Temporal Patterns Of Gene Expression Research Articles

Salicylic acid and reactive oxygen species interplay in the transcriptional control of defense genes expression.

It is well established that salicylic acid (SA) plays a critical role in the transcriptional reprograming that occurs during the plant defense response against biotic and abiotic stress. In the course of the defense response, the transcription of different sets of defense genes is controlled in a spatio-temporal manner via SA-mediated mechanisms. Interestingly, different lines of evidence indicate that SA interplays with reactive oxygen species (ROS) and glutathione (GSH) in stressed plants. In this review we focus on the evidence that links SA, ROS, and GSH signals to the transcriptional control of defense genes. We discuss how redox modifications of regulators and co-regulators involved in SA-mediated transcriptional responses control the temporal patterns of gene expression in response to stress. Finally, we examine how these redox sensors are coordinated with the dynamics of cellular redox changes occurring in the defense response to biotic and abiotic stress.

Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation.

BackgroundSocial amoebae are lower eukaryotes that inhabit the soil. They are characterized by the construction of a starvation-induced multicellular fruiting body with a spore ball and supportive stalk. In most species, the stalk is filled with motile stalk cells, as represented by the model organism Dictyostelium discoideum, whose developmental mechanisms have been well characterized. However, in the genus Acytostelium, the stalk is acellular and all aggregated cells become spores. Phylogenetic analyses have shown that it is not an ancestral genus but has lost the ability to undergo cell differentiation.ResultsWe performed genome and transcriptome analyses of Acytostelium subglobosum and compared our findings to other available dictyostelid genome data. Although A. subglobosum adopts a qualitatively different developmental program from other dictyostelids, its gene repertoire was largely conserved. Yet, families of polyketide synthase and extracellular matrix proteins have not expanded and a serine protease and ABC transporter B family gene, tagA, and a few other developmental genes are missing in the A. subglobosum lineage. Temporal gene expression patterns are astonishingly dissimilar from those of D. discoideum, and only a limited fraction of the ortholog pairs shared the same expression patterns, so that some signaling cascades for development seem to be disabled in A. subglobosum.ConclusionsThe absence of the ability to undergo cell differentiation in Acytostelium is accompanied by a small change in coding potential and extensive alterations in gene expression patterns.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1278-x) contains supplementary material, which is available to authorized users.

Identification of Differentially Expressed Genes in Sugarcane During Pathogenesis of Colletotrichum falcatum by Suppression Subtractive Hybridization (SSH)

A suppression subtractive hybridization technique was used to identify differentially expressed genes in sugarcane in response to Colletotrichum falcatum, the fungal pathogen causing red rot in sugarcane. Messenger RNA (mRNA) samples collected from red rot resistant cv. Co 93009 at 6, 12, 24 and 48 h after pathogen challenge were pooled together and used as tester population. mRNA samples collected from red rot susceptible cv. CoC 671 at 6, 12, 24 and 48 h after pathogen challenge and control of samples of cv. Co 93009 and cv. CoC 671 were pooled together and used as the driver population. A forward subtraction enriched for differentially expressed ESTs in the resistant cultivar was carried out. At the end of subtraction, cloning and sequencing, 136 EST sequences were assembled into ten clusters/contigs. Based on TIGR homology search, the clusters were found to be involved in reactive oxygen species signaling, defense and the secretory pathway of plant innate immunity associated with hypersensitive response—mediated programmed cell death. Temporal gene expression pattern of the EST clusters by quantitative real time PCR revealed that, resistant cultivar had a higher level of gene expression than the susceptible cultivar in all the clusters till 48 h after pathogen inoculation. In conclusion, this study identified for the first time a set of differentially expressed EST clusters in red rot resistant sugarcane cultivar in response to C. falcatum infection.

Gene regulatory systems that control gene expression in the Ciona embryo.

