Published in Genome Biology
BackgroundChromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance pl...
Published in Genomics
The nucleosome is the fundamental structural unit of eukaryotic chromatin and plays an essential role in the epigenetic regulation of cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to identify nucleosome positions in the genome. Our previous model based on DNA deformation energy, in which a set...
Published in Molecular Neurobiology
Although important information is available on the molecular mechanisms of long-term memory formation, little is known about the processes underlying memory persistence in the brain. Here, we report that persistent gene expression of CaMKIIδ isoform participates in object recognition long-lasting memory storage in mice hippocampus. We found that Ca...
Published in Seminars in cell & developmental biology
In nature plants are exposed to frequent changes in their abiotic and biotic environment. While some environmental cues are used to gauge the environment and align growth and development, others are beyond the regularly encountered spectrum of a species and trigger stress responses. Such stressful conditions provide a potential threat to survival a...
Published in Plant Molecular Biology
Key messageThe maize chromatin remodeler ZmCHB101 plays an essential role in the osmotic stress response. ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes.AbstractDrought and osmotic stresses are recurring conditions that severely constrain crop production. Evidence accumulated in the mode...
Published in Methods in molecular biology (Clifton, N.J.)
Nucleosomes are the basic repeating units of eukaryotic chromatin. They play important roles in chromatin compaction and gene regulation. Therefore, it is important to profile the in vivo locations of nucleosomes in the genome. Here we illustrate how to profile nucleosome occupancy at genome-wide scale using micrococcal nuclease (MNase) digestion c...
Nucleosomes are the basic repeating units of eukaryotic chromatin. They play important roles in chromatin compaction and gene regulation. Therefore, it is important to profile the in vivo locations of nucleosomes in the genome. Here we illustrate how to profile nucleosome occupancy at genome-wide scale using micrococcal nuclease (MNase) digestion c...
Published in The international journal of biochemistry & cell biology
Maintaining a stable and balanced histone pool is of paramount importance for genome stability and fine regulation of DNA replication and transcription. This involves a complex regulatory machinery, exploiting transcription factors as well as histone chaperones, chromatin remodelers and modifiers. The functional details of this machinery are as yet...
Published in BMC Genomics
BackgroundCryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell or whether CUTs represent noise in the yeast transcriptome.We sought to ascertain the extent of conserved CUT expression across a...
Published in Methods in molecular biology (Clifton, N.J.)
Nucleosome occupancy in promoter and genic regions can severely influence the transcription levels. Few methods have been established to investigate the nucleosome occupancy along the DNA. In this chapter we describe a detailed protocol to analyze the nucleosome occupancy at a specific locus using MNase-pPCR.
