A simple and versatile system for the ATP-dependent assembly of chromatin

Khuong, Mai T.; Jia, Fu; Cruz‐Becerra, Grisel; Kadonaga, James T.

doi:10.1074/jbc.m117.815365

Cited by 12 publications

(23 citation statements)

References 49 publications

(51 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To complement the studies with mononucleosomes, we tested whether Rv Dsup can be incorporated into extended periodic nucleosome arrays. In these experiments, we assembled nucleosomes onto plasmid DNA by using a purified and defined ATP-dependent chromatin assembly system with the ACF motor protein and the dNLP core histone chaperone (Fyodorov and Kadonaga, 2003; Khuong et al, 2017). We also included separate reactions with histone H1 (reviewed in Woodcock et al, 2006; Happel and Doenecke, 2009; Kalashnikova et al, 2016) as a positive control for a nucleosome-binding factor.…”

Section: Resultsmentioning

confidence: 99%

The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals

Chavez

Cruz‐Becerra

Fei

et al. 2019

eLife

Self Cite

View full text Add to dashboard Cite

Tardigrades, also known as water bears, are animals that can survive extreme conditions. The tardigrade Ramazzottius varieornatus contains a unique nuclear protein termed Dsup, for damage suppressor, which can increase the resistance of human cells to DNA damage under conditions, such as ionizing radiation or hydrogen peroxide treatment, that generate hydroxyl radicals. Here we find that R. varieornatus Dsup is a nucleosome-binding protein that protects chromatin from hydroxyl radicals. Moreover, a Dsup ortholog from the tardigrade Hypsibius exemplaris similarly binds to nucleosomes and protects DNA from hydroxyl radicals. Strikingly, a conserved region in Dsup proteins exhibits sequence similarity to the nucleosome-binding domain of vertebrate HMGN proteins and is functionally important for nucleosome binding and hydroxyl radical protection. These findings suggest that Dsup promotes the survival of tardigrades under diverse conditions by a direct mechanism that involves binding to nucleosomes and protecting chromosomal DNA from hydroxyl radicals.

show abstract

Section: Resultsmentioning

confidence: 99%

The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals

Chavez

Cruz‐Becerra

Fei

et al. 2019

eLife

Self Cite

View full text Add to dashboard Cite

show abstract

“…Human p300 protein was synthesized in Sf9 cells and purified as described in Kraus and Kadonaga (1998). Recombinant Drosophila melanogaster core histones were synthesized in E. coli and purified by the method of Khuong et al (2017). The catalytic domain of Drosophila topoisomerase I was synthesized and purified as described by Fyodorov and Kadonaga (2003).…”

Section: Purification Of Recombinant Proteinsmentioning

confidence: 99%

NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes

et al. 2018

Self Cite

View full text Add to dashboard Cite

Our understanding of transcription by RNA polymerase II (Pol II) is limited by our knowledge of the factors that mediate this critically important process. Here we describe the identification of NDF, a nucleosome-destabilizing factor that facilitates Pol II transcription in chromatin. NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner, and facilitates transcription by Pol II through nucleosomes in a purified and defined transcription system as well as in cell nuclei. Upon transcriptional induction, NDF is recruited to the transcribed regions of thousands of genes and colocalizes with a subset of H3K36me3-enriched regions. Notably, the recruitment of NDF to gene bodies is accompanied by an increase in the transcript levels of many of the NDF-enriched genes. In addition, the global loss of NDF results in a decrease in the RNA levels of many genes. In humans, NDF is present at high levels in all tested tissue types, is essential in stem cells, and is frequently overexpressed in breast cancer. These findings indicate that NDF is a nucleosome-destabilizing factor that is recruited to gene bodies during transcriptional activation and facilitates Pol II transcription through nucleosomes.

show abstract

“…Mass spectrometry was used in one study to identify histone H3K9, H3K27, H3K36, and H3K37 as sites of p300-catalyzed acetylation in promoter-proximal nucleosomes in such a reconstituted system (123). Chromatin reconstitution from defined components continues to be an area of active investigation, and a recent report from Kadonaga and co-workers (124) described the refinement of such a system for ATPdependent assembly of chromatin using a histone chaperone (Drosophila nucleoplasmin-like protein (dNLP)), an ATP-remodeling enzyme (imitation switch (ISWI)), core histones, and various DNA substrates. This experimental resource will benefit future detailed mechanistic studies on the relationship between chromatin and transcription.…”

Section: In Vitro Reconstitution Of Active Chromatin Templatesmentioning

confidence: 99%

Milestones in transcription and chromatin published in the Journal of Biological Chemistry

Gottesfeld

2019

Journal of Biological Chemistry

View full text Add to dashboard Cite

During Herbert Tabor's tenure as Editor-in-Chief from 1971 to 2010, JBC has published many seminal papers in the fields of chromatin structure, epigenetics, and regulation of transcription in eukaryotes. As of this writing, more than 21,000 studies on gene transcription at the molecular level have been published in JBC since 1971. This brief review will attempt to highlight some of these ground-breaking discoveries and show how early studies published in JBC have influenced current research. Papers published in the Journal have reported the initial discovery of multiple forms of RNA polymerase in eukaryotes, identification and purification of essential components of the transcription machinery, and identification and mechanistic characterization of various transcriptional activators and repressors and include studies on chromatin structure and post-translational modifications of the histone proteins. The large body of literature published in the Journal has inspired current research on how chromatin organization and epigenetics impact regulation of gene expression.

show abstract

A simple and versatile system for the ATP-dependent assembly of chromatin

Cited by 12 publications

References 49 publications

The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals

The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals

NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes

Milestones in transcription and chromatin published in the Journal of Biological Chemistry

Contact Info

Product

Resources

About