Transcriptional control of gene expression is one of the most important regulatory systems in animal development. Specific gene expression is basically determined by combinatorial regulation mediated by multiple sequence-specific transcription factors. The decoding of animal genomes has provided an opportunity for us to systematically examine gene regulatory networks consisting of successive layers of control of gene expression. It remains to be determined to what extent combinatorial regulation encoded in gene regulatory networks can explain spatial and temporal gene-expression patterns. The ascidian Ciona intestinalis is one of the animals in which the gene regulatory network has been most extensively studied. In this species, most specific gene expression patterns in the embryo can be explained by combinations of upstream regulatory genes encoding transcription factors and signaling molecules. Systematic scrutiny of gene expression patterns and regulatory interactions at the cellular resolution have revealed incomplete parts of the network elucidated so far, and have identified novel regulatory genes and novel regulatory mechanisms.

Study of the obp5 gene in Apis mellifera ligustica and Apis cerana cerana.

Apis mellifera ligustica and A. cerana cerana exhibit differences in olfactory sensitivity to odors from nectariferous plants and diseased broods. It is presumed that the differences in odorant-binding proteins (OBPs) between these 2 species contribute to their olfactory sensitivity. We compared the sequences, temporal expression pattern, and binding properties of the 2 OBP-encoding genes. We cloned the Amobp5 and Acobp5 genes. Among the ligands tested, phenethyl acetate was the most variable, with AcOBP5 showing high affinity and AmOBP5 having no apparent affinity for this ligand. While AmOBP5 had high affinity to both benzyl alcohol and 2-phenylethanol, the binding affinity of AcOBP5 to these compounds was moderate. However, the fluorescence intensity of these compounds was not decreased below 50%; thus, the dissociation constants could not be calculated. The Amobp5 gene showed significantly higher expression in 10- and 15-day-old workers than in other stages, while the Acobp5 gene had the highest expression in 30-day-old workers. Both the Amobp5 and Acobp5 genes had the lowest expression level in 1-day-old workers. These results suggest that the binding properties and temporal expression patterns of the obp5 genes in A. mellifera and A. cerana play a critical role in the olfactory sensitivity of workers.

Comparative analysis of temporal gene expression patterns in the developing ovary of the embryonic chicken.

Many genes participate in the process of ovarian germ cell development, while the combined action mechanisms of these molecular regulators still need clarification. The present study was focused on determination of differentially expressed genes and gene functions at four critical time points in chicken ovarian development. Comparative transcriptional profiling of ovaries from embryonic day 5.5 (E5.5), E12.5, E15.5 and E18.5 was performed using an Affymetrix GeneChip chicken genome microarray. Differential expression patterns for genes specifically depleted and enriched in each stage were identified. The results showed that most of the up- and downregulated genes were involved in the metabolism of retinoic acid (RA) and synthesis of hormones. Among them, a higher number of up- and downregulated genes in the E15.5 ovary were identified as being involved in steroid biosynthesis and retinol metabolism, respectively. To validate gene changes, expressions of twelve candidate genes related to germ cell development were examined by real-time PCR and found to be consistent with the of GeneChip data. Moreover, the immunostaining results suggested that ovarian development during different stages was regulated by different genes. Furthermore, a Raldh2 knockdown chicken model was produced to investigate the fundamental role of Raldh2 in meiosis initiation. It was found that meiosis occurred abnormally in Raldh2 knockdown ovaries, but the inhibitory effect on meiosis was reversed by the addition of exogenous RA. This study offers insights into the profile of gene expression and mechanisms regulating ovarian development, especially the notable role of Raldh2 in meiosis initiation in the chicken.

Transcriptome sequencing reveals the virulence and environmental genetic programs of Vibrio vulnificus exposed to host and estuarine conditions.

