancer with high mortality.
Recent advances in understanding SCLC genomics and breakthroughs of immunotherapy …
Recent advances in understanding SCLC genomics and breakthroughs of immunotherapy …
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems
Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to
investigate slow biological processes that involve multiple proteins, nucleic acids, and their …
investigate slow biological processes that involve multiple proteins, nucleic acids, and their …