However, the related underlying mechanisms remain conjectural in that DNA methylation at CpG sites was proposed to play a role in repression of Pol III transcription ( Besser et al. SINEs exhibit tissue-specific expression patterns, implying they undergo epigenetic regulation. Moreover, it has been shown that a variety of ancient SINE families-LF-SINE, AmnSINE1, MIR, B3, B4, SINEC, and Mar1-have provided cis regulatory sequences during the course of mammalian evolution ( Nishihara 2019). Due to the absence of protein-coding genes within these elements, SINE transcription alone does not cause a mutation by retrotransposition rather, it has been proposed that SINE RNAs have functions regulating gene transcription and translation ( Chu et al. While SINEs do not encode a protein, long interspersed elements (LINEs) present in the same genome provide a reverse transcriptase activity for SINE retrotransposition ( Kajikawa and Okada 2002 Dewannieux et al. Transposition involves reverse transcription of SINE RNAs and integration of the resultant cDNAs into a genomic DNA site, a process termed retrotransposition ( Ichiyanagi 2013). Short interspersed elements (SINEs) are a class of transposable elements present in a wide variety of organisms ( Vassetzky and Kramerov 2013) that originated from RNA polymerase III (Pol III)-transcribed genes such as tRNAs, 7SL RNA, and 5S rRNA ( Ullu and Tschudi 1984 Daniels and Deininger 1985 Sakamoto and Okada 1985 Kapitonov and Jurka 2003), thus, SINE transcription depends on Pol III.
SINE, epigenetics, intra-specific difference, chromatin boundary, transposable elements Introduction These results suggest that the currently active B2 copies are mobile boundary elements that can modulate chromatin modifications and gene expression, and are likely involved in epigenomic and phenotypic diversification of the mouse species. Moreover, genomic B2 copies were enriched at the boundary of various histone modifications, and chromatin insulator protein, CCCTC-binding factor, a well-known chromatin boundary protein, bound to >100 polymorphic and >10,000 non-polymorphic B2 insertions. DNA methylation and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses in liver revealed that polymorphic B2 insertions served as a boundary element inhibiting the expansion of DNA hypomethylated and histone hyperacetylated regions, and decreased the expression of neighboring genes. Using a novel RNA sequencing method designated as melRNA-seq, we detected the expression of SINEs in male germ cells at both the subfamily and genomic copy levels: the vast majority of B1 RNAs originated from evolutionarily young subfamilies, whereas B2 RNAs originated from both young and old subfamilies. To study the mobility, expression, and function of SINE copies, we first identified about 2,000 insertional polymorphisms of SINE B1 and B2 families within Mus musculus. However, it remains unclear whether currently active SINEs contribute to the expansion of TF binding sites. Evidence has accumulated that ancient SINE sequences have acquired new binding sites for transcription factors (TFs) through multiple mutations following retrotransposition, and as a result have rewired the host regulatory network during the course of evolution. More than one million copies of short interspersed elements (SINEs), a class of retrotransposons, are present in the mammalian genomes, particularly within gene-rich genomic regions.
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