Vibrio vulnificus is a natural inhabitant of estuarine waters worldwide and is of medical relevance due to its ability to cause grievous wound infections and/or fatal septicemia. Genetic polymorphisms within the virulence-correlated gene (vcg) serve as a primary feature to distinguish clinical (C-) genotypes from environmental (E-) genotypes. C-genotypes demonstrate superior survival in human serum relative to E-genotypes, and genome comparisons have allowed for the identification of several putative virulence factors that could potentially aid C-genotypes in disease progression. We used RNA sequencing to analyze the transcriptome of C-genotypes exposed to human serum relative to seawater, which revealed two divergent genetic programs under these two conditions. In human serum, cells displayed a distinct “virulence profile” in which a number of putative virulence factors were upregulated, including genes involved in intracellular signaling, substrate binding and transport, toxin and exoenzyme production, and the heat shock response. Conversely, the “environmental profile” exhibited by cells in seawater revealed upregulation of transcription factors such as rpoS, rpoN, and iscR, as well as genes involved in intracellular signaling, chemotaxis, adherence, and biofilm formation. This dichotomous genetic switch appears to be largely governed by cyclic-di-GMP signaling, and remarkably resembles the dual life-style of V. cholerae as it transitions from host to environment. Furthermore, we found a “general stress response” module, known as the stressosome, to be upregulated in seawater. This signaling system has been well characterized in Gram-positive bacteria, however its role in V. vulnificus is not clear. We examined temporal gene expression patterns of the stressosome and found it to be upregulated in natural estuarine waters indicating that this system plays a role in sensing and responding to the environment. This study advances our understanding of gene regulation in V. vulnificus, and brings to the forefront a number of previously overlooked genetic networks.

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing sites; and transcription, processing, and degradation rates of each transcript at a splice junction resolution during the LPS response of mouse dendritic cells. Four key regulatory strategies, dominated by RNA transcription changes, generate most temporal gene expression patterns. Noncanonical strategies that also employ dynamic posttranscriptional regulation control only a minority of genes, but provide unique signal processing features. We validate Tristetraprolin (TTP) as a major regulator of RNA degradation in one noncanonical strategy. Applying DRiLL to the regulation of noncoding RNAs and to zebrafish embryogenesis demonstrates its broad utility. Our study provides a new quantitative approach to discover transcriptional and posttranscriptional events that control dynamic changes in transcript levels using RNA sequencing data.

MicroRNA-dependent temporal gene expression in the ureteric bud epithelium during mammalian kidney development.

Our previous study on mouse mutants with the ureteric bud (UB) epithelium-specific Dicer deletion (Dicer UB mutants) demonstrated the significance of UB epithelium-derived miRNAs in UB development. Our whole-genome transcriptional profiling showed that the Dicer mutant UB epithelium abnormally retained transcriptional features of the early UB epithelium and failed to express many genes associated with collecting duct differentiation. Furthermore, we identified a temporal expression pattern of early UB genes during UB epithelium development in which gene expression was detected at early developmental stages and became undetectable by embryonic day 14.5. In contrast, expression of early UB genes persisted at later stages in the Dicer mutant UB epithelium and increased at early stages. Our bioinformatic analysis of the abnormally persistently expressed early genes in the Dicer mutant UB epithelium showed significant enrichment of the let-7 family miRNA targets. We further identified a temporal expression pattern of let-7 miRNAs in the UB epithelium that is anti-parallel to that of some early UB genes during kidney development. We propose a model in which the let-7 family miRNAs silence the expression of a subset of early genes in the UB epithelium at later developmental stages to promote collecting duct differentiation. Developmental Dynamics 244:444-456, 2015. © 2014 Wiley Periodicals, Inc.

Prevalence of cycling genes and drug targets calls for prospective chronotherapeutics.

