Got Headache?

Source: Campillos et al (2008). Drug Target Identification Using Side-Effect Similarity. Science 321:263-266.

Living organisms are highly complex systems and when a foreign molecule is introduced (i.e. injected) into the body, non-specific bindings may occur that result in unwanted (and sometimes harmful) side-effects. Target prediction is usually done through structural similarities; where similar compounds affect identical targets. However, two completely different molecules may also share targets which is overlooked in this classic method. The authors of this paper combine the strength of structure-based similarities with symptoms-based knowledge to draw more conclusive predictions. They start with ~700 drugs and extract their reported side-effects. They remove the inherent redundancy (e.g. vomiting and nausea largely overlap) and also normalize the probability of sharing a target based on the total number of occurrences (e.g. dizziness is quite common but other side-effect are more specific).

Following their prediction step, they also validate 20 predicted drugs with significant probabilities of sharing a target (note that all of these drugs are selected so that they represent different classes of drugs with varying therapeutic purposes). They succeed in validating 13/20 of these cases using in vitro and in vivo experiments which is quite impressive.

Graded Expression of A Protein Under Positive Selection

Source: Neuenschwander et al. (2008). A simple selection strategy for evolving highly efficient enzymes. Nat Biotech 25 (10): 1145-47.

This paper discusses a more robust method for directed evolution. Many enzymes can be subjected to evolution if they can be engineered into a background where their activity is essential for growth and survival of the host. This approach works find but there are a number of obstacles. For example, growth is a broad phenotype; even a limited activity of the enzyme might be sufficient to sustain growth resulting in the saturation of the evolution process. In this paper, he authors make the case that by a gradual decrease in the transcription, translation and half-life of the protein of interest, we can reduce the concentration of the available enzyme thus pushing it back into the optimization process. As shown below, their experimental set-up includes an inducible tet promoter and an ssrA for protein degradation and lowerig half life.

Multiplex Color Coded Probe Pairs to Replace Microarrays

Source: Geiss et al. (2008). Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat biotech 26(3):317-325.

This is a very cool paper with an exciting approach... The authors claim that their method is more sensitive compared to chip-based microarrays. Their method involves synthesizing two probes (a capture probe and a reporter probe). The capture probe is simply a biotinylated oligo with a 35-50 complementary region to the target mRNA; whereas, the reporter probe, in addition to a complementary region contains a series of sequences that can be targeted by colored probes. The sequence of these colors along the reporter oligo is unique for each mRNA (Figure a).

The pair of probes for each target is added to the mRNA solution along with the colored probes. Upon the formation of the complex, the oligos are bound to a surface from the biotin group on the capture probe and subjected to a electric field to extend all the molecules to alinear format. The resulting image is then analysed and the number of transcripts for each type is counted (see Figures b-c).


This method (as cool as it seems) is quite expensive and the fact that it is more sensitive does not make it a viable protocol. Specially, with the current emergence of RNA-seq it seems difficult to establish a competitive method.

Modifying the Translation Efficiency: The Role of Codon Pair Biases

Source: Coleman et al (2008). Virus Attenuation by Genome-Scale Changes in Codon Pair Bias. Science 320: 1784-1787.

While there is a huge number of possibilities for two adjacent codons, many of them rarely happen and some of them occur more frequently than predicted by chance alone. This distribution of codon frequencies, in part, can be explained by the amino acid usages in the proteins; however, even synonymous codons show drastically different codon-pair biases. Although the actual mechanism is not known, these biases are believed to affect translation efficiency.

In this paper, the authors use the concept of codon pair biases to synthesize polioviruses with maximum or minimum codon-pair biases. For example, in the min version, for every two amino acids they choose the least frequent codon pair. They subsequentlu show that these altered codon-pair usages drastically affects the virulence of polio virus. These viruses are highly attenuated can be actually used as vaccines to boost the immunity of the tested rats.

The Path to Pluripotency: Dissecting the Reprogrammed Cells

Source: Mikkelsen et al (2008). Dissecting direct reprogramming through integrative genomic analysis. Nature 454: 49-55.

I am not really familiar with this field but I found this paper interesting in the sense that it employs whole-genome methods to tackle a specific and important problem. Human and mouse cells can be transformed back into a pluripotent stage (termed iPS cells) through re-expression of specific transcription factors. However, the success rate of this method is low and the molecular characteristics of this transition is poorly understood.

The first step in reprogramming involves the ectopic expressin of Oct4, Sox2, Klf4 and c-Myc transcription factors. De-differentitation and proliferation of the cells is marked by a decrease in the expression of tissue-specific genes (in this case Snai1 and Snai2) and an increase in DNA replication and cell-cycle progression genes. A parallel boost in the expression of anti-proliferative genes suggests that the mechanism to inhibit uncontrolled prliferation is intact.

Reprogrammed iPS cells, by large, share the expression of key genes with the embryonic stem cells. In this study, however, the authors have extended this similarity to the chromatin structure as well. Much of the details, in this paper, come from studying the partially reprogrammed cells. For example, MCV8, a cell line achieved as a byproduct of an unsuccessful reprogramming, can give rise to both iPS and differentiated cells with an inherent stochasticity involved.

Based on their observations, the authors argue that the cells fail to reprogram because:

1. The cells may induce anti-proliferative genes in response to proliferative stress;
2. They may inappropriately activate or fail to repress endogenous or ectopic transcription factors, and become ‘trapped’ in differentiated states;
3. They may fail to reactivate hypermethylated pluripotency genes.

The bottom line is the fact that reprogramming can be facilitated through another layer of gene regulation (besides the initial four transcription factors).

Fine-tuning Transcription Level: Cyclical Methylation of Promoters

Source: Kangaspeska et al. (2008). Transient cyclical methylation of promoter DNA. Nature 452:112-115.

Apart from nuclear compartmentalization (see previous post), effect of transcription factors and histone modifications, another general regulation mechanism of gene expression exists which transcedes the generations and carries the epigenetic information. Methylation at CpG sites in the promoters is a known repressor of transcription; these methylations however portray a rather static landscape of gene regulation; i.e. until now. Authors of this paper make the case for a dynamic scene regarding methylation status at the CpG dinucleotides. Their results (e.g. see the figure below) show a cyclical methylation and de-methylation of pS2 promoter with a periodocity of ~100 minutes (compared to the constitutively expressed promoter PPIA).The role of this sinuoidal methylation/de-methylation is unknown but one can envisage many key properties that may emerge from this behavior. For example, a general circadian rhythm may be in charge, thus controling the time-scale in which the genes are expressed relative to each other. Moreover, this rhythmic expression, in fact, is capable of increasing the efficiency by which the transcript levels can be controlled.

Repression by Exile: Repositioning to Nuclear Lamina Represses Expression

Source: Reddy et al. (2008). Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452:243-247.

The correlation between nuclear compartmentalization and gene expression is long known; however, we don't know whether the observed repression of transcription is a by-product of switching compartments or they simply co-occur for other reasons. This paper makes the case for the former; the authors design a construct that can be attached to nuclear membrane upon induction. The reporter set-up (shown below) involves a hygromycin resistance gene (Tk-hyg) as well as multiple copies of Lac operators (lacO) that constitute binding sites for the E. coli Lac repressor (LacI). A GFP-LacI-ΔEMD which is tethered to the nuclear membrane through ΔEMD can be induced by IPTG to recruite lacO sites on the reporter. The localization of the reporter can be simultaneouly monitored using a GFP-LacI fusion.

Using this set-up the authors make the case for a general repression mechanism through membrane tethering. They also employ other methods (e.g. FISH and DamID) to further validate their results which I don't get into.