Dynamic Nucleosome Organization at hox Promoters during Zebrafish Embryogenesis
Document Type
Journal ArticlePublication Date
2013-05-09Keywords
NucleosomesEmbryonic Development
Zebrafish
Genes, Homeobox
Amino Acids, Peptides, and Proteins
Animal Experimentation and Research
Cell and Developmental Biology
Cells
Embryonic Structures
Genetic Phenomena
Genetics and Genomics
Investigative Techniques
Metadata
Show full item recordAbstract
Nucleosome organization at promoter regions plays an important role in regulating gene activity. Genome-wide studies in yeast, flies, worms, mammalian embryonic stem cells and transformed cell lines have found well-positioned nucleosomes flanking a nucleosome depleted region (NDR) at transcription start sites. This nucleosome arrangement depends on DNA sequence (cis-elements) as well as DNA binding factors and ATP-dependent chromatin modifiers (trans-factors). However, little is understood about how the nascent embryonic genome positions nucleosomes during development. This is particularly intriguing since the embryonic genome must undergo a broad reprogramming event upon fusion of sperm and oocyte. Using four stages of early embryonic zebrafish development, we map nucleosome positions at the promoter region of 37 zebrafish hox genes. We find that nucleosome arrangement at the hox promoters is a progressive process that takes place over several stages. At stages immediately after fertilization, nucleosomes appear to be largely disordered at hox promoter regions. At stages after activation of the embryonic genome, nucleosomes are detectable at hox promoters, with positions becoming more uniform and more highly occupied. Since the genomic sequence is invariant during embryogenesis, this progressive change in nucleosome arrangement suggests that trans-factors play an important role in organizing nucleosomes during embryogenesis. Separating hox genes into expressed and non-expressed groups shows that expressed promoters have better positioned and occupied nucleosomes, as well as distinct NDRs, than non-expressed promoters. Finally, by blocking the retinoic acid-signaling pathway, we disrupt early hox gene transcription, but observe no effect on nucleosome positions, suggesting that active hox transcription is not a driving force behind the arrangement of nucleosomes at the promoters of hox genes during early development.Source
PLoS One. 2013 May 9;8(5):e63175. doi: 10.1371/journal.pone.0063175. Print 2013. Link to article on publisher's site
DOI
10.1371/journal.pone.0063175Permanent Link to this Item
http://hdl.handle.net/20.500.14038/30016PubMed ID
23671670Related Resources
Rights
Copyright: © 2013 Weicksel et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ae974a485f413a2113503eed53cd6c53
10.1371/journal.pone.0063175