Posts tagged: RBPome

The RBPome: unlocking a new layer in gene regulation

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In 2012, Genome Biology joined with a number of other journals to publish articles describing the ENCODE project, which set out to catalog how proteins bind to the genome in order to regulate transcription. With a similar goal, we published a special issue focused on epigenomics, which looked at both DNA-bound proteins and epigenetic modifications to the DNA molecule itself, again with a view to better understanding the regulation of transcription.

Although we continue to publish many epigenomics articles, we were keen this year to turn our attention to a new frontier of gene regulation: the RBPome. Just as proteins bind DNA to regulate transcription, RNA-binding proteins (RBPs) bind to the transcriptome in order to regulate RNA …

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Ready yourself for the RBPome

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Genome Biology today publishes the first set of articles in this month's special issue focused on 'the RBPome'. We will continue to publish RBPome articles throughout January, so look out for a heady mix of Research, Method, Software, Review, Research Highlight and Editorial articles.

'The RBPome' is our term for the rather wordy concept of 'RNA-binding proteins (RBPs) and their recognition elements within the transcriptome'. We hope to put the spotlight on gene regulation by RBPs, who until now have received less attention in the literature than gene regulatory components that act on DNA, such as transcription factors and histone modifications.

Who and what will be included in the issue?

One reason why the RBPome has been somewhat neglected is that …

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Binded by the light

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A major focus of Genome Biology's RBPome issue is the role that RNA-binding proteins play in regulating splicing within the transcriptome.

But what are the triggers that cause these proteins to change their binding patterns, and so modify splicing programs? Might environmental cues such as light be responsible?

A new article published today in our RBPome issue suggests that this might very well be the case.

In the study, Shih-Long Tu and colleagues (Academia Sinica, Taiwan) use the moss Physcomitrella patens to report the first example of light-mediated splicing in plants.

The moss was exposed to different light conditions, following which high-throughput sequencing was employed to monitor changes in splicing. The sequencing data suggested that light induces a …

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John Rinn and Jernej Ule: Guest Editors for Genome Biology RBPome issue

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Genome Biology is very pleased to announce the Guest Editors of our special issue on the RBPome as John Rinn and Jernej Ule. The issue will be published in January 2014.

RNA binding proteins and their recognition elements within the transcriptome
The issue will focus on RNA binding proteins (RBPs), and the RNA molecules and motifs to which they bind: it is this RNA landscape, sculpted by RBPs, that we believe to be a particularly exciting and fast-moving area of research at the present time.

Or, as John puts it: "Almost all RNA genes function through protein interactions - with the ongoing explosion of RNA genes being …

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The RBPome: submissions open for a new Genome Biology special issue

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Genome Biology is now inviting submissions for a special issue on "the RBPome". Advances in genomics have vastly improved our ability to investigate the cellular landscape of RNA-binding proteins (RBPs), and have uncovered a vast territory of gene regulation previously hidden from view. The interest in the RBPome that has arisen from these recent advances makes the topic a timely one, and we are confident that our special issue will stand out as an important contribution to this emerging field.

You might be wondering by now if we are guilty of 'badomics' when we use the term the RBPome? You be the judge – and we would welcome suggestions of whether there is a more succinct way to …

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Spicing up splicing – with poison exons

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Regulatory networks in which proteins bind to DNA to alter gene expression are a well established feature of cell biology, but less is known about whether this concept is mirrored by proteins that form interactions with RNA.

In a new article published in Genome Biology, an international team of researchers led by Karla Neugebauer (Max Planck Institute of Molecular Cell Biology and Genetics) show that the RNA-binding protein SRSF3 sits at the heart of an extensive regulatory network.

Using state-of-the-art iCLIP technology developed by co-author Jernej Ule, the study begins with a detailed exploration of the RNA binding targets for SRSF3 and its close relative SRSF4, two proteins known to function in RNA splicing. A large number of …

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