Results 31 to 40 of about 70,917 (227)

Linking stochastic fluctuations in chromatin structure and gene expression. [PDF]

PLoS Biology, 2013
The number of mRNA and protein molecules expressed from a single gene molecule fluctuates over time. These fluctuations have been attributed, in part, to the random transitioning of promoters between transcriptionally active and inactive states, causing ...
Christopher R Brown, Changhui Mao, Elena Falkovskaia, Melissa S Jurica, Hinrich Boeger   +4 more
doaj   +1 more source

A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure [PDF]

Scientific Reports, 2018
AbstractChromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo.
Korolev, Nikolay, Lyubartsev, Alexander P., Nordenskiöld, Lars   +2 more
openaire   +3 more sources

Nucleosome-coupled expression differences in closely-related species

BMC Genomics, 2011
Background Genome-wide nucleosome occupancy is negatively related to the average level of transcription factor motif binding based on studies in yeast and several other model organisms.
Gebbia Marinella, Tsui Kyle, Yao Victoria, Guan Yuanfang, Dunham Maitreya J, Nislow Corey, Troyanskaya Olga G   +6 more
doaj   +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

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

Conserved structural motifs in PAS, LOV, and CRY proteins regulate circadian rhythms and are therapeutic targets

FEBS Letters, EarlyView.
Cryptochrome and PAS/LOV proteins play intricate roles in circadian clocks where they act as both sensors and mediators of protein–protein interactions. Their ubiquitous presence in signaling networks has positioned them as targets for small‐molecule therapeutics. This review provides a structural introduction to these protein families.
Eric D. Brinckman, Anna E. Lester, Brian D. Zoltowski   +2 more
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, Kim Sneppen, Jan O. Haerter   +2 more
doaj   +1 more source

Plasma extrachromosomal circular DNA as a biomarker in EGFR‐targeted therapy of non‐small cell lung cancer

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, Sarmad Mehmood, Eva Boysen Fynboe Ebert, Peter Meldgaard, Anindya Dutta, Boe S. Sorensen   +5 more
wiley   +1 more source

Nucleosome footprinting in plasma cell-free DNA for the pre-surgical diagnosis of ovarian cancer

npj Genomic Medicine, 2022
Fragmentation patterns of plasma cell-free DNA (cfDNA) are known to reflect nucleosome positions of cell types contributing to cfDNA. Based on cfDNA fragmentation patterns, the deviation in nucleosome footprints was quantified between diagnosed ovarian ...
Adriaan Vanderstichele, Pieter Busschaert, Chiara Landolfo, Siel Olbrecht, An Coosemans, Wouter Froyman, Liselore Loverix, Nicole Concin, Elena Ioana Braicu, Pauline Wimberger, Els Van Nieuwenhuysen, Sileny N. Han, Toon Van Gorp, Tom Venken, Ruben Heremans, Patrick Neven, Tom Bourne, Ben Van Calster, Dirk Timmerman, Diether Lambrechts, Ignace Vergote   +20 more
doaj   +1 more source

Metformin promotes mitochondrial integrity through AMPK‐signaling in Leber's hereditary optic neuropathy

FEBS Open Bio, EarlyView.
Metformin mediates mitochondrial quality control in Leber's hereditary optic neuropathy (LHON) fibroblasts carrying mtDNA mutations. At therapeutic levels, metformin activates AMPK signaling to restore mitochondrial dynamics by promoting fusion and restraining fission, while preserving mitochondrial mass, enhancing autophagy/mitophagy and biogenesis ...
Chatnapa Panusatid, Rapasviranda Soiyangsuk, Maneeluck Tanadjindarat, Chayanon Peerapittayamongkol   +3 more
wiley   +1 more source