There are two main threads in biomedical research: One is to discover how biological systems work, basic science; and the other is to use knowledge obtained from basic research in medicine, translation. The availability of genome sequences has brought an unprecedented opportunity for discovery (1). As one of several initial efforts toward the interpretation of the human and mouse genomes, Hogenesch and coworkers built the Gene Atlas in 2004 (2) in which the protein-coding genes were profiled for their expression against a panel of over 100 human and mouse tissues and cells. In the current study by Zhang et al. a decade later (3), Hogenesch and his team have now added the temporal dimension to construct the Circadian Gene Atlas in which gene expression is profiled across 12 different mouse tissues at different times of the day. For more than a decade, circadian researchers have examined the cycling transcriptomes in many tissues (reviewed in ref. 4). Notably, this new dataset represents by far the most comprehensive profiling of protein-coding and noncoding genes and provides not only a panoramic view of temporal gene expression patterns at the genome-wide level, but also a nucleotide view of any gene. As you delve into the data and its analysis, it is easy to see that circadian biology is not just for chronobiologists; it is important for all biologists and has important implications in medicine.

Common microRNAs Target Established ASD Genes.

COMPLEX GENETIC ARCHITECTURE IN AUTISM Autism spectrum disorder (ASD) encompasses a range of early-onset neurodevelopmental disorders characterized by impaired social interactions and communications, together with repetitive stereotypic behaviors (MIM20895; DSM5). Individuals with ASD can display a broad clinical profile ranging in symptom severity and comorbidities. A strong genetic component underlying ASD has been firmly established; hundreds of genes and chromosomal loci are known to be associated with the disorder and have been cataloged in ASD-specific genetic databases such as AutDB (1). The potential genetic risk factors range from candidate genes reported from genetic association studies to rare, recurrent gene-disruptive mutations identified in ASD individuals using high-throughput technologies such as whole exome sequencing (2). A number of recurrent copy number variants (CNVs) that overlap with related neurodevelopmental and neuropsychiatric disorders such as intellectual disability and schizophrenia have been implicated in ASD as well. Two recent studies, in particular, provide a deeper understanding of the complex genetic architecture of ASD. First, a genome-wide analysis revealed shared risk loci between five major psychiatric disorders including ASD, attention deficit hyperactivity disorder (ADHD), bipolar disorder, major depressive disorder, and schizophrenia (3). The second study examined the detailed structure of the type of genetic liability in ASD and showed that inherited common variants contributed to 49.4% heritability, whereas rare de novo variants accounted for only 2.6% (4). Despite this progress in ASD genetics, the underlying perturbations in brain development that contributes to the emergence of specific symptoms along developmental time points, whether in the first years of life in ASD or during adolescence in the case of schizophrenia, remains largely unresolved. The regulatory mechanisms that orchestrate the precise temporal and spatial patterns of gene expression in the brain are at the forefront of research for brain-based disorders. The importance of various types of non-coding RNAs is being increasingly recognized in this regulatory process, with microRNAs (miRNAs) emerging as a leading candidate. miRNAs are highly conserved small non-coding RNAs approximately 22 nucleotides in length that regulate gene expression mostly by binding to the 3 UTR of target messenger RNAs (mRNAs). miRNAs recognize their targets primarily through complementarity with the seed sequence at nucleotides 2–8 of the 5 end of the miRNA. A distinguishing feature of miRNAs lies in the ability of a single miRNA molecule to bind to the recognition site on many mRNAs and subsequently regulate their expression (5). By this mechanism, miRNA–mRNA interactions can potentially modulate expression of hundreds of target genes and influence the corresponding cellular networks. Any disturbances of such a system within a neuronal context could lead to altered brain circuits and synaptic function – processes implicated in disorders such as autism or schizophrenia.

Temporal and anatomic patterns of immediate-early gene expression in the forebrain of C57BL/6 and DBA/2 mice after morphine administration

