Differential Transcript Abundance Research Articles

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

Metatranscriptomes generated by pyrosequencing hold significant potential for describing functional processes in complex microbial communities. Meeting this potential requires protocols that maximize mRNA recovery by reducing the relative abundance of ribosomal RNA, as well as systematic comparisons to identify methodological artifacts and test for reproducibility across data sets. Here, we implement a protocol for subtractive hybridization of bacterial rRNA (16S and 23S) that uses sample-specific probes and is applicable across diverse environmental samples. To test this method, rRNA-subtracted and unsubtracted transcriptomes were sequenced (454 FLX technology) from bacterioplankton communities at two depths in the oligotrophic open ocean, yielding 10 data sets representing approximately 350 Mbp. Subtractive hybridization reduced bacterial rRNA transcript abundance by 40-58%, increasing recovery of non-rRNA sequences up to fourfold (from 12% to 20% of total sequences to 40-49%). In testing this method, we established criteria for detecting sequences replicated artificially via pyrosequencing errors and identified such replicates as a significant component (6-39%) of total pyrosequencing reads. Following replicate removal, statistical comparisons of reference genes (identified via BLASTX to NCBI-nr) between technical replicates and between rRNA-subtracted and unsubtracted samples showed low levels of differential transcript abundance (<0.2% of reference genes). However, gene overlap between data sets was remarkably low, with no two data sets (including duplicate runs from the same pyrosequencing library template) sharing greater than 17% of unique reference genes. These results indicate that pyrosequencing captures a small subset of total mRNA diversity and underscores the importance of reliable rRNA subtraction procedures to enhance sequencing coverage across the functional transcript pool.

Histidine kinase and response regulator genes as they relate to salinity tolerance in rice

We have previously shown that Oryza sativa L. Pokkali maintains higher levels of transcripts under non-saline conditions, which are otherwise induced under salinity in the sensitive genotype-IR64. We wanted to test this hypothesis of differential gene regulation further, within the members of a given stress responsive gene family, which share significant structural and functional similarities. For this purpose, we chose to work on the two-component system (TCS family) which plays an important role in stress perception and signal transduction under hormonal, abiotic stress, light and developmental regulation. We present data to show that all members of TCS family, including sensory histidine kinases, phosphotransfer proteins and response regulators, are having differential transcript abundance (under both non-stress and salinity stress conditions) in contrasting rice genotypes. Further, under non-stress conditions, transcript abundance for all TCS members (except RR21) was found to be higher in the salt-tolerant genotype-Pokkali. TCS transcripts are otherwise induced by salinity stress to a relatively higher level in the sensitive cultivar IR64. A few of these members were also found to be localised within important salinity-related quantitative trait loci identified earlier. Based on the above findings, we propose that the TCS members may have a significant role in salinity tolerance in rice and can serve as useful 'candidate genes' for raising salinity-tolerant crop plants.

Differential transcript regulation in Arabidopsis thaliana and the halotolerant Lobularia maritima indicates genes with potential function in plant salt adaptation

Salt stress is an environmental factor that severely impairs plant growth and productivity. Salinity-induced transcript accumulation was monitored in the salt-sensitive Arabidopsis thaliana and the related salt-tolerant Lobularia maritima using cDNA-arrays with expressed sequence tags derived from a cDNA subtraction library of salt-stressed L. maritima. The expression profiles revealed differences of the steady state transcript regulation in A. thaliana and L. maritima in response to salt stress. The differentially expressed transcripts include those involved in the control of gene expression as a transcription factor II homologue as well as signal transduction elements such as a serine/threonine protein kinase, a SNF1-related protein kinase AKIN10 homologue, and protein phosphatase 2C. Other ESTs with differential regulation patterns included transcripts encoding proteins with function in general stress responses and defense and included a peroxidase, dehydrins, enzymes of lipid and nitrogen metabolism, and functionally unclassified proteins. In a more detailed analysis the basic leucine zipper transcription factor AtbZIP24 showed differential transcript abundance in A. thaliana and L. maritima in response to salt stress. Transgenic AtbZIP24-RNAi lines showed improved growth and development under salt stress that was correlated with changed Cl − accumulation. The data indicate that AtbZIP24 functions as a transcriptional repressor in salt-stressed A. thaliana that negatively regulates growth and development under salinity in context of controlling Cl − homeostasis. Monitoring the differential and tissue specific global regulation of gene expression during adaptation to salinity in salt-sensitive and halotolerant plants is a promising and powerful approach to identify novel elements of plant salt stress adaptation.

Dietary restriction by growth in axenic medium induces discrete changes in the transcriptional output of genes involved in energy metabolism in Caenorhabditis elegans

Dietary restriction increases life span in a wide range of species, including the nematode worm Caenorhabditis elegans. The mechanism by which it does so remains largely unknown, although it is commonly thought that a reduction of reactive oxygen species (ROS) plays a pivotal role. More specifically, for C. elegans, it has been proposed that food restriction reduces energy expenditure, possibly in conjunction with an anaerobic shift in energy production, with consequent reduction in the formation of ROS. We have measured differential transcript abundance of 49 genes known to play roles in energy metabolism in axenic culture medium, which causes a nutritional deficit and leads to a substantial increase of life span. We found no evidence for a reduction in metabolic rate or a shift to anaerobic metabolism in axenic culture. Major changes induced by growth in axenic medium include down-regulation of lipid degradation and up-regulation of glyoxylate cycle activity glyceroneogenesis and, possibly, gluconeogenesis. The activities determined in worm extracts for pyruvate kinase, phosphoenolpyruvate carboxykinase and isocitrate lyase followed a similar trend. We conclude that growth in axenic culture is marked by a general up-regulation of replenishing pathways.

