Seung Gu Park

Expression breadth and expression abundance behave differently in correlations with evolutionary rates

BackgroundOne of the main objectives of the molecular evolution and evolutionary systems biology field is to reveal the underlying principles that dictate protein evolutionary rates. Several studies argue that expression abundance is the most critical component in determining the rate of evolution, especially in unicellular organisms. However, the expression breadth also needs to be considered for multicellular organisms.ResultsIn the present paper, we analyzed the relationship between the two expression variables and rates using two different genome-scale expression datasets, microarrays and ESTs. A significant positive correlation between the expression abundance (EA) and expression breadth (EB) was revealed by Kendalls rank correlation tests. A novel random shuffling approach was applied for EA and EB to compare the correlation coefficients obtained from real data sets to those estimated based on random chance. A novel method called a Fixed Group Analysis (FGA) was designed and applied to investigate the correlations between expression variables and rates when one of the two expression variables was evenly fixed.ConclusionsIn conclusion, all of these analyses and tests consistently showed that the breadth rather than the abundance of gene expression is tightly linked with the evolutionary rate in multicellular organisms.

SMG5–PNRC2 is functionally dominant compared with SMG5–SMG7 in mammalian nonsense-mediated mRNA decay

In mammals, nonsense-mediated mRNA decay (NMD) functions in post-transcriptional gene regulation as well as mRNA surveillance. A key NMD factor, Upf1, becomes hyperphosphorylated by SMG1 kinase during the recognition of NMD substrates. Hyperphosphorylated Upf1 interacts with several factors including SMG5, SMG6, SMG7 and PNRC2 to trigger rapid mRNA degradation. However, the possible cross-talk among these factors and their selective use during NMD remain unknown. Here, we show that PNRC2 is preferentially complexed with SMG5, but not with SMG6 or SMG7, and that downregulation of PNRC2 abolishes the interaction between SMG5 and Dcp1a, a component of the decapping complex. In addition, tethering experiments reveal the function of Upf1, SMG5 and PNRC2 at the same step of NMD and the requirement of SMG6 for Upf1 for efficient mRNA degradation. Intriguingly, microarray results reveal the significant overlap of SMG5-dependent NMD substrates more with PNRC2-dependent NMD substrates than with SMG7-dependent NMD substrates, suggesting the functional dominance of SMG5-PNRC2, rather than SMG5-SMG7, under normal conditions. The results provide evidence that, to some extent, endogenous NMD substrates have their own binding preference for Upf1-interacting adaptors or effectors.

Interleukin-1 Promotes Coagulation, Which Is Necessary for Protective Immunity in the Lung Against Streptococcus pneumoniae Infection

Interleukin (IL)-1 is a well-known cytokine for the initiation of innate immunity in bacterial infection. However, the underlying mechanism of IL-1 on the respiratory infection is not fully elucidated. We studied how IL-1 contributes to the host defense against Streptococcus pneumoniae. IL-1R(-/-) mice showed high mortality, local cytokine storm, and substantial infiltrates in the lower respiratory tract after intratracheal challenge with S. pneumoniae. The IL-1-deficient condition did not suppress the propagation of bacteria in the lung, although the recruitment and the bacteria-killing ability of neutrophils (CD11b(+)Ly6C(+)Ly6G(+)) were not defective compared with wild-type mice. Unexpectedly, we found that the transcription of fibrinogen alpha and gamma genes were highly activated in the lungs of wild-type mice after the infection, whereas no significant changes were found in IL-1R(-/-) mice. Of note, synthesis of fibrinogen was dependent on the IL-1-IL-6-Stat3 cascade. Treatment with recombinant fibrinogen improved survival and bacterial propagation in the IL-1R(-/-) mice and blockade of the coagulation increased the susceptibility of wild-type mice to pneumococcal pneumonia. Our findings suggest that IL-1 signaling leads to the synthesis of fibrinogen in the lung after pneumococcus infection and is followed by coagulation, which contributes to the control of bacterial infection in the pulmonary tract.

