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

被引:75
作者
Igolkina, Anna A. [1 ,2 ]
Zinkevich, Arsenii [3 ]
Karandasheva, Kristina O. [4 ]
Popov, Aleksey A. [3 ]
Selifanova, Maria, V [3 ]
Nikolaeva, Dania [3 ]
Tkachev, Victor [5 ]
Penzar, Dmitry [3 ,6 ]
Nikitin, Daniil M. [5 ,7 ]
Buzdin, Anton [5 ,7 ,8 ]
机构
[1] Peter Great St Petersburg Polytech Univ, Math Biol & Bioinformat Lab, Inst Appl Math & Mech, Polytech Skaya 29, St Petersburg 195251, Russia
[2] All Russia Res Inst Agr Microbiol, Lab Microbiol Monitoring & Bioremediat Soil, Podbelskogo 3, St Petersburg 196608, Russia
[3] Lomonosov Moscow State Univ, Vorobiovy Gory 1, Moscow 119991, Russia
[4] Res Ctr Med Genet, Moskvorechie St 1, Moscow 115478, Russia
[5] Omicsway Corp, Walnut, CA 91789 USA
[6] Russian Acad Sci, Vavilov Inst Gen Genet, Gubkina 3, Moscow 119991, Russia
[7] Shemyakin Ovchinnikov Inst Bioorgan Chem, Moscow 117997, Russia
[8] IM Sechenov First Moscow State Med Univ, Moscow 119991, Russia
基金
俄罗斯基础研究基金会;
关键词
human genome molecular evolution; histone modifications; transposable elements; retrotransposons; molecular pathway analysis; gene ontology; epigenetics; gene regulation; promoter; chromatin structure; ENCODE DATA; IN-VIVO; EXPRESSION; ELEMENTS; CANCER; ENCYCLOPEDIA; ENHANCER; GENES; TOOL;
D O I
10.3390/cells8091034
中图分类号
Q2 [细胞生物学];
学科分类号
071009 ; 090102 ;
摘要
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.
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页数:16
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