Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo

Li, Tzu-Huey; Spearow, Jimmy L.; Rubin, Carol M.; Schmid, Carl W.

doi:10.1016/s0378-1119(99)00384-4

Cited by 132 publications

(99 citation statements)

References 24 publications

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“…The tissue-specific expression of B1 and B2 SINE RNAs of mice in vivo, together with evidence for regulated changes in their expression by physiological stresses is highly suggestive that these elements perform a function important to their hosts (Li et al 1999).…”

Section: Broad-spectrum Mutator Mechanismsmentioning

confidence: 99%

Perspective: Transposable Elements, Parasitic Dna, and Genome Evolution

2001

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Abstract. The nature of the role played by mobile elements in host genome evolution is reassessed considering numerous recent developments in many areas of biology. It is argued that easy popular appellations such as ''selfish DNA'' and ''junk DNA'' may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism. Transposable elements are potent, broad spectrum, endogenous mutators that are subject to the influence of chance as well as selection at several levels of biological organization. Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions.

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Section: Broad-spectrum Mutator Mechanismsmentioning

confidence: 99%

Perspective: Transposable Elements, Parasitic Dna, and Genome Evolution

2001

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“…The DNA methylation level at B1 elements (high in somatic cells and relatively low in germ cells and preimplantation embryos) negatively correlates with the B1 RNA abundance (Ichiyanagi et al, 2011), suggesting transcriptional regulation by DNA methylation. On the other hand, mouse B2 transcripts can be detected in some somatic tissues (Bachvarova, 1988;Li et al, 1999), despite that B2 elements (up to 6 CpG sites in ~190 bp; Fig. 2C) are DNA-methylated in somatic cells (Ichiyanagi et al, unpublished data).…”

Section: Epigenetic Regulation Of Sine Transcriptionmentioning

confidence: 99%

“…SINEs produce RNAs that are similar to functional cellular RNAs and the expression of some mammalian SINEs, human Alu, mouse B1 and B2, and rabbit C, is induced upon cell stress such as heat shock (Fornace and Mitchell, 1986;Liu et al, 1995;Li et al, 1999), suggesting that SINE-derived RNAs have a functional role in stress response (Schmid, 1998). Indeed, the Alu and B2 RNAs, of different origins (7SL vs. tRNA), inhibit Pol II transcription via direct interaction with the Pol II enzyme in vitro, which is implicated in the transcriptional gene repression observed during heat shock Espinoza et al, 2004;Mariner et al, 2008).…”

Section: Possible Sine Functionsmentioning

confidence: 99%

Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs

Ichiyanagi

2013

Genes Genet. Syst.

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Short interspersed elements (SINEs) are a class of retrotransposons, which amplify their copy numbers in their host genomes by retrotransposition. More than a million copies of SINEs are present in a mammalian genome, constituting over 10% of the total genomic sequence. In contrast to the other two classes of retrotransposons, long interspersed elements (LINEs) and long terminal repeat (LTR) elements, SINEs are transcribed by RNA polymerase III. However, like LINEs and LTR elements, the SINE transcription is likely regulated by epigenetic mechanisms such as DNA methylation, at least for human Alu and mouse B1. Whereas SINEs and other transposable elements have long been thought as selfish or junk DNA, recent studies have revealed that they play functional roles at their genomic locations, for example, as distal enhancers, chromatin boundaries and binding sites of many transcription factors. These activities imply that SINE retrotransposition has shaped the regulatory network and chromatin landscape of their hosts. Whereas it is thought that the epigenetic mechanisms were originated as a host defense system against proliferation of parasitic elements, this review discusses a possibility that the same mechanisms are also used to regulate the SINE-derived functions.

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“…B2 and Alu RNAs are transcribed by RNA polymerase III from short interspersed elements (SINEs) (5). Upon heat shock, the levels of B2 RNA and Alu RNA increase (6,7) and they function as general repressors of mRNA transcription (3,4). Biochemical experiments showed that B2 and Alu RNAs bind directly to core Pol II with low nM affinity (4,8).…”

mentioning

confidence: 99%

B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes

Yakovchuk

Goodrich

Kugel

2009

Proc. Natl. Acad. Sci. U.S.A.

145

135

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Noncoding RNAs (ncRNAs) are now recognized as transregulators of eukaryotic transcription, a role once attributed exclusively to protein factors. Two ncRNAs in mammalian cells have been shown to repress general mRNA transcription by RNA polymerase II (Pol II) in response to heat shock: mouse B2 RNA and human Alu RNA. B2 and Alu RNAs bind directly and tightly to Pol II and co-occupy the promoters of repressed genes along with the polymerase. Here, we identified the molecular mechanism by which mouse B2 RNA and human Alu RNA repress Pol II transcription. Biochemical assays to probe the network of protein-DNA interactions at the promoter revealed that B2 and Alu RNAs prevent Pol II from establishing contacts with the promoter both upstream and downstream of the TATA box during closed complex formation. Disruption of these contacts correlates with transcriptional repression. We conclude that B2 and Alu RNA prevent Pol II from properly engaging the DNA during closed complex formation, resulting in complexes with an altered conformation that are transcriptionally inert. In the absence of its normal contacts with the promoter, Pol II is likely held in these inactive complexes on DNA through interactions with promoter-bound TATA box-binding protein and transcription factor IIB.T ranscription is an intricate biological process in which DNA is copied into RNA; it is the critical first step in gene expression. In eukaryotes, the enzyme RNA polymerase II (Pol II) transcribes protein-encoding genes into mRNA with assistance of general transcription factors (GTFs; specifically TFIIA, TFIID, TFIIB, TFIIF, TFIIE, and TFIIH) that are thought to function at most promoters (1). Transcriptional regulation of specific genes occurs through the remarkably balanced interplay of auxiliary factors such as promoter-specific activators and repressors, coregulators, and chromatin-modifying complexes (1). Traditionally, it was thought that all of these factors were proteins, but now it is becoming clear that noncoding RNAs (ncRNAs) also play important roles in regulating transcription. Indeed, diverse ncRNAs have been identified as regulators of nearly every step in the process of mRNA transcription from controlling chromatin structure through regulating transcript elongation (2).Our laboratory reported that 2 ncRNAs, mouse B2 RNA and human Alu RNA, repress mRNA transcription by binding to Pol II during the cellular heat shock response (3, 4). B2 and Alu RNAs are transcribed by RNA polymerase III from short interspersed elements (SINEs) (5). Upon heat shock, the levels of B2 RNA and Alu RNA increase (6, 7) and they function as general repressors of mRNA transcription (3, 4). Biochemical experiments showed that B2 and Alu RNAs bind directly to core Pol II with low nM affinity (4, 8). Other SINE RNAs have been identified in mammalian cells, including mouse B1 RNA and human scAlu RNA (5), the latter of which is likely derived from cleavage of full-length Alu RNA (9). The biological functions for B1 and scAlu RNAs are not known. In vitro both of...

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Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo

Cited by 132 publications

References 24 publications

Perspective: Transposable Elements, Parasitic Dna, and Genome Evolution

Perspective: Transposable Elements, Parasitic Dna, and Genome Evolution

Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs

B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes

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