Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP

Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) has revolutionized our understanding of chromatin-related biological processes. The method, however, requires thousands of cells and has therefore limited applications in situations where cell numbers are limited. Here...

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Bibliographic Details
Published in:PloS one 2019-11, Vol.14 (11), p.e0225801-e0225801
Main Authors: Org, Tõnis, Hensen, Kati, Kreevan, Rita, Mark, Elina, Sarv, Olav, Andreson, Reidar, Jaakma, Ülle, Salumets, Andres, Kurg, Ants
Format: Article
Language:English
Subjects:
Algorithms
Animals
Binding sites
Biological activity
Biology
Biology and life sciences
Biotechnology
Blastocyst - cytology
Blastocyst - metabolism
Blastocyst Inner Cell Mass - metabolism
Blastocysts
Breeding of animals
Cattle
Cell division
Cell Line
Chromatin
Chromatin - chemistry
Chromatin - metabolism
Chromatin Immunoprecipitation
Criminal investigation
Deoxyribonucleic acid
DNA
EDTA
Embryonic development
Embryos
Fertilization in Vitro
Gene expression
Gene mapping
Genome
Genomes
Genomics
Gynecology
High-Throughput Nucleotide Sequencing
Histones
Histones - genetics
Histones - metabolism
Humans
Immunoprecipitation
Life sciences
Medicine
Methods
Next-generation sequencing
Novels
Obstetrics
Oocytes - cytology
Protein Processing, Post-Translational
Proteins
Research and Analysis Methods
Scientific equipment industry
Sequence Analysis, DNA
Stem cells
Technology application
Trophectoderm
Trophoblasts - metabolism
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Summary:Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) has revolutionized our understanding of chromatin-related biological processes. The method, however, requires thousands of cells and has therefore limited applications in situations where cell numbers are limited. Here we describe a novel method called Restriction Assisted Tagmentation Chromatin Immunoprecipitation (RAT-ChIP) that enables global histone modification profiling from as few as 100 cells. The method is simple, cost-effective and takes a single day to complete. We demonstrate the sensitivity of the method by deriving the first genome-wide maps of histone H3K4me3 and H3K27me3 modifications of inner cell mass and trophectoderm of bovine blastocyst stage embryos.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0225801