Cell
MinireviewSINEs and LINEs: Highly repeated short and long interspersed sequences in mammalian genomes
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Genome-wide expression analysis of a new class of lncRNAs driven by SINE B2
2021, GeneCitation Excerpt :The acknowledgment of genome-wide effects of B2-AS lncRNAs has been growing, ever since B2 was shown to provide a mobile polymerase II promoter (Ferrigno et al., 2001). B2 elements have been known to encode sense/antisense lncRNAs (B2-S and B2-AS) (Lunyak et al., 2007; Fan and Papadopoulos, 2012), which also produce a variety of RNA molecules, including the extension of B2-S into long transcripts (BS-S lncRNAs), which may retrotranspose by the aid of LINE-1 element(s) (Singer, 1982); the B2-AS lncRNAs are transcribed from the B2-mediated mobile polymerase II promoter in the mouse genome (Ferrigno et al., 2001), with variable sizes of RNA molecules and an intra-molecule stem-loop structure (Fig. 1). Apparently, both B2-S and B2-AS lncRNAs can form double-stranded RNAs (dsRNAs), at least in the B2-conserved region, which possess the potential to be processed into small interference RNAs (siRNAs) (Song and Rossi, 2017).
Non-full-length Water-Soluble CXCR4<sup>QTY</sup> and CCR5<sup>QTY</sup> Chemokine Receptors: Implication for Overlooked Truncated but Functional Membrane Receptors
2020, iScienceCitation Excerpt :4) Are they synthesized and subsequently cleared? It is plausible that there are a few means of generating non-full-length receptors and proteins in general through (1) alternative RNA splicing (Ambros, 2004; Chaudhary et al., 2019), (2) SINE and LINE transposon insertions and deletions (Adams et al., 1980; Cordaux and Batzer, 2009; Deininger et al., 1981; Ewing and Kazazian, 2011; Singer, 1982; Vassetzky and Kramerov, 2013; Wicker et al., 2007), (3) frameshift mutations resulting in premature translational termination, and (4) non-AUG translation initiation (Ghosh et al., 1967; Kearse and Wilusz, 2017). Many gene identification bioinformatics search for receptors and proteins with AUG as the translational initiation, and most experiments probe for RNA, rather than proteins.
Evaluating the applicability of mouse SINEs as an alternative normalization approach for RT-qPCR in brain tissue of the APP23 model for Alzheimer's disease
2019, Journal of Neuroscience MethodsCitation Excerpt :These drawbacks, in addition to the unstable expression of historical RGs (e.g. GAPDH, ACTB and 18S rRNA), motivate the search for alternative normalization approaches. Short interspersed nuclear elements (SINEs) are a class of highly occurring retrotransposons, which are generally 100–500 base pairs (bp) in length (Ichiyanagi, 2013; Singer, 1982). Since SINEs make up approximately 10% of the total mammalian genome (Bovine Genome Sequencing Analysis Consortium et al., 2009; Mouse Genome Sequencing Consortium et al., 2002; Lander et al., 2001; Lindblad-Toh et al., 2005; Mikkelsen et al., 2007) and since they are mainly located in intronic and untranslated regions of many genes (Tsirigos and Rigoutsos, 2009), it is hypothesized that temporary or event-related changes in a certain number of genes will not have a large impact on the overall SINE content in the transcriptome (Renard et al., 2018; Crans et al., 2019).