Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features

Abstract Ten-eleven translocation (TET) family enzymes convert 5-methylcytosine to 5-hydroxylmethylcytosine. However, the molecular mechanism that regulates this biological process is not clear. Here, we show the evidence that PGC7 (also known as Dppa3 or Stella) interacts with TET2 and TET3 both in vitro and in vivo to suppress the enzymatic activity of TET2 and TET3. Moreover, lacking PGC7 induces the loss of DNA methylation at imprinting loci. Genome-wide analysis of PGC7 reveals a consensus DNA motif that is recognized by PGC7. The CpG islands surrounding the PGC7-binding motifs are hypermethylated. Taken together, our study demonstrates a molecular mechanism by which PGC7 protects DNA methylation from TET family enzyme-dependent oxidation.

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Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity

Gene ◽

10.1016/j.gene.2005.01.012 ◽

2005 ◽

Vol 350 (2) ◽

pp. 129-136 ◽

Cited By ~ 63

Author(s):

Riu Yamashita ◽

Yutaka Suzuki ◽

Sumio Sugano ◽

Kenta Nakai

Keyword(s):

Strong Correlation ◽

Tissue Specificity ◽

Cpg Islands ◽

Transcription Start ◽

Transcription Start Sites ◽

Genome Wide Analysis ◽

Genome Wide

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Genome-wide analysis reveals the genomic features of the turkey vulture (Cathartes aura) as a scavenger

Molecular Genetics and Genomics ◽

10.1007/s00438-019-01541-3 ◽

2019 ◽

Vol 294 (3) ◽

pp. 679-692 ◽

Cited By ~ 3

Author(s):

Chuang Zhou ◽

Guannan Wang ◽

Haoran Yu ◽

Yang Geng ◽

Wei Wu ◽

...

Keyword(s):

Cathartes Aura ◽

Genomic Features ◽

Genome Wide Analysis ◽

Turkey Vulture ◽

Genome Wide

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Genome Wide Analysis of Dinucleotide Distribution along the Genomes of Species and its Biological Implication

10.1101/2020.02.20.957142 ◽

2020 ◽

Author(s):

Zhicheng Cai ◽

Sirui Liu ◽

Yue Xue ◽

Hui Quan ◽

Ling Zhang ◽

...

Keyword(s):

Body Temperature ◽

Biological Function ◽

Local Density ◽

Density Fluctuations ◽

Biological Impact ◽

Genomic Features ◽

Genome Wide Analysis ◽

Multi Scale ◽

Biological Implication ◽

Genome Wide

AbstractGenome compositions vary among species and nucleotides are unevenly distributed in the genomes in correlation with genomic functions. The multi-scale organizations of dinucleotides in the genome and their evolution are important genomic features informative on biological function and evolution, but remain to be fully analyzed. Here, we investigated the distributions of dinucleotides, especially that of CpG due to its biological importance, in a variety of species. Among all dinucleotides, we found that CpG is the most unevenly distributed and the distributions of all dinucleotides are correlated and organized in blocks in high species, suggesting their biological impact on regulation. By comparing the local density fluctuations and the hierarchical distribution of CpG at different scales of genomic lengths, we found that CpG distributions of different species have distinct characteristics. The clustering of species based on the CpG distribution is consistent with the phylogenetic tree. Interestingly, the heterogeneity of CpG density appears to correlate with species’ body temperature control. We propose a phase separation hypothesis to explain the dependence of chromatin structure and body temperature range on the genome sequence.

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Genome-wide analysis of DNA methylation status of CpG islands in embryoid bodies, teratomas, and fetuses

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2003.10.078 ◽

2003 ◽

Vol 311 (4) ◽

pp. 884-890 ◽

Cited By ~ 43

Author(s):

Maksym Kremenskoy ◽

Yuliya Kremenska ◽

Jun Ohgane ◽

Naka Hattori ◽

Satoshi Tanaka ◽

...

Keyword(s):

Dna Methylation ◽

Methylation Status ◽

Cpg Islands ◽

Embryoid Bodies ◽

Genome Wide Analysis ◽

Genome Wide

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Comparative Analysis of CpG Islands in Four Fish Genomes

Comparative and Functional Genomics ◽

10.1155/2008/565631 ◽

2008 ◽

Vol 2008 ◽

pp. 1-6 ◽

Cited By ~ 21

Author(s):

Leng Han ◽

Zhongming Zhao

Keyword(s):

Comparative Analysis ◽

Cpg Islands ◽

Gc Content ◽

Fish Genome ◽

Systematic Analysis ◽

Gene Markers ◽

Cpg Dinucleotides ◽

Genome Wide Analysis ◽

Genome Wide ◽

Distinct Distribution

There has been much interest in CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, because they are considered gene markers and involved in gene regulation. To date, there has been no genome-wide analysis of CGIs in the fish genome. We first evaluated the performance of three popular CGI identification algorithms in four fish genomes (tetraodon, stickleback, medaka, and zebrafish). Our results suggest that Takai and Jones' (2002) algorithm is most suitable for comparative analysis of CGIs in the fish genome. Then, we performed a systematic analysis of CGIs in the four fish genomes using Takai and Jones' algorithm, compared to other vertebrate genomes. We found that both the number of CGIs and the CGI density vary greatly among these genomes. Remarkably, each fish genome presents a distinct distribution of CGI density with some genomic factors (e.g., chromosome size and chromosome GC content). These findings are helpful for understanding evolution of fish genomes and the features of fish CGIs.

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