ArticleNucleic acids research2018
MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 16 citations in OpenAlex.
- An MNase-ChIP-Seq Protocol to Profile Histone Modifications at a DNA Break in Yeast.Methods and protocols · 2026Article
- FRET analysis of the unwrapping of nucleosomal DNA containing a sequence characteristic of the + 1 nucleosome.Scientific reports · 2025Article
- Evaluation by Experimentation and Simulation of a FRET Pair Comprising Fluorescent Nucleobase Analogs in Nucleosomes.Chemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin.Biochemical Society transactions · 2022Review
- Hi-CO: 3D genome structure analysis with nucleosome resolution.Nature protocols · 2021Article
- Transcription factor competition at the γ-globin promoters controls hemoglobin switching.Nature genetics · 2021Article
- Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Epigenome Regulation by Dynamic Nucleosome Unwrapping.Trends in biochemical sciences · 2020Review
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The first nucleosomes in the downstream of transcription starting sites are called +1 nucleosomes, which are expected to be readily unwrapped for DNA transcription. To investigate DNA accessibility in +1 nucleosomes, MNase-seq experiments were carried out with 20 reconstituted +1 nucleosomes of budding yeast. Although MNase has been known for its sequence preference in DNA digestions, we confirmed that this sequence preference is overwhelmed by DNA accessibility by identifying the sequence-driven and accessibility-driven cleavages. Specifically, we find that sequences favoured by MNase at the end regions such as TA dinucleotide are prohibited from cleavage at the internal sites in the early stage of digestion. Nevertheless, sequences less favoured by MNase at the end regions such as AA/TT dinucleotide are predominantly cleaved at the internal sites in the early stage of digestion. Since AA/TT is known as a rigid dinucleotide step resistant to DNA bending, these internal cleavages reflect the local site exposures induced by DNA mechanics. As the DNA entry site of +1 nucleosomes in yeast is found AA/TT-rich, this sequence element may play a role in gene activation by reducing DNA-histone affinities along the direction of DNA transcription.
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