Cell
Volume 28, Issue 3, March 1982, Pages 433-434
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SINEs 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, Gene
    Citation 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, iScience
    Citation 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 Methods
    Citation 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).

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