Chromatin endogenous cleavage (ChEC) is a technique which allows to monitor protein-DNA interaction in the nucleus of eukaryotic cells. In addition to mapping of genomic interaction sites ChEC may also yield quantitative information about the occupancy of proteins at their genomic target regions. Here, we provide a protocol for ChEC experiments in S. cerevisiae, downstream DNA analysis and quantification of ChEC-mediated degradation. The potential of the method is exemplified in ChEC experiments with RNA polymerase I and the yeast homolog of linker histone H1.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-4939-2877-4_14 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Methyl-dependent auto-regulation of the DNA N6-adenine methyltransferase AMT1 in the unicellular eukaryote Tetrahymena thermophila.
Nucleic Acids Res
January 2025
MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
DNA N6-methyladenine (6mA) is a potential epigenetic mark involved in gene transcription in eukaryotes, yet the regulatory mechanism governing its methyltransferase (MTase) activity remains obscure. Here, we exploited the 6mA MTase AMT1 to elucidate its auto-regulation in the unicellular eukaryote Tetrahymena thermophila. The detailed endogenous localization of AMT1 in vegetative and sexual stages revealed a correlation between the 6mA reestablishment in the new MAC and the occurrence of zygotically expressed AMT1.
View Article and Find Full Text PDFChemical catalyst manipulating cancer epigenome and transcription.
Nat Commun
January 2025
Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
The number and variety of identified histone post-translational modifications (PTMs) are continually increasing. However, the specific consequences of each histone PTM remain largely unclear, primarily due to the lack of methods for selectively and rapidly introducing a desired histone PTM in living cells without genetic engineering. Here, we report the development of a cell-permeable histone acetylation catalyst, BAHA-LANA-PEG-CPP44, which selectively enters leukemia cells, binds to chromatin, and acetylates H2BK120 of endogenous histones in a short reaction time.
View Article and Find Full Text PDFHigh-resolution analysis of human centromeric chromatin.
Life Sci Alliance
April 2025
National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, USA
Centromeres are marked by the centromere-specific histone H3 variant CENP-A/CENH3. Throughout the cell cycle, the constitutive centromere-associated network is bound to CENP-A chromatin, but how this protein network modifies CENP-A nucleosome conformations in vivo is unknown. Here, we purify endogenous centromeric chromatin associated with the CENP-C complex across the cell cycle and analyze the structures by single-molecule imaging and biochemical assays.
View Article and Find Full Text PDFIdentification and characterization of cold-responsive cis-element in the OsPHD13 and OsPHD52 promoter and its upstream regulatory proteins in rice.
Plant Sci
January 2025
Anhui Province Key Laboratory of Rice Germplasm Innovation and Molecular Improvement, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China. Electronic address:
Rice (Oryza sativa L.) is one of the most important grain crops in the world. Abiotic stress such as low temperature is an important factor affecting the yield and quality of rice.
View Article and Find Full Text PDFIdentification of MORF4L1 as an endogenous substrate of CRBN and its potential role as a therapeutic target in cancer.
Sci Rep
January 2025
Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China.
The ubiquitin-proteasome system (UPS) is essential for cellular homeostasis, regulating the degradation of proteins involved in key processes such as cell cycle, apoptosis, and DNA repair. Dysregulation of the UPS is implicated in hepatocellular carcinoma (HCC), contributing to tumor progression and therapeutic resistance. The cereblon (CRBN) E3 ubiquitin ligase complex is a crucial component of the UPS, particularly in modulating protein degradation in response to small-molecule modulators like thalidomide.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!