Eesha Sharma3, Tim Sterne-Weiler3, Dave O’Hanlon, Benjamin J. Blencowe correspondence email
3Co-first author
Highlights
• LIGR-seq is a method for the global-scale mapping RNA-RNA interactions in vivo
• LIGR-seq data reveal a complex RNA-RNA interactome in human cells
• Hundreds of trans-interactions involving known and orphan ncRNAs are detected
• The orphan snoRNA SNORD83B regulates levels of its LIGR-seq-detected target mRNAs
Summary
The majority of the human genome is transcribed into non-coding (nc)RNAs that lack known biological functions or else are only partially characterized. Numerous characterized ncRNAs function via base pairing with target RNA sequences to direct their biological activities, which include critical roles in RNA processing, modification, turnover, and translation. To define roles for ncRNAs, we have developed a method enabling the global-scale mapping of RNA-RNA duplexes crosslinked in vivo, “LIGation of interacting RNA followed by high-throughput sequencing” (LIGR-seq). Applying this method in human cells reveals a remarkable landscape of RNA-RNA interactions involving all major classes of ncRNA and mRNA. LIGR-seq data reveal unexpected interactions between small nucleolar (sno)RNAs and mRNAs, including those involving the orphan C/D box snoRNA, SNORD83B, that control steady-state levels of its target mRNAs. LIGR-seq thus represents a powerful approach for illuminating the functions of the myriad of uncharacterized RNAs that act via base-pairing interactions.
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NOTA DESTE BLOGGER:
Veja como o EurekAlert (da AAAS - American Association for the Advancement of Science, a SBPC dos gringos) destacou o uso desta tecnologia:
Shedding light on the 'dark matter' of the genome
New tool allows scientists to understand the role of non-coding RNAs
UNIVERSITY OF TORONTO
What used to be dismissed by many as "junk DNA" is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) -- genome's messages that do not code for proteins -- in development and disease. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions.
...
ncRNAs come in multiple flavours: there's rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA's place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control what goes on in the cell, nor how they do this. The new technology developed by Blencowe's group has been able to pick up new interactions involving all classes of RNAs and has already revealed some unexpected findings.
The team discovered new roles for small nucleolar RNAs (snoRNAs) that normally guide chemical modifications of other ncRNAs. It turns out that some snoRNAs can also regulate stability of a set of protein-coding mRNAs. In this way, snoRNAs can also directly influence which proteins are made, as well as their abundance, adding a new level of control in cell biology. And this is only the tip of the iceberg as the researchers plan to further develop and apply their technology to investigate the ncRNAs in different settings.
[NOTA BENE: Foram "eles" que disseram isso]
O que foi considerado pela Nomenklatura científica como DNA "lixo", está se mostrando cada vez mais um tesouro de informação genética. Pensar que em 1998, William Dembski, um dos principais teóricos da TDI afirmou:
William Dembski predicted function for non-coding "junk"-DNA based upon intelligent design:
But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it.
in "Intelligent Science and Design", First Things, Vol. 86:21-27 (October 1998).
PERGUNTA CÁUSTICA DESTE BLOGGER:
Então, quem é que impede o avanço da ciência, cara-pálida? Os darwinistas ou a turma do Design Inteligente???
O que foi considerado pela Nomenklatura científica como DNA "lixo", está se mostrando cada vez mais um tesouro de informação genética. Pensar que em 1998, William Dembski, um dos principais teóricos da TDI afirmou:
William Dembski predicted function for non-coding "junk"-DNA based upon intelligent design:
But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it.
in "Intelligent Science and Design", First Things, Vol. 86:21-27 (October 1998).
PERGUNTA CÁUSTICA DESTE BLOGGER:
Então, quem é que impede o avanço da ciência, cara-pálida? Os darwinistas ou a turma do Design Inteligente???
