FACT caught in the act of manipulating the nucleosome
Nature, 2019 The organization of genomic DNA into nucleosomes profoundly affects all DNA-related processes in eukaryotes. The histone chaperone known as ‘facilitates chromatin transcription’ (FACT 1 ) (consisting of subunits SPT16 and SSRP1) promotes both disassembly
Yang Liu +9 more
semanticscholar +1 more source
Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. [PDF]
PLoS Computational Biology, 2013 Because DNA packaging in nucleosomes modulates its accessibility to transcription factors (TFs), unraveling the causal determinants of nucleosome positioning is of great importance to understanding gene regulation.
Evgeniy A Ozonov, Erik van Nimwegen
doaj +1 more source
Statistical mechanics of nucleosome ordering by chromatin structure-induced two-body interactions
, 2011 One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes.
Chereji, Răzvan V. +3 more
core +1 more source
Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites [PDF]
, 2010 The positions of nucleosomes in eukaryotic genomes determine which parts of the DNA sequence are readily accessible for regulatory proteins and which are not.
A Flaus +46 more
core +5 more sources
The role of histone modifications in transcription regulation upon DNA damage
FEBS Letters, EarlyView.This review discusses the critical role of histone modifications in regulating gene expression during the DNA damage response (DDR). By modulating chromatin structure and recruiting repair factors, these post‐translational modifications fine‐tune transcriptional programmes to maintain genomic stability.
Angelina Job Kolady, Siyao Wang
wiley +1 more source
Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation [PDF]
, 2019 DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors.
Chereji, Razvan V. +4 more
core +1 more source
Integration of circadian and hypoxia signaling via non‐canonical heterodimerization
FEBS Letters, EarlyView.CLOCK, BMAL1, and HIFs are basic helix‐loop‐helix and Per‐Arnt‐Sim domain (bHLH‐PAS) proteins, which function as transcription factors. bHLH‐PAS proteins are designated in two classes. Many class I proteins are regulated by environmental signals via their PAS domains, but such signals have not been identified for all.
Sicong Wang, Katja A. Lamia
wiley +1 more source
Exploring the Link between Nucleosome Occupancy and DNA Methylation
Frontiers in Genetics, 2018 Near promoters, both nucleosomes and CpG sites form characteristic spatial patterns. Previously, nucleosome depleted regions were observed upstream of transcription start sites and nucleosome occupancy was reported to correlate both with CpG density and ...
Cecilia Lövkvist +2 more
doaj +1 more source
High-throughput sequencing reveals a simple model of nucleosome energetics
, 2010 We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size ...
A. V. Morozov +26 more
core +1 more source
Molecular Oncology, EarlyView.Detection of extrachromosomal circular DNA (eccDNA) in plasma samples from EGFR‐mutated non‐small cell lung cancer patients. Plasma was collected before and during treatment with the EGFR‐tyrosine kinase inhibitor osimertinib. Plasma eccDNA was detected in all cancer samples, and the presence of the EGFR gene on eccDNA serves as a potential biomarker ...
Simone Stensgaard +5 more
wiley +1 more source