Protein interactions with<i><i>piALU</i></i>RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly

Blackwell, Benjamin; Lopez, Mary F.; Wang, Jianrong; Krastins, Bryan; Sarracino, David; Tollervey, James; Dobke, Marek; Jordan, I. King; Lunyak, Victoria V.

doi:10.4161/mge.19032

Cited by 21 publications

(26 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2). First, within the lncRNA, the TE sequence continues to perform a similar function as that for which it evolved in the ancestral TE, most likely through protein binding (Blackwell et al 2012). Alternatively the TE sequence might mediate hybridization to other, homologous nucleic acid sequences (Gong and Maquat 2011).…”

Section: Hypothesis: Transposable Elements As Functional Domains Of Lmentioning

confidence: 99%

“…RNPs, such as Alu or LINE1, have been shown to interact with a diverse range of host proteins, including chromatin modifiers, transcription factors, DNA repair factors, RNA binding proteins, and RNA Polymerase II (Mariner et al 2008;Blackwell et al 2012;Goodier et al 2013). It is reasonable to infer that fresh insertion of TE repeats within lncRNA may confer binding to the same complexes, thereby constituting preformed protein-binding domains.…”

Section: Type I: Protein Interactionmentioning

confidence: 99%

“…It is reasonable to infer that fresh insertion of TE repeats within lncRNA may confer binding to the same complexes, thereby constituting preformed protein-binding domains. Among those protein classes recently found to interact with Alu and LINE1 are many, such as chromatin regulatory complexes, that are highly relevant to known functional roles of lncRNA (Blackwell et al 2012;Goodier et al 2013). Thus, there is a relationship, at least at early evolutionary stages, between the TE's activity in the lncRNA context and its role in its original TE context.…”

Section: Type I: Protein Interactionmentioning

confidence: 99%

“…It was recently shown that age-related macular degeneration arises from aberrant Dicer processing in the retina, leading to the accumulation of Alu transcripts, which results in toxicity and consequently retinal neuronal degeneration (Kaneko et al 2011). A recent screen for binding partners of Alu sequence discovered a diverse repertoire of protein partners, including a number of chromatin remodeling factors and transcription factors (Blackwell et al 2012). Indeed, ongoing work by Kugel and Goodrich have demonstrated that Alu and other SINE transcripts are capable of binding and repressing RNA Polymerase II activity through the adoption of a modular structure, thereby repressing global gene transcription during heat shock (Mariner et al 2008).…”

Section: Transposable Element Rna Is Biologically Activementioning

confidence: 99%

“…In the case in which this involves the adoption of a structure for protein binding, then we might expect that the TE fragment will confer binding of the host lncRNA to natural partners of the TE, specifically the TE RNP ( Fig. 2; Blackwell et al 2012;Goodier et al 2013). Such RNPs are known to interact with a wide range of proteins, including those with regulatory functions of clear relevance to lncRNA function (Blackwell et al 2012).…”

Section: Tes and The Evolution Of Complex Lncrna Regulatory Networkmentioning

confidence: 99%

See 4 more Smart Citations

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

Johnson

Guigó

2014

RNA

282

231

View full text Add to dashboard Cite

Our genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which are likely to have genetic regulatory functions. It has been proposed that lncRNA are organized into combinations of discrete functional domains, but the nature of these and their identification remain elusive. One class of sequence elements that is enriched in lncRNA is represented by transposable elements (TEs), repetitive mobile genetic sequences that have contributed widely to genome evolution through a process termed exaptation. Here, we link these two concepts by proposing that exonic TEs act as RNA domains that are essential for lncRNA function. We term such elements Repeat Insertion Domains of LncRNAs (RIDLs). A growing number of RIDLs have been experimentally defined, where TE-derived fragments of lncRNA act as RNA-, DNA-, and protein-binding domains. We propose that these reflect a more general phenomenon of exaptation during lncRNA evolution, where inserted TE sequences are repurposed as recognition sites for both protein and nucleic acids. We discuss a series of genomic screens that may be used in the future to systematically discover RIDLs. The RIDL hypothesis has the potential to explain how functional evolution can keep pace with the rapid gene evolution observed in lncRNA. More practically, TE maps may in the future be used to predict lncRNA function.

show abstract

Section: Hypothesis: Transposable Elements As Functional Domains Of Lmentioning

confidence: 99%

Section: Type I: Protein Interactionmentioning

confidence: 99%

Section: Type I: Protein Interactionmentioning

confidence: 99%

Section: Transposable Element Rna Is Biologically Activementioning

confidence: 99%

Section: Tes and The Evolution Of Complex Lncrna Regulatory Networkmentioning

confidence: 99%

See 3 more Smart Citations

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

Johnson

Guigó

2014

RNA

282

231

View full text Add to dashboard Cite

show abstract

Untangling the web: The diverse functions of the PIWI/piRNA pathway

Mani

Juliano

2013

Molecular Reproduction Devel

View full text Add to dashboard Cite

SUMMARY Small RNAs impact several cellular processes through gene regulation. Argonaute proteins bind small RNAs to form effector complexes that control transcriptional and post-transcriptional gene expression. PIWI proteins belong to the Argonaute protein family, and bind PIWI-interacting RNAs (piRNAs). They are highly abundant in the germline, but are also expressed in some somatic tissues. The PIWI/piRNA pathway has a role in transposon repression in Drosophila, which occurs both by epigenetic regulation and post-transcriptional degradation of transposon mRNAs. These functions are conserved, but clear differences in the extent and mechanism of transposon repression exist between species. Mutations in piwi genes lead to the upregulation of transposon mRNAs. It is hypothesized that this increased transposon mobilization leads to genomic instability and thus sterility, although no causal link has been established between transposon upregulation and genome instability. An alternative scenario could be that piwi mutations directly affect genomic instability, and thus lead to increased transposon expression. We propose that the PIWI/piRNA pathway controls genome stability in several ways: suppression of transposons, direct regulation of chromatin architecture and regulation of genes that control important biological processes related to genome stability. The PIWI/piRNA pathway also regulates at least some, if not many, protein-coding genes, which further lends support to the idea that piwi genes may have broader functions beyond transposon repression. An intriguing possibility is that the PIWI/piRNA pathway is using transposon sequences to coordinate the expression of large groups of genes to regulate cellular function.

show abstract

Genome-wide identification, functional prediction and expression profiling of long non-coding RNAs in Camelina sativa

Subburaj

Jeon

et al. 2018

Plant Growth Regul

View full text Add to dashboard Cite

Protein interactions withpiALURNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly

Cited by 21 publications

References 47 publications

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

Untangling the web: The diverse functions of the PIWI/piRNA pathway

Genome-wide identification, functional prediction and expression profiling of long non-coding RNAs in Camelina sativa

Contact Info

Product

Resources

About