pRNA

Wehner, Stefanie; Dörrich, Anja K.; Ciba, P.; Wilde, Annegret; Marz, Manja

doi:10.4161/rna.27448

Cited by 17 publications

(12 citation statements)

References 23 publications

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“…Specifically, these non-coding RNAs interact with complementary sequences within the rDNA promoter forming a RNA–DNA–DNA triplex [ 73 ] that is specifically recognized by the DNA methyltransferase DNMT3b, thereby inducing DNA methylation and transcriptional silencing [ 74 , 75 ]. Indeed, the pRNA triplex structure with DNA displaces the transcription factor, TTF-I, from its binding site [ 73 ].…”

Section: Mechanisms Of Regulation Mediated By Antisense Lncrnamentioning

confidence: 99%

Neighboring Gene Regulation by Antisense Long Non-Coding RNAs

Villegas

Zaphiropoulos

2015

IJMS

251

213

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Antisense transcription, considered until recently as transcriptional noise, is a very common phenomenon in human and eukaryotic transcriptomes, operating in two ways based on whether the antisense RNA acts in cis or in trans. This process can generate long non-coding RNAs (lncRNAs), one of the most diverse classes of cellular transcripts, which have demonstrated multifunctional roles in fundamental biological processes, including embryonic pluripotency, differentiation and development. Antisense lncRNAs have been shown to control nearly every level of gene regulation—pretranscriptional, transcriptional and posttranscriptional—through DNA–RNA, RNA–RNA or protein–RNA interactions. This review is centered on functional studies of antisense lncRNA-mediated regulation of neighboring gene expression. Specifically, it addresses how these transcripts interact with other biological molecules, nucleic acids and proteins, to regulate gene expression through chromatin remodeling at the pretranscriptional level and modulation of transcriptional and post-transcriptional processes by altering the sense mRNA structure or the cellular compartmental distribution, either in the nucleus or the cytoplasm.

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Section: Mechanisms Of Regulation Mediated By Antisense Lncrnamentioning

confidence: 99%

Neighboring Gene Regulation by Antisense Long Non-Coding RNAs

Villegas

Zaphiropoulos

2015

IJMS

251

213

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“…23,33 In Tip5 the deacetylation of a lysine residue within the second AT-hook leads to increased binding of the evolutionarily conserved non-coding pRNA, and to enhanced heterochromatin formation at the rDNA locus. 24,34 Additionally, ncRNA binding of the insulator protein CTCF was also described recently and the RNA-binding domain was mapped to the C-terminus of the protein. 35 This chromatin regulator protein does not possess known RNA-binding domains but it contains an AT-hook at its C-terminus.…”

Section: The Relationship Of Eat-hooks To Other Short K/r-rich Proteimentioning

confidence: 99%

The extended AT-hook is a novel RNA binding motif

et al. 2015

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The AT-hook has been defined as a DNA binding peptide motif that contains a glycine-arginine-proline (G-R-P) tripeptide core flanked by basic amino acids. Recent reports documented variations in the sequence of AT-hooks and revealed RNA binding activity of some canonical AT-hooks, suggesting a higher structural and functional variability of this protein domain than previously anticipated. Here we describe the discovery and characterization of the extended AT-hook peptide motif (eAT-hook), in which basic amino acids appear symmetrical mainly at a distance of 12–15 amino acids from the G-R-P core. We identified 80 human and 60 mouse eAT-hook proteins and biochemically characterized the eAT-hooks of Tip5/BAZ2A, PTOV1 and GPBP1. Microscale thermophoresis and electrophoretic mobility shift assays reveal the nucleic acid binding features of this peptide motif, and show that eAT-hooks bind RNA with one order of magnitude higher affinity than DNA. In addition, cellular localization studies suggest a role for the N-terminal eAT-hook of PTOV1 in nucleocytoplasmic shuttling. In summary, our findings classify the eAT-hook as a novel nucleic acid binding motif, which potentially mediates various RNA-dependent cellular processes.

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“…Conserved across eutharians, various levels of sequence conservation, and highly conserved secondary-structure motifs Mayer et al, 2006Mayer et al, , 2008Santoro et al, 2010;Schmitz et al, 2010;Guetg et al, 2012;Jacob et al, 2013;Savić et al, 2014;Wehner et al, Rinn et al, 2007;Gupta et al, 2010;Tsai et al, 2010;Li et al, 2013;Somarowthu et al, 2015;Zhang et al, 2015;Portoso et al, 2017 ncSRA Activation of steroid receptors (isoforms of SRA code for protein)…”

Section: Discussionmentioning

confidence: 99%

Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans

Ramírez-Colmenero¹,

Oktaba

2020

Front. Genet.

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Long non-coding RNAs (lncRNAs) have important regulatory functions across eukarya. It is now clear that many of these functions are related to gene expression regulation through their capacity to recruit epigenetic modifiers and establish chromatin interactions. Several lncRNAs have been recently shown to participate in modulating chromatin within the spatial organization of the genome in the three-dimensional space of the nucleus. The identification of lncRNA candidates is challenging, as it is their functional characterization. Conservation signatures of lncRNAs are different from those of protein-coding genes, making identifying lncRNAs under selection a difficult task, and the homology between lncRNAs may not be readily apparent. Here, we review the evidence for these higher-order genome organization functions of lncRNAs in animals and the evolutionary signatures they display.

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pRNA

Cited by 17 publications

References 23 publications

Neighboring Gene Regulation by Antisense Long Non-Coding RNAs

Neighboring Gene Regulation by Antisense Long Non-Coding RNAs

The extended AT-hook is a novel RNA binding motif

Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans

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