ArticleBMC genomics2010
Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in Saccharomyces cerevisiae.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed, 13 citations in OpenAlex.
- Gene Repositioning Is Under Constraints After Evolutionary Conserved Gene Neighborhood Separate.Frontiers in genetics · 2019Article
- Intrachromosomal colocalization strengthens co-expression, co-modification and evolutionary conservation of neighboring genes.BMC genomics · 2018Article
- Histone modifications facilitate the coexpression of bidirectional promoters in rice.BMC genomics · 2016Article
- The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast.Genome biology and evolution · 2016Article
- The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes.BMC genomics · 2012Article
- Young intragenic miRNAs are less coexpressed with host genes than old ones: implications of miRNA-host gene coevolution.Nucleic acids research · 2012Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNeighboring gene pairs in the genome of Saccharomyces cerevisiae have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. However, the extent of the contribution of histone modifications to the coexpression of neighboring genes is unclear.
resultsWe investigated the similarity of histone modification between neighboring genes using autocorrelation analysis and composite profiles. Our analysis showed that neighboring genes had similar levels or changes of histone modifications, especially those transcribed in the same direction. The similarities, however, were restricted to 1 or 2 neighboring genes. Moreover, the expression of a gene was significantly correlated with histone modification of its neighboring gene(s), but this was limited to only 1 or 2 neighbors. Using a hidden Markov model (HMM), we found more than 2000 chromatin domains with similar acetylation changes as the cultures changed and a considerable number of these domains covered 2-4 genes. Gene pairs within domains exhibited a higher level of coexpression than random pairs and shared similar functions.
conclusionsThe results of this study suggest that similar histone modifications occur within only a small local chromatin region in yeast. The modifications generally have an effect on coexpression with only 1 or 2 neighboring genes. Some blocking mechanism(s) might strictly restrain the distribution of histone modifications in yeast.
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