ArticleBMC molecular biology2011
Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays.
Article in BMC molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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Who cites it
21 citing papers in PubMed, 31 citations in OpenAlex.
- Development, characterization, and inter-laboratory validation of methylated human cell free DNA candidate reference materials.Clinical epigenetics · 2026Article
- Analysis of DNA Methylation in Gliomas: Assessment of Preanalytical Variables.Laboratory investigation; a journal of technical methods and pathology · 2024Article
- A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes.Laboratory investigation; a journal of technical methods and pathology · 2024Article
- CryoGrid-PIXUL-RNA: high throughput RNA isolation platform for tissue transcript analysis.BMC genomics · 2023Article
- dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region.Cell reports · 2022Article
- Single cell epigenetic visualization assay.Nucleic acids research · 2021Article
- PIXUL-ChIP: integrated high-throughput sample preparation and analytical platform for epigenetic studies.Nucleic acids research · 2019Article
- Distinct patterns of transcriptional and epigenetic alterations characterize acute and chronic kidney injury.Scientific reports · 2018Article
- Article
- Methylation-Demethylation Dynamics: Implications of Changes in Acute Kidney Injury.Analytical cellular pathology (Amsterdam) · 2018Review
- Treacher Collins syndrome mutations in Saccharomyces cerevisiae destabilize RNA polymerase I and III complex integrity.Human molecular genetics · 2017Article
- Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy.Nucleic acids research · 2016Article
- Regulation of ribosomal RNA expression across the lifespan is fine-tuned by maternal diet before implantation.Biochimica et biophysica acta · 2016Article
- Heterogeneity of epigenetic changes at ischemia/reperfusion- and endotoxin-induced acute kidney injury genes.Kidney international · 2015Article
- Experimental acute lung injury induces multi-organ epigenetic modifications in key angiogenic genes implicated in sepsis-associated endothelial dysfunction.Critical care (London, England) · 2015Article
- Mechanisms of maladaptive repair after AKI leading to accelerated kidney ageing and CKD.Nature reviews. Nephrology · 2015Review
- Epigenetic-Mediated Downregulation of μ-Protocadherin in Colorectal Tumours.Gastroenterology research and practice · 2015Article
- Beads-free protein immunoprecipitation for a mass spectrometry-based interactome and posttranslational modifications analysis.Proteome science · 2015Article
- Losartan reverses permissive epigenetic changes in renal glomeruli of diabetic db/db mice.Kidney international · 2014Article
- Epigenetic alterations in acute kidney injury.Seminars in nephrology · 2013Review
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundThe processes that compose expression of a given gene are far more complex than previously thought presenting unprecedented conceptual and mechanistic challenges that require development of new tools. Chromatin structure, which is regulated by DNA methylation and histone modification, is at the center of gene regulation. Immunoprecipitations of chromatin (ChIP) and methylated DNA (MeDIP) represent a major achievement in this area that allow researchers to probe chromatin modifications as well as specific protein-DNA interactions in vivo and to estimate the density of proteins at specific sites genome-wide. Although a critical component of chromatin structure, DNA methylation has often been studied independently of other chromatin events and transcription.
resultsTo allow simultaneous measurements of DNA methylation with other genomic processes, we developed and validated a simple and easy-to-use high throughput microplate-based platform for analysis of DNA methylation. Compared to the traditional beads-based MeDIP the microplate MeDIP was more sensitive and had lower non-specific binding. We integrated the MeDIP method with a microplate ChIP assay which allows measurements of both DNA methylation and histone marks at the same time, Matrix ChIP-MeDIP platform. We illustrated several applications of this platform to relate DNA methylation, with chromatin and transcription events at selected genes in cultured cells, human cancer and in a model of diabetic kidney disease.
conclusionThe high throughput capacity of Matrix ChIP-MeDIP to profile tens and potentially hundreds of different genomic events at the same time as DNA methylation represents a powerful platform to explore complex genomic mechanism at selected genes in cultured cells and in whole tissues. In this regard, Matrix ChIP-MeDIP should be useful to complement genome-wide studies where the rich chromatin and transcription database resources provide fruitful foundation to pursue mechanistic, functional and diagnostic information at genes of interest in health and disease.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.