Although morphine was previously reported to produce an instant induction of c-fos in the striatum, our recent studies have demonstrated that the expression of numerous immediate early genes (IEGs) is significantly elevated at delayed time-points (several hours) after morphine administration. To better dissect the time-course of opioid-produced IEG induction, we used in situ hybridization to examine the expression of the IEGs c-fos, zif268 and arc in the mouse forebrain at several time-points after acute morphine injection. To link drug-produced behavioral changes with the activity of specific neuronal complexes, this study was performed comparatively in the C57BL/6 and DBA/2 mouse strains, which differ markedly in their locomotor responses to opioids and opioid reward.Our study demonstrates that morphine produces two episodes of IEG induction, which are separate in time (30min vs. 4–6h) and which have different neuroanatomic distribution. At 30min, one or more IEGs were induced in circumscribed subregions of the dorsal striatum (dStr) and of the nucleus accumbens (NAc) shell, as well as in the lateral septum. The observed inter-strain differences in IEG expression at 30min support earlier proposals that activation of the dorsomedial striatum may mediate morphine-elicited locomotor stimulation (both effects were present only in the C57BL/6 strain). In contrast, NAc shell activation does not appear to be linked to morphine-elicited changes in locomotor behavior. The second IEG induction (of arc and of zif268) was more widespread, involving most of the dStr and the cortex. The second IEG induction peaked earlier in the DBA/2 mice than in the C57BL/6 mice (4h compared with 6h) and displayed no apparent relation to locomotor behavior. This delayed episode of IEG activation, which has largely been overlooked thus far, may contribute to the development of long-term effects of opioids such as tolerance, dependence and/or addiction.

RNA sequencing reveals high resolution expression change of major plant hormone pathway genes after young seedless grape berries treated with gibberellin

Seedless varieties are of particular importance to the table-grape and raisin industries. Gibberellin (GA) application is widely used in the early stages of seedless berry development to increase berry size and economic value. However, the underlying mechanism of GA induction of berry enlargement is not well understood. Here, RNA-sequencing analysis of ‘Centennial Seedless’ (Vitis vinifera L.) berries treated with GA3 12 days after flowering is reported. Pair-wise comparison of GA3-treated and control samples detected 165, 444, 463 genes with an over two-fold change in expression 1, 3, and 7 days after GA3 treatment, respectively. The number of differentially expressed genes increased with time after GA3 treatment, and the differential expression was dominated by downregulation. Significantly modulated expression included genes encoding synthesis and catabolism to manage plant hormone homeostasis, hormone transporters, receptors and key components in signaling pathways; exogenous GA3 induced multipoint cross talk with auxin, cytokinin, brassinosteroid, ABA and ethylene. The temporal gene-expression patterns of cell-wall-modification enzymes, cytoskeleton and membrane components and transporters revealed a pivotal role for cell-wall-relaxation genes in GA3-induced berry enlargement. Our results provide the first sequential transcriptomic atlas of exogenous GA3-induced berry enlargement and reveal the complexity of GA3's effect on berry sizing.

Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis.

BackgroundThe genetic cascades underpinning vertebrate early eye morphogenesis are poorly understood. One gene family essential for eye morphogenesis encodes the retinal homeobox (Rx) transcription factors. Mutations in the human retinal homeobox gene (RAX) can lead to gross morphological phenotypes ranging from microphthalmia to anophthalmia. Zebrafish rx3 null mutants produce a similar striking eyeless phenotype with an associated expanded forebrain. Thus, we used zebrafish rx3-/- mutants as a model to uncover an Rx3-regulated gene network during early eye morphogenesis.ResultsRx3-regulated genes were identified using whole transcriptomic sequencing (RNA-seq) of rx3-/- mutants and morphologically wild-type siblings during optic vesicle morphogenesis. A gene co-expression network was then constructed for the Rx3-regulated genes, identifying gene cross-talk during early eye development. Genes highly connected in the network are hub genes, which tend to exhibit higher expression changes between rx3-/- mutants and normal phenotype siblings. Hub genes down-regulated in rx3-/- mutants encompass homeodomain transcription factors and mediators of retinoid-signaling, both associated with eye development and known human eye disorders. In contrast, genes up-regulated in rx3-/- mutants are centered on Wnt signaling pathways, associated with brain development and disorders. The temporal expression pattern of Rx3-regulated genes was further profiled during early development from maternal stage until visual function is fully mature. Rx3-regulated genes exhibited synchronized expression patterns, and a transition of gene expression during the early segmentation stage when Rx3 was highly expressed. Furthermore, most of these deregulated genes are enriched with multiple RAX-binding motif sequences on the gene promoter.ConclusionsHere, we assembled a comprehensive model of Rx3-regulated genes during early eye morphogenesis. Rx3 promotes optic vesicle morphogenesis and represses brain development through a highly correlated and modulated network, exhibiting repression of genes mediating Wnt signaling and concomitant enhanced expression of homeodomain transcription factors and retinoid-signaling genes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-825) contains supplementary material, which is available to authorized users.

