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Implications of CpG islands on chromosomal architectures and modes of global gene regulation

ABSTRACT: In this study, we present the critical implication of CpG islands (CGI) on the general rules for chromatin structural architectures and gene regulation mechanisms. Through integrative biological big data analyses, we found that the linear gene arrangements in chromosomes harbor the critical evidences for spatial gene segregation and different modes of gene localization between CGI-containing (CGI+) and CGI-less (CGI-) genes within the nucleus. CGI- genes, which are generally located within the nuclear periphery (chromosomal territories) as heterochromatin, are converted to euchromatin and internalized into the nuclear center only when activated. However, CGI-centered regulations keep CGI+ genes from heterochromatin formation and located within nuclear center regardless of their activities. We also show these different localization behaviors make CGI+ and CGI- genes to be regulated by distinct transcriptional regulation mechanisms: CGI- genes are regulated by local bindings of transcription factors, while CGI+ genes are strongly engaged in the 3-dimensional long-range chromosomal interactions. This SuperSeries is composed of the SubSeries listed below.

OTHER RELATED OMICS DATASETS IN: PRJNA319990PRJNA319987PRJNA319992PRJNA319996PRJNA319994PRJNA319989

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE80799 | GEO | 2018/02/15

REPOSITORIES: GEO

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Project description:Dynamic nuclear architecture and chromatin organizations are the key features of the mid- prophase I in mammalian meiosis. Where the chromatin undergoes major changes, including meiosis-specific spatiotemporal arrangements and remodelling, the establishment of chromatin loop–axis structure, pairing, and crossing over between homologous chromosomes, any deficiencies in these events may induce genome instability, subsequently leading to failure to produce gametes and infertility. Despite the significance of chromatin structure, little is known about the location of chromatin marks and the necessity of their balance during meiosis prophase I. Here, we show a thorough cytological study of the surface-spread meiotic chromosomes of mouse spermatocytes for H3K9,14,18,23,27,36, H4K12,16 acetylation, and H3K4,9,27,36 methylation. Active acetylation and methylation marks on H3 and H4, such as H3K9ac, H3K14ac, H3K18ac, H3K36ac, H3K56ac, H4K12ac, H4K16ac, and H3K27me3 and H3K36me3 exhibited pan-nuclear localization away from heterochromatin. In comparison, repressive marks like H3K9me3 are localized to heterochromatin. In addition, we found that the intensities of H3K23ac, H3K27ac, and H3K9me3 enhanced during meiotic prophase I. Further, taking advantage of the delivery of small-molecule chemical inhibitors Methotrexate (MTX; heterochromatin enhancer), HMS-I1 (heterochromatin inhibitor), Anacardic acid (AA; histone acetyltransferase inhibitor), Trichostatin A (TSA; histone deacetylase inhibitor), IOX1 (JmjC demethylases inhibitor), and AZ505 (methyl transferase inhibitor) in seminiferous tubules through the rete testis route, revealed that alteration in histone modifications enhanced the centromere mislocalization, chromosome breakage, altered meiotic recombination and reduced sperm count. Notably, an imbalance in the histone modifications influences the chromosome axis length and chromatin loop size via transcriptional regulation of meiosis- specific genes. Our findings highlight the importance of balanced chromatin modifications in meiotic prophase I chromosome organization and instability.

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Implications of CpG islands on chromosomal architectures and modes of global gene regulation

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