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

BackgroundGenomes of higher eukaryotes have surprisingly long first introns and in some cases, the first introns have been shown to have higher conservation relative to other introns. However, the functional relevance of conserved regions in the first introns is poorly understood. Leveraging the recent ENCODE data, here we assess potential regulatory roles of conserved regions in the first intron of human genes.ResultsWe first show that relative to other downstream introns, the first introns are enriched for blocks of highly conserved sequences. We also found that the first introns are enriched for several chromatin marks indicative of active regulatory regions and this enrichment of regulatory marks is correlated with enrichment of conserved blocks in the first intron; the enrichments of conservation and regulatory marks in first intron are not entirely explained by a general, albeit variable, bias for certain marks toward the 5’ end of introns. Interestingly, conservation as well as proportions of active regulatory chromatin marks in the first intron of a gene correlates positively with the numbers of exons in the gene but the correlation is significantly weakened in second introns and negligible beyond the second intron. The first intron conservation is also positively correlated with the gene’s expression level in several human tissues. Finally, a gene-wise analysis shows significant enrichments of active chromatin marks in conserved regions of first introns, relative to the conserved regions in other introns of the same gene.ConclusionsTaken together, our analyses strongly suggest that first introns are enriched for active transcriptional regulatory signals under purifying selection.

Positive selection signatures in the TLR7 family

While adaptive immunity genes evolve rapidly under the influence of positive selection, innate immune system genes are known to evolve slowly due to strong purifying selection. Among the sensors of the innate immune system, Toll-like receptors (TLRs) are particularly important due to their ability to recognize and respond to pathogen-associated molecular patterns (PAMP), such as lipopolysaccharides, peptidoglycans, and nucleic acids from bacteria or viruses. In the present study, we examine the evolutionary process that has operated on the TLR7 family genes TLR7, TLR8, and TLR9. The results demonstrate that the average Ka/Ks (the ratio between nonsynonymous and synonymous substitution rates) of each TLR family gene is far lower than one regardless of estimating methods, supporting previous observations of strong purifying selection in this gene family. Interestingly, however, analysis of Ka/Ks ratios along the coding regions of TLR7 family genes by sliding-window analysis reveals a few narrow high peaks (Ka/Ks > 1). The most prominent peak corresponds to a specific region in the ectodomain, which exists only in the TLR7 family, suggesting that this unique structure of the TLR7 family might have been a target of positive selection in a variety of lineages. Furthermore, maximum likelihood model tests suggest that positive selection is the best explanation for a certain fraction of the amino acid substitutions in the TLR9.

Putative functional genes in idiopathic dilated cardiomyopathy

Idiopathic dilated cardiomyopathy (DCM) is a complex disorder with a genetic and an environmental component involving multiple genes, many of which are yet to be discovered. We integrate genetic, epigenetic, transcriptomic, phenotypic, and evolutionary features into a method – Hridaya, to infer putative functional genes underlying DCM in a genome-wide fashion, using 213 human heart genomes and transcriptomes. Many genes identified by Hridaya are experimentally shown to cause cardiac complications. We validate the top predicted genes, via five different genome-wide analyses: First, the predicted genes are associated with cardiovascular functions. Second, their knockdowns in mice induce cardiac abnormalities. Third, their inhibition by drugs cause cardiac side effects in human. Fourth, they tend to have differential exon usage between DCM and normal samples. Fifth, analyzing 213 individual genotypes, we show that regulatory polymorphisms of the predicted genes are associated with elevated risk of cardiomyopathy. The stratification of DCM patients based on cardiac expression of the functional genes reveals two subgroups differing in key cardiac phenotypes. Integrating predicted functional genes with cardiomyocyte drug treatment experiments reveals novel potential drug targets. We provide a list of investigational drugs that target the newly identified functional genes that may lead to cardiac side effects.

