Posts tagged: Genome Biology

Word of caution: a new method to study RNA-seq biases

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Shaury Nash CC BY-SA

As next generation sequencing methods quickly become ubiquitous tools of genomics, more and more effort is directed to understand what are the limitations of these approaches. These limitations present themselves quite often in the form of coverage biases.

Last year Genome Biology published a study from David Jaffe and colleagues that looked at coverage biases in DNA sequencing. The authors used a suite of computational tools for bias assessment and applied them to a number of commonly used technologies. It turned out that, for instance, PacBio coverage is the least biased; and that high- and low-CG regions and long runs of homopolymers are very prone to coverage biases. They emphasized that the presence of such biases may lead to …

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Genome regulation: it’s the geometry, stupid!

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Transcription factories (from Cope et al.)

The emerging realization that cells modify the three dimensional arrangement of DNA in order to regulate the genome is changing the way that scientists think about how and when genes are expressed. A new study in Genome Biology goes so far as to show that information about the shape of the genome is sufficient on its own to accurately classify cells according to leukemia subtype.

Traditional genomics studies have examined the genome as a linear DNA sequence. According to this viewpoint, each gene is surrounded by adjacent sequence – in particular the region of the genome immediately upstream – that regulates its expression: when the gene is turned off and on, and to what degree.

It has long been known that …

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It’s in your genes: a new method for cancer drug response prediction

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source: flickr;  viZZZual.com (CC BY)

One of the greatest challenges of current medicine is predicting how a patient will respond to a given drug. In an ideal world, where time, money and – most importantly – the patient’s well-being and survival are not an issue, we would simply either keep trying different treatments until hitting the jackpot, or perhaps harvest the patient’s cells and try a range of treatments in vitro. The problem is, of course, that the world is not ideal and such in vitro testing is usually not practical and, in general, especially in the case of many of the most debilitating diseases, patients often don’t have time to waste.

It is then not really surprising that many researchers have been …

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Methylating much?

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source: flickr, calciostreaming (CC BY)

Our readers might have gotten distracted this month by discussions on whether it is right or wrong for Illumina to limit researchers’ use of their kit, and so we are here to help you regain focus: after a deliberately thematic issue on the RBPome, we have just published an accidentally thematic issue on DNA methylation.

Useful tools

This month Genome Biology publishes three tools that many working on DNA methylation should find quite handy.

Mark Robinson (of edgeR, which he published together with another of this issue’s authors, Gordon Smyth) and company present a new method, BayMeth, for the effective quantification of data generated with DNA-methylation-capture-seq techniques (MBD-seq, MeDIP-seq and so on). So if you …

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Why mosquitoes resist – a new molecular marker sheds light on insecticide resistance

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Mosquito

This guest blog is written by Vera Unwin. With an MSc in Medical Parasitology and experience as a Parasitology Research Technician, Vera regularly writes for Bugbitten, our blog on parasites and vectors.

Insecticides are fundamental to vector control programs for vector borne diseases. Malaria is one of the most dangerous of these diseases, with an estimated 627,000 deaths per year. Reducing transmission by targeting mosquito populations is an integral strategy for controlling this disease. Such programs are heavily reliant on the use of insecticides- in the form of Insecticide Treated bed Nets (ITNS) and Indoor Residual Spraying (IRS)- to decrease mosquito populations and so lower transmission of the disease.

 

The widespread use of insecticides has inevitably …

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Uniform diversity: a genome-wide study of PRC1 ortholog localization

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Poly-combs! /source: Sean McMenemy (CC BY)

Polycomb-group proteins are a well-characterized family of proteins involved in chromatin remodeling. In mammals, Polycomb-group proteins form two multiprotein complexes: Polycomb repressive complex 2 (PRC2), which represses gene expression, and PRC1.

PRC1, unlike its highly conserved sister, is a masterpiece of variety. It comprises the subunits Polycomb (Pc), Posterior sex combs (Psc), Polyhomeotic (Ph) and Sex combs extra (Sce) – but in humans there are five orthologs of Pc, six of Psc, three of Ph and two of Sce, which can, in theory, give rise to up to 180 different versions of PRC1. And while we don’t know for sure how many versions of PRC1 are to be found in human cells, one thing is clear: there doesn’t …

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The RBPome: unlocking a new layer in gene regulation

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gblogo_small

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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Cancer progression Genome Biology special issue: call for papers

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cancer-prog-genome-biology_v6

Genome Biology would like to announce that we are now inviting Research, Method or Software manuscript submissions for publication in a special issue on cancer progression and heterogeneity, which is planned for late summer 2014.

Recent advances, such as single-cell sequencing technologies, are allowing us to study cancer genomics at a depth that was not previously possible. Now, Genome Biology wants to highlight the importance of this field by publishing a special issue with an emphasis on cancer progression and heterogeneity. We will consider Research, Method and Software manuscripts describing insights into, or developing methods for studying, all aspects of the genomics of cancer progression, including the clonal evolution of cancer, cancer heterogeneity, metastasis, single-cell …

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Ready yourself for the RBPome

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gblogo_small

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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moss

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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