Related Experiment Video
Updated: Oct 16, 2025
08:53
Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
Published on: May 2, 2025
550
Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis
David A Bates1, Charles E Bates2, Andrew S Earl1
1Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America.
Plos One
|October 21, 2021
Summary
Nucleosome formation in vitro is biased towards DNA ends. This study confirms this end bias but shows it does not skew experimental results or their interpretation.
Area of Science:
- Molecular Biology
- Genetics
- Epigenetics
Background:
- Eukaryotic gene regulation fundamentally relies on nucleosome positioning on DNA.
- In vitro studies are common for understanding in vivo nucleosome patterns, but may introduce biases.
- Nucleosome formation in vitro is influenced by DNA fragment length and end proximity.
Purpose of the Study:
- To investigate and confirm the phenomenon of nucleosome end bias in in vitro DNA fragmentation.
- To develop a method for analyzing nucleosomes forming at the terminal ends of DNA fragments.
- To assess the impact of nucleosome end bias on the interpretation of experimental results.
Main Methods:
- Confirmation of nucleosome end bias using in vitro reconstituted nucleosomes.
- Development of a novel library preparation method utilizing nearly identical libraries with distinct known DNA ends.
- Analysis of nucleosome occupancy near the terminal ends of fragmented DNA.
Main Results:
- The study confirms that nucleosomes exhibit a preference for forming on the terminal ends of linear DNA fragments in vitro.
- A method was successfully developed to identify and analyze nucleosomes positioned at DNA fragment ends.
- Despite the observed end bias, the overall interpretation of nucleosome occupancy data remained unaffected.
Conclusions:
- Nucleosome end bias is a confirmed phenomenon in in vitro DNA studies.
- The developed method allows for the recovery and analysis of end-localized nucleosomes.
- Nucleosome end bias does not significantly skew the interpretation of eukaryotic gene regulation studies.
Related Concept Videos
02:36Chromatin Immunoprecipitation- ChIP
11.5K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
11.5K
02:54Nucleosome Remodeling
9.9K
Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
9.9K