Sources and predictors of resolvable indel polymorphism assessed using rice as a model

The principal sources of genetic variation that can be assayed with restriction enzymes are base substitutions and insertions/deletions (indels). The likelihood of detecting indels as restriction fragment length polymorphisms (RFLPs) is determined by the size and frequency of the indels, and the ability to resolve small indels as RFLPs is limited by the distribution of restriction fragment sizes. In this study, we use aligned sequences from the indica and japonica subspecies of rice ( Oryza sativa L.) to quantify and compare the ability of restriction enzymes to detect indels. We look specifically at two abundant transposable element-derived indel sources: miniature inverted repeat transposable elements (MITEs) and long terminal repeat (LTR) retroelements. From this analysis we conclude that indels rather than base substitutions are the prevailing source of the polymorphism detected in rice. We show that, although MITE derived indels are more abundant than LTR-retroelement derived indels, LTR-retroelements have a greater capacity to generate visible restriction fragment length polymorphism because of their larger size. We find that the variation in the detectability of indels among restriction enzymes can be explained by differences in the frequency and dispersion of their restriction sites in the genome. The parameters that describe the fragment size distributions obtained with the restriction enzymes are highly correlated across the sequenced genomes of rice, Arabidopsis and human, with the exception of some extreme deviations in frequency for particular recognition sequences corresponding to variations in the levels and modes of DNA methylation in the three disparate organisms. Thus, we can predict the relative ability of a restriction enzyme to detect indels derived from a specific source based on the distribution of restriction fragment sizes, even when this is estimated for a distantly related genome.Electronic Supplementary Material Supplementary Material is available in the online version of this article at Communicated by M.-A. Grandbastien     

Genome-wide DNA polymorphism analyses using VariScan

Background  

DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis.     

Genome-wide annotation and functional identification of aphid GLUT-like sugar transporters

Background

Phloem feeding insects, such as aphids, feed almost continuously on plant phloem sap, a liquid diet that contains high concentrations of sucrose (a disaccharide comprising of glucose and fructose). To access the available carbon, aphids hydrolyze sucrose in the gut lumen and transport its constituent monosaccharides, glucose and fructose. Although sugar transport plays a critical role in aphid nutrition, the molecular basis of sugar transport in aphids, and more generally across all insects, remains poorly characterized. Here, using the latest release of the pea aphid, Acyrthosiphon pisum, genome we provide an updated gene annotation and expression profile of putative sugar transporters. Finally, gut expressed sugar transporters are functionally expressed in yeast and screened for glucose and fructose transport activity.

Results

In this study, using a de novo approach, we identified 19 sugar porter (SP) family transporters in the A. pisum genome. Gene expression analysis, based on 214, 834 A. pisum expressed sequence tags, supports 17 sugar porter family transporters being actively expressed in adult female aphids. Further analysis, using quantitative PCR identifies 4 transporters, A. pisum sugar transporter 1, 3, 4 and 9 (ApST1, ApST3, ApST4 and ApST9) as highly expressed and/or enriched in gut tissue. When expressed in a Saccharomyces cerevisiae hexose transporter deletion mutant (strain EBY.VW4000), only ApST3 (previously characterized) and ApST4 (reported here) transport glucose and fructose resulting in functional rescue of the yeast mutant. Here we characterize ApST4, a 491 amino acid protein, with 12 predicted transmembrane regions, as a facilitative glucose/fructose transporter. Finally, phylogenetic reconstruction reveals that ApST4, and related, as yet uncharacterized insect transporters are phylogenetically closely related to human GLUT (SLC2A) class I facilitative glucose/fructose transporters.

Conclusions

The gut enhanced expression of ApST4, and the transport specificity of its product is consistent with ApST4 functioning as a gut glucose/fructose transporter. Here, we hypothesize that both ApST3 (reported previously) and ApST4 (reported here) function at the gut interface to import glucose and fructose from the gut lumen.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-647) contains supplementary material, which is available to authorized users.     

Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication

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Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

Background

Recent studies have shown that the regulatory effect of microRNAs can be investigated by examining expression changes of their target genes. Given this, it is useful to define an overall metric of regulatory effect for a specific microRNA and see how this changes across different conditions.

Results

Here, we define a regulatory effect score (RE-score) to measure the inhibitory effect of a microRNA in a sample, essentially the average difference in expression of its targets versus non-targets. Then we compare the RE-scores of various microRNAs between two breast cancer subtypes: estrogen receptor positive (ER⁺) and negative (ER^-). We applied this approach to five microarray breast cancer datasets and found that the expression of target genes of most microRNAs was more repressed in ER^- than ER⁺; that is, microRNAs appear to have higher RE-scores in ER^- breast cancer. These results are robust to the microRNA target prediction method. To interpret these findings, we analyzed the level of microRNA expression in previous studies and found that higher microRNA expression was not always accompanied by higher inhibitory effects. However, several key microRNA processing genes, especially Ago2 and Dicer, were differentially expressed between ER^- and ER⁺ breast cancer, which may explain the different regulatory effects of microRNAs in these two breast cancer subtypes.

Conclusions

The RE-score is a promising indicator to measure microRNAs' inhibitory effects. Most microRNAs exhibit higher RE-scores in ER^- than in ER⁺ samples, suggesting that they have stronger inhibitory effects in ER^- breast cancers.     

Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq

Faithful replication of the entire genome requires replication forks to copy large contiguous tracts of DNA, and sites of persistent replication fork stalling present a major threat to genome stability. Understanding the distribution of sites at which replication forks stall, and the ensuing fork processing events, requires genome-wide methods that profile replication fork position and the formation of recombinogenic DNA ends. Here, we describe Transferase-Activated End Ligation sequencing (TrAEL-seq), a method that captures single-stranded DNA 3′ ends genome-wide and with base pair resolution. TrAEL-seq labels both DNA breaks and replication forks, providing genome-wide maps of replication fork progression and fork stalling sites in yeast and mammalian cells. Replication maps are similar to those obtained by Okazaki fragment sequencing; however, TrAEL-seq is performed on asynchronous populations of wild-type cells without incorporation of labels, cell sorting, or biochemical purification of replication intermediates, rendering TrAEL-seq far simpler and more widely applicable than existing replication fork direction profiling methods. The specificity of TrAEL-seq for DNA 3′ ends also allows accurate detection of double-strand break sites after the initiation of DNA end resection, which we demonstrate by genome-wide mapping of meiotic double-strand break hotspots in a dmc1Δ mutant that is competent for end resection but not strand invasion. Overall, TrAEL-seq provides a flexible and robust methodology with high sensitivity and resolution for studying DNA replication and repair, which will be of significant use in determining mechanisms of genome instability.

TrAEL-seq provides genome-wide base pair resolution maps of exposed DNA 3’ ends; this reveals replication fork stalling and normal replication profiles in asynchronous, unlabelled wildtype cell populations, along with the sites of resected DNA breaks.     

Genome-wide functional analysis of human 5' untranslated region introns

Background  

Approximately 35% of human genes contain introns within the 5' untranslated region (UTR). Introns in 5'UTRs differ from those in coding regions and 3'UTRs with respect to nucleotide composition, length distribution and density. Despite their presumed impact on gene regulation, the evolution and possible functions of 5'UTR introns remain largely unexplored.     

Evolution of human mitochondrial DNA: Evidence for departure from a pure neutral model of populations at equilibrium

Summary Human mitochondrial DNA (mtDNA) data from 18 populations have been carefully reexamined. A phylogeny of 77 mtDNA types found among the 1389 individuals analyzed for restriction fragment length polymorphisms (RFLPs) was established using the parsimony principle and compared to a UPGMA tree of the 18 populations. Both analyses agreed in separating African samples from the other populations, though the mtDNA type phylogeny suggested close relations between Africans and other continental groups. Conformity of observed mtDNA type frequency distributions with the infinite allele model was studied for 31 human populations. Several Oriental and Caucasoid populations were found to be overly homogeneous, generally due to an elevated frequency of one particular type. Contrastingly, all African samples conformed to the neutral model of populations at equilibrium and presented more diversified distributions. This suggested that part of the apparent African divergence was due to heterogeneous evolutionary processes and confirmed that some diversity reducing factors were at work in Caucasoids and Orientals. Several nonexclusive hypotheses accounting for the rejection of the neutrality tests were discussed. Alternative hypotheses concerning modern human emergence were also reviewed in the light of present results.     

Genome-wide identification and expression profiling of DNA methyltransferase gene family in maize

Key message

In this study, we identified eight DNA MTase genes in maize and the diversity of expression patterns of them was presented by EST mining, microarray and semi-quantitative expression profile analyses.

Abstract

DNA methylation plays a pivotal role in promoting genomic stability through diverse biological processes including regulation of gene expression during development and chromatin organization. Although this important biological process is mainly regulated by several conserved Cytosine-5 DNA methyltransferases encoded by a smaller multigene family in plants, investigation of the plant C5-MTase-encoding gene family will serve to elucidate the epigenetic mechanism diversity in plants. Recently, genome-wide identification and evolutionary analyses of the C5-MTase-encoding gene family have been characterized in multiple plant species including Arabidopsis, rice, carrot and wheat. However, little is known regarding the C5-MTase-encoding genes in the entire maize genome. Here, genome-wide identification and expression profile analyses of maize C5-MTase-encoding genes (ZmMETs) were performed from the latest version of the maize (B73) genome. Phylogenetic analysis indicated that the orthologs from the three species (maize, Arabidopsis and rice) were categorized into four classes. Chromosomal location of these genes revealed that they are unevenly distributed on 6 of all 10 chromosomes with three chromosomal/segmental duplication events, suggesting that gene duplication played a key role in expansion of the maize C5-MTase-encoding gene family. Furthermore, EST expression data mining, microarray data and semi-quantitative expression profile analyses detected in the leaves by two different abiotic stress treatments have demonstrated that these genes had temporal and spatial expression pattern and exhibited different expression levels in stress treatments, suggesting that functional diversification of ZmMET genes family. Overall, our study will serve to present signification insights to explore the plant C5-MTase-encoding gene expression and function and also be beneficial for future experimental research to further unravel the mechanisms of epigenetic regulation in plants.     

Genome-wide identification of WD40 genes reveals a functional diversification of COP1-like genes in Rosaceae

Plant Molecular Biology - Genome-wide identification of WD40-like genes reveals a duplication of COP1-like genes, one of the key players involved in regulation of flowering time and...     

Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays

DNA microarray technology has become an important research tool for microbiology and biotechnology as it allows for comprehensive DNA and RNA analyses to characterize genetic diversity and gene expression in a genome-wide manner. DNA microarrays have been applied extensively to study the biology of many bacteria including Mycobacterium tuberculosis, but only recently have they been used for the related high-GC Gram-positive Corynebacterium glutamicum, which is widely used for biotechnological amino acid production. Besides the design and generation of microarrays as well as their use in hybridization experiments and subsequent data analysis, recent applications of DNA microarray technology in C. glutamicum including the characterization of ribose-specific gene expression and the valine stress response will be described. Emerging perspectives of functional genomics to enlarge our insight into fundamental biology of C. glutamicum and their impact on applied biotechnology will be discussed.