Distinctive structures between chimpanzee and humanin a brain noncoding RNA

Бениаминов, А. Д.; Westhof, Éric; Krol, Alain

doi:10.1261/rna.1054608

Cited by 56 publications

(48 citation statements)

References 11 publications

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“…HAR1 was identified to be bidirectionally transcribed as part of two longer lncRNAs in a sense-antisense pair: the lncRNA HAR1A (HAR1 forward) on the forward genomic strand, and the lncRNA HAR1B (HAR1 reverse) on the opposite strand. The HAR1 region was found to be 118 nt long, to reside precisely in the exon-to-exon sense-antisense overlap of these two lncRNA genes (whose reference transcripts range from 900 to nearly 3,000 nt in length, including the HAR1 118 nt sequence), and to fold into an organized secondary RNA structure whose differences between human and chimpanzee have been biochemically confirmed by independent studies 18,20 . Interestingly, it was suggested that the mutations in the human HAR1 compared to the chimpanzee sequence, stabilized this RNA structure further and were therefore evolutionary produced through positive selection 20 .…”

Section: Lack Of Conservation Does Not Imbue a Lack Of Functionmentioning

confidence: 85%

“…The HAR1 region was found to be 118 nt long, to reside precisely in the exon-to-exon sense-antisense overlap of these two lncRNA genes (whose reference transcripts range from 900 to nearly 3,000 nt in length, including the HAR1 118 nt sequence), and to fold into an organized secondary RNA structure whose differences between human and chimpanzee have been biochemically confirmed by independent studies 18,20 . Interestingly, it was suggested that the mutations in the human HAR1 compared to the chimpanzee sequence, stabilized this RNA structure further and were therefore evolutionary produced through positive selection 20 . Alternatively, this varied secondary structure may be involved in sense antisense pairing of HAR1B and HAR1A, which are reverse complement and overlapping one another, thus allowing for RNA:RNA pairing and higher ordered secondary structures to form.…”

Section: Lack Of Conservation Does Not Imbue a Lack Of Functionmentioning

confidence: 85%

See 1 more Smart Citation

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

Johnsson

Lipovich

Grandér

et al. 2014

Biochimica et Biophysica Acta (BBA) - General Subjects

631

465

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Background Recent advances in genome wide studies have revealed the abundance of long non-coding RNAs (lncRNAs) in mammalian transcriptomes. The ENCODE Consortium has elucidated the prevalence of human lncRNA genes, which are as numerous as protein-coding genes. Surprisingly, many lncRNAs do not show the same pattern of high interspecies conservation as protein-coding genes. The absence of functional studies and the frequent lack of sequence conservation therefore make functional interpretation of these newly discovered transcripts challenging. Many investigators have suggested the presence and importance of secondary structural elements within lncRNAs, but mammalian lncRNA secondary structure remains poorly understood. It is intriguing to speculate that in this group of genes, RNA secondary structures might be preserved throughout evolution and that this might explain the lack of sequence conservation among many lncRNAs. Scope of review Here, we review the extent of interspecies conservation among different lncRNAs, with a focus on a subset of lncRNAs that have been functionally investigated. The function of lncRNAs is widespread and we investigate whether different forms of functionalities may be conserved. Major conclusions Lack of conservation does not imbue a lack of function. We highlight several examples of lncRNAs where RNA structure appears to be the main functional unit and evolutionary constraint. We survey existing genomewide studies of mammalian lncRNA conservation and summarize their limitations. We further review specific human lncRNAs which lack evolutionary conservation beyond primates but have proven to be both functional and therapeutically relevant. General significance Pioneering studies highlight a role in lncRNAs for secondary structures, and possibly the presence of functional “modules”, which are interspersed with longer and less conserved stretches of nucleotide sequences. Taken together, high-throughput analysis of conservation and functional composition of the still-mysterious lncRNA genes is only now becoming feasible.

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Section: Lack Of Conservation Does Not Imbue a Lack Of Functionmentioning

confidence: 85%

Section: Lack Of Conservation Does Not Imbue a Lack Of Functionmentioning

confidence: 85%

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

Johnsson

Lipovich

Grandér

et al. 2014

Biochimica et Biophysica Acta (BBA) - General Subjects

631

465

View full text Add to dashboard Cite

show abstract

“…Evidence that many of these RNAs are likely to be functional is provided by the high temporal and spatial specificity of their transcription, especially in the brain [50,51] and by sequence and structural conservation within or across phylogenetic groups. Moreover, given that the numbers, types and even sequences of proteins are highly conserved among mammals, and even among animals of all kinds, evidence is accumulating that evolutionary processes producing new animal species, for example the emergence of humans from the great ape lineage, may be driven in part by rapid RNA evolution [52–54]. Understanding the functions of new RNAs can be aided by predictions of their 2D and 3D structures.…”

Section: Introductionmentioning

confidence: 99%

The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs

Parlea

Sweeney

Hosseini-Asanjan

et al. 2016

Methods

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RNA 3D motifs occupy places in structured RNA molecules that correspond to the hairpin, internal and multi-helix junction “loops” of their secondary structure representations. As many as 40% of the nucleotides of an RNA molecule can belong to these structural elements, which are distinct from the regular double helical regions formed by contiguous AU, GC, and GU Watson-Crick basepairs. With the large number of atomic- or near atomic-resolution 3D structures appearing in a steady stream in the PDB/NDB structure databases, the automated identification, extraction, comparison, clustering and visualization of these structural elements presents an opportunity to enhance RNA science. Three broad applications are: (1) identification of modular, autonomous structural units for RNA nanotechnology, nanobiology and synthetic biology applications; (2) bioinformatic analysis to improve RNA 3D structure prediction from sequence; and (3) creation of searchable databases for exploring the binding specificities, structural flexibility, and dynamics of these RNA elements. In this contribution, we review methods developed for computational extraction of hairpin and internal loop motifs from a non-redundant set of high-quality RNA 3D structures. We provide a statistical summary of the extracted hairpin and internal loop motifs in the most recent version of the RNA 3D Motif Atlas. We also explore the reliability and accuracy of the extraction process by examining its performance in clustering recurrent motifs from homologous ribosomal RNA (rRNA) structures. We conclude with a summary of remaining challenges, especially with regard to extraction of multi-helix junction motifs.

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“…7a, b Evidence is rapidly accumulating that much of this RNA production plays critical roles in gene regulation, development, adaptation to environmental changes, and evolutionary plasticity. 7c, 46 Still, the structures and functions of most ncRNAs remain unknown. Thus, another task is to predict the secondary (2D) and tertiary (3D) structures of ncRNAs identified in the genomic sequences or discovered by transcriptome projects.…”

Section: What Is the Scope Of Rna Structural Bioinformatics?mentioning

confidence: 99%

Quantum Chemical Studies of Nucleic Acids: Can We Construct a Bridge to the RNA Structural Biology and Bioinformatics Communities?

Šponer

Petrov²,

Leontis³

2010

J. Phys. Chem. B

123

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In this feature article, we provide a side-by-side introduction for two research fields: quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics. Our main aim is to demonstrate that these research areas, while largely separated in contemporary literature, have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids. We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures, while also assessing the limitations of these approaches. The ultimate aim is to attain valuable physico-chemical insights regarding the nature of the fundamental molecular interactions and how they shape RNA structures, dynamics, function and evolution.

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Distinctive structures between chimpanzee and humanin a brain noncoding RNA

Cited by 56 publications

References 11 publications

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs

Quantum Chemical Studies of Nucleic Acids: Can We Construct a Bridge to the RNA Structural Biology and Bioinformatics Communities?

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