A gene expression signature of confinement in peripheral blood of red wolves (Canis rufus)

The stresses that animals experience as a result of modification of their ecological circumstances induce physiological changes that leave a signature in profiles of gene expression. We illustrate this concept in a comparison of free range and confined North American red wolves (Canis rufus). Transcription profiling of peripheral blood samples from 13 red wolf individuals in the Alligator River region of North Carolina revealed a strong signal of differentiation. Four hundred eighty-two out of 2980 transcripts detected on Illumina HumanRef8 oligonucleotide bead arrays were found to differentiate free range and confined wolves at a false discovery rate of 12.8% and P < 0.05. Over-representation of genes in focal adhesion, insulin signalling, proteasomal, and tryptophan metabolism pathways suggests the activation of pro-inflammatory and stress responses in confined animals. Consequently, characterization of differential transcript abundance in an accessible tissue such as peripheral blood identifies biomarkers that could be useful in animal management practices and for evaluating the impact of habitat changes on population health, particularly as attention turns to the impact of climate change on physiology and in turn species distributions.

Arabidopsis–rice–wheat gene orthologues for Na+ transport and transcript analysis in wheat–L. elongatum aneuploids under salt stress

Lophopyrum elongatum is a wild relative of wheat that provides a source of novel genes for improvement of the salt tolerance of bread wheat. Improved Na(+) 'exclusion' is associated with salt tolerance in a wheat-L. elongatum amphiploid, in which a large proportion (ca. 50%) of the improved regulation of leaf Na(+) concentrations is controlled by chromosome 3E. In this study, genes that might control Na(+) accumulation, such as for transporters responsible for Na(+) entry (HKT1) and exit (SOS1) from cells, or compartmentalisation within vacuoles (NHX1, NHX5, AVP1, AVP2) in the model plant, Arabidopsis thaliana, were targeted for comparative analyses in wheat. Putative rice orthologues were identified and characterised as a means to bridge the large evolutionary distance between genomes from the model dicot and the more complex grass species. Wheat orthologues were identified through BLAST searching to identify either FL-cDNAs or ESTs and were subsequently used to design primers to amplify genomic DNA. The probable orthologous status of the wheat genes was confirmed through demonstration of similar intron-exon structure with their counterparts in Arabidopsis and rice. The majority of exons for Arabidopsis, rice and wheat orthologues of NHX1, NHX5 and SOS1 were conserved except for those at the amino and carboxy terminal ends. However, additional exons were identified in the predicted NHX1 and SOS1 genes of rice and wheat, as compared with Arabidopsis, indicating gene rearrangement events during evolution from a common ancestor. Nullisomic-tetrasomic, deletion and addition lines in wheat were used to assign gene sequences to chromosome regions in wheat and L. elongatum. Most sequences were assigned to homoeologous chromosomes, however, in some instances, such as for SOS1, genes were mapped to other unpredicted locations. Differential transcript abundance under salt stress indicated a complex pattern of expression for wheat orthologues that may regulate Na(+) accumulation in wheat lines containing chromosomes from L. elongatum. The identification of wheat orthologues to well characterized Arabidopsis genes, map locations and gene expression profiles increases our knowledge on the complex mechanisms regulating Na(+) transport in wheat and wheat-L. elongatum lines under salt stress.

Differential gene expression between pigmented and non-pigmented cell culture lines of Daucus carota

RNA differential display was used to look at differential transcript abundance between cell culture lines of wild carrot (Daucus carota L.) that either produce no pigments, or carotenoids only, or carotenoids and cyanidin-based anthocyanins. Nineteen partial cDNA clones were isolated and used in northern RNA analysis, confirming that seven of the corresponding genes were preferentially expressed in particular cell lines. For six of the seven differential clones, longer cDNAs were isolated from a cDNA library. Nucleotide sequence analysis allowed putative identification of the encoded products of three. The isolation of the cDNAs allowed the temporal variation in transcript abundance to be examined. For two out of five cDNAs tested the differential expression pattern was lost after a period of 24 months, representing approximately 52 subcultures. The results demonstrate the relevance of a differential RNA approach to trying to understanding the nature of mechanisms causing variability in plant cell cultures, the first step in bringing it under control for the improvement of culture technologies.

Protein-Tyrosine Phosphatases in the Vessel Wall

Many protein-tyrosine phosphatases (PTPases) have now been identified, but little is known about PTPase expression and regulation in vascular tissue and in vascular disease. Polymerase chain reaction (PCR) amplification and cDNA fingerprinting of PTPase catalytic domains, combined with random sequencing of PCR product libraries, identified 18 (8 receptor-like and 10 cytosolic) PTPases in the rat carotid artery and revealed differential expression of 5 of these PTPases during neointima formation after balloon catheter injury. In situ hybridization was used to localize mRNA expression in vessel cross sections for the 5 differentially expressed PTPases. This revealed that for 3 PTPases (SHP1, CD45, and PTPbeta), differential transcript abundance was due to appearance/loss of the cell types by which they were expressed (leukocytes for SHP1 and CD45, endothelial cells for PTPbeta). However, mRNA expression of 2 PTPases (PTPL1 and PTP1B) was specifically upregulated by proliferating and migrating smooth muscle cells (SMCs) in characteristic temporal and regional patterns in response to vessel damage. Quantitative PCR analysis showed that PTP1B and PTPL1 were induced approximately 30-fold and approximately 60-fold, respectively, by 2 weeks after injury in the damaged vessels compared with the uninjured vessels. PTP1B was rapidly upregulated in the media after vessel injury and remained highly expressed in the developing neointima. By contrast, PTPL1 expression did not increase dramatically until the SMCs had migrated into the intima. The differential expression of PTP1B and PTPL1 by SMCs after injury suggests roles for these PTPases in the regulation of vessel wall remodeling.