2013 IEEE Scientific Visualization Contest winner: Observing genomics and phenotypical patterns in the developing mouse brain.

The 2013 IEEE Scientific Visualization Contest focused on developmental neuroscience related to the mouse brain. In developmental neuroscience, researchers examine spatiotemporal patterns of gene expression to understand how brain structures evolve and vary over an organism's life. The Allen Developing Mouse Brain Atlas project generated expression data for thousands of genes with high spatial resolution over multiple developmental stages. These data have become an invaluable resource for neuroscientists and developmental biologists exploring interesting spatial and temporal patterns of gene expression. Given the extremely large amounts of data, it's desirable to apply visualization techniques to their access, analysis, and interpretation. The proposed visual-analytics system enables clear, insightful observations of the gene expression patterns for such data, focusing on structural patterns that vary across gene expression levels over six developmental stages. Users can explore patterns through specialized data-driven representations that capture emerging structure-function associations in the developing mouse brain. The system also provides an effective characterization of certain processes in the developing brain that could lead to further analysis.

Temporal transcriptome analysis of the chicken embryo yolk sac.

BackgroundThe yolk sac (YS) is an extra-embryonic tissue that surrounds the yolk and absorbs, digests and transports nutrients during incubation of the avian embryo as well as during early term mammalian embryonic development. Understanding YS functions and development may enhance the efficient transfer of nutrients and optimize embryo development. To identify temporal large-scale patterns of gene expression and gain insights into processes and mechanisms in the YS, we performed a transcriptome study of the YS of chick embryos on embryonic days (E) E13, E15, E17, E19, and E21 (hatch).Results3547 genes exhibited a significantly changed expression across days. Clustering and functional annotation of these genes as well as histological sectioning of the YS revealed that we monitored two cell types: the epithelial cells and the erythropoietic cells of the YS. We observed a significant up-regulation of epithelial genes involved in lipid transport and metabolism between E13 and E19. YS epithelial cells expressed a vast array of lipoprotein receptors and fatty acid transporters. Several lysosomal genes (CTSA, PSAP, NPC2) and apolipoproteins genes (apoA1, A2, B, C3) were among the highest expressed, reflecting the intensive digestion and re-synthesis of lipoproteins in YS epithelial cells. Genes associated with cytoskeletal structure were down-regulated between E17 and E21 supporting histological evidence of a degradation of YS epithelial cells towards hatch.Expression patterns of hemoglobin synthesis genes indicated a high erythropoietic capacity of the YS between E13 and E15, which decreased towards hatch. YS histological sections confirmed these results. We also observed that YS epithelial cells expressed high levels of genes coding for plasma carrier proteins (ALB, AFP, LTF, TTR), normally produced by the liver.ConclusionsHere we expand current knowledge on developmental, nutritional and molecular processes in the YS. We demonstrate that in the final week of chick embryonic development, the YS plays different roles to support or replace the functions of several organs that have not yet reached their full functional capacity. The YS has a similar functional role as the intestine in digestion and transport of nutrients, the liver in producing plasma carrier proteins and coagulation factors, and the bone marrow in synthesis of blood cells.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-690) contains supplementary material, which is available to authorized users.

LIN-42, the Caenorhabditis elegans PERIOD homolog, negatively regulates microRNA transcription.