Crowdsourcing: Spatial clustering of low-affinity binding sites amplifies in vivo transcription factor occupancy

To predict in vivo occupancy of a transcription factor (TF), current models consider only the immediate genomic context of a putative binding site (BS) – impact of the site’s spatial chromatin context is not known. Using clusters of spatially proximal enhancers, or archipelagos, and DNase footprints to quantify TF occupancy, we report for the first time an emergent group-level effect on occupancy, whereby BS within an archipelago experience greater in vivo occupancy than comparable BS outside archipelagos, i.e. BS not in spatial proximity with other homotypic BS. This occupancy boost is tissue-specific and scales robustly with the total number of BS, or enhancers, for the TF in the archipelago. Interestingly, enhancers within an archipelago are non-uniformly impacted by the occupancy boost; specifically, archipelago enhancers that are enriched for BS corresponding to degenerate motifs exhibit the greatest occupancy boost, as well as the highest overall accessibility, evolutionary selection, and expression at neighboring gene loci. Strikingly, archipelago-wide activity scales with expression of TFs with degenerate, but not specific, motifs. We explain these results through biophysical modelling, which suggests that spatially proximal homotypic BS facilitate TF diffusion, and induce boosts in local TF concentration and occupancy. Together, we demonstrate for the first time cooperativity among genomically distal homotypic BS that is contingent upon their spatial proximity, consistent with a TF diffusion model. Through leveraging of three-dimensional chromatin structure and TF availability, weak archipelago binding sites crowdsource their occupancy as well as context specificity, with coordinated switch-like effect on overall archipelago activity.

First intron length in mammals is associated with 5′ exon skipping rate

The first introns in eukaryotes are much longer than downstream introns. While the functional roles of large first introns have been studied extensively, investigations into the mechanisms leading up to extreme lengths are limited. Prominently, Hong et al. noted that the first introns are predominantly in 5’ UTR and suggested that its lengthening may have resulted from a 5’-ward shifting of donor site due to a lower selection on splice site, as well as a selection to occlude upstream cryptic translation start sites. Here we suggest exon skipping as an alternative mechanism for first intron lengthening. Exon skipping results in consecutive introns becoming part of a single longer intron. We reasoned that a 5’-biased exon skipping rate could lead to longer introns toward the 5’-end of the gene, especially the first intron. Based on multiple datasets in human and mouse, we indeed found that internal exons toward the 5’-end of the gene are skipped significantly more frequently than the downstream exons. Importantly, we show that 5’-biased exon skipping is supported by consistent 5’-bias in several genomic, epigenomic, contextual, and evolutionary features that can be functionally linked to exon skipping. Interestingly, we found that first introns are enriched for relics of, now defunct, exons, some of which may have been recruited for regulatory functions; a significantly greater-than-expected fraction of such exons are included in cDNAs in other mammals. Overall, our results offer 5’-biased exon skipping as a novel, and arguably more potent, alternative explanation for substantially lengthening of first introns.

Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy

Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. Many of these events involve synthetic rescue (SR) interactions, where the reduction in cancer cell viability caused by targeted gene inactivation is rescued by an adaptive alteration of another gene (the rescuer). Here we perform a genome-wide prediction of SR rescuer genes by analyzing tumor transcriptomics and survival data of 10,000 TCGA cancer patients. Predicted SR interactions are validated in new experimental screens. We show that SR interactions can successfully predict cancer patients’ response and emerging resistance. Inhibiting predicted rescuer genes sensitizes resistant cancer cells to therapies synergistically, providing initial leads for developing combinatorial approaches to overcome resistance proactively. Finally, we show that the SR analysis of melanoma patients successfully identifies known mediators of resistance to immunotherapy and predicts novel rescuers.

Analysis of putative miRNA function using a novel approach, GAPPS-miRTarGE

Deciphering the function of miRNA is one of the most important research subjects directed toward understanding the regulation of gene expression. Several experimental methodologies and bioinformatics programs have been developed, however, elucidating miRNA function has not been an easy task. Herein, we suggest a new method, GAPPS-miRTarGE, which is a novel methodology for predicting miRNA function based on the proportion of mRNA targets expressed during embryonic developmental stages, the Theilers stages (TS), in mice. GAPPS-miRTarGE is essentially a computational approach that groups miRNAs using shared expression patterns of their target genes during the 28 different TS. In this study, we present not only several examples derived from the GAPPS-miRTarGE analyses that confirm previously known miRNA functions but also examples of function prediction for valid but functionally unknown miRNAs. Furthermore, we show that tissue-centered GAPPS-miRTarGE, such as brain-centered or heart-centered, is useful for predicting miRNA function on a more detailed level.