H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks

Abstract

Background: Transposons are selfish genetic elements that self-reproduce in host DNA. They were active during evolutionary history and now occupy almost half of mammalian genomes. Close insertions of transposons reshaped structure and regulation of many genes considerably. Co-evolution of transposons and host DNA frequently results in the formation of new regulatory regions. Previously we published a concept that the proportion of functional features held by transposons positively correlates with the rate of regulatory evolution of the respective genes. Methods: We ranked human genes and molecular pathways according to their regulatory evolution rates based on high throughput genome-wide data on five histone modifications (H3K4me3, H3K9ac, H3K27ac, H3K27me3, H3K9me3) linked with transposons for five human cell lines. Results: Based on the total of approximately 1.5 million histone tags, we ranked regulatory evolution rates for 25075 human genes and 3121 molecular pathways and identified groups of molecular processes that showed signs of either fast or slow regulatory evolution. However, histone tags showed different regulatory patterns and formed two distinct clusters: promoter/active chromatin tags (H3K4me3, H3K9ac, H3K27ac) vs. heterochromatin tags (H3K27me3, H3K9me3). Conclusion: In humans, transposon-linked histone marks evolved in a coordinated way depending on their functional roles.

Parental Effects on Epigenetic Programming in Gametes and Embryos of Dairy Cows

“…Basically, genes with higher expression are most likely located at open chromatin regions which are generally modified by active epigenetic marks: such as H3K4me3 on proximal promoters, H3K27-ac on enhancers, and low DNA methylated promoters ( Gaspar-Maia et al, 2011 ; Tian et al, 2011 ). Repressed expression genes are found in closed chromatin regions bound with inactive epigenetic marks including H3K37me3, hypermethylation at transcription start sites, and long non-coding RNA bound regions ( Saxena and Carninci, 2011 ; Ando et al, 2019 ; Igolkina et al, 2019 ). During gametogenesis and embryogenesis, chromatin states undergo extensive remodeling to reach totipotency.…”

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“…H3K27ac and H3K4me3 modi cation indicate active gene transcription [27,28]. To understand if these modi cations contribute to circSOD2 upregulation in HCC.…”

Identification of AR-V7 downstream genes commonly targeted by AR/AR-V7 and specifically targeted by AR-V7 in castration resistant prostate cancer

“…H3K4me1, H3K4me3 and H3K27ac are major histone epigenetic modification marks. H3K4me1 commonly associates with active enhancers, H3K4me3 is highly enriched at active promotors, and H3K27ac is known as an active transcription mark [15] .…”