During C. elegans development, microRNAs (miRNAs) function as molecular switches that define temporal gene expression and cell lineage patterns in a dosage-dependent manner. It is critical, therefore, that the expression of miRNAs be tightly regulated so that target mRNA expression is properly controlled. The molecular mechanisms that function to optimize or control miRNA levels during development are unknown. Here we find that mutations in lin-42, the C. elegans homolog of the circadian-related period gene, suppress multiple dosage-dependent miRNA phenotypes including those involved in developmental timing and neuronal cell fate determination. Analysis of mature miRNA levels in lin-42 mutants indicates that lin-42 functions to attenuate miRNA expression. Through the analysis of transcriptional reporters, we show that the upstream cis-acting regulatory regions of several miRNA genes are sufficient to promote highly dynamic transcription that is coupled to the molting cycles of post-embryonic development. Immunoprecipitation of LIN-42 complexes indicates that LIN-42 binds the putative cis-regulatory regions of both non-coding and protein-coding genes and likely plays a role in regulating their transcription. Consistent with this hypothesis, analysis of miRNA transcriptional reporters in lin-42 mutants indicates that lin-42 regulates miRNA transcription. Surprisingly, strong loss-of-function mutations in lin-42 do not abolish the oscillatory expression patterns of lin-4 and let-7 transcription but lead to increased expression of these genes. We propose that lin-42 functions to negatively regulate the transcriptional output of multiple miRNAs and mRNAs and therefore coordinates the expression levels of genes that dictate temporal cell fate with other regulatory programs that promote rhythmic gene expression.

Evidence for species-specific clock gene expression patterns in hamster peripheral tissues.

Rhythmic oscillations that repeat every 24h can be found in numerous behavioral and physiological functions. Beside the endogenous master clock in the suprachiasmatic nucleus (SCN), peripheral oscillators exist that can disengage from the master clock rhythm by different mechanisms. The fact that core clock genes in peripheral tissues do not always have the same characteristics as in the SCN suggests that their function may vary in different organs. Additionally, suggestions about species-specific variation in expression peak and nadir times, especially in the testis, led to the need for systematical investigations on clock gene expression patterns in different organs and species under standardized methodological conditions. Therefore, daily gene expression patterns of the clock genes Bmal1, Period1, Period2, Clock, Cryptochrome1 and Cryptochrome2 were recorded at each of eight time points during a 24 hour period in the testis, kidney, liver, spleen and heart of three hamster species (Phodopus sungorus, Phodopus roborovskii and Cricetulus griseus; family: Cricetidae). Clock gene expression was found to be rhythmic in all investigated organs, however with inconsistent results in the testis. Complex cosinor analysis revealed species differences in temporal gene expression patterns regarding their orthophase, number of peaks, and amplitude for all genes and organs with most pronounced differences in the testis. The results of this study strongly indicate that clock gene expression in peripheral tissues is species-specific and that their functions might be at least partly connected to clock-unrelated traits that vary between the investigated species. Further studies should aim at clarifying the specific roles of clock genes in the testis.

Genome-wide survey and expression analysis of the bHLH-PAS genes in the amphioxus Branchiostoma floridae reveal both conserved and diverged expression patterns between cephalochordates and vertebrates.

BackgroundThe bHLH-PAS transcription factors are found in both protostomes and deuterostomes. They are involved in many developmental and physiological processes, including regional differentiation of the central nervous system, tube-formation, hypoxia signaling, aromatic hydrocarbon sensing, and circadian rhythm regulation. To understand the evolution of these genes in chordates, we analyzed the bHLH-PAS genes of the basal chordate amphioxus (Branchiostoma floridae).ResultsFrom the amphioxus draft genome database, we identified ten bHLH-PAS genes, nine of which could be assigned to known orthologous families. The tenth bHLH-PAS gene could not be assigned confidently to any known bHLH family; however, phylogenetic analysis clustered this gene with arthropod Met family genes and two spiralian bHLH-PAS-containing sequences, suggesting that they may share the same ancestry. We examined temporal and spatial expression patterns of these bHLH-PAS genes in developing amphioxus embryos. We found that BfArnt, BfNcoa, BfSim, and BfHifα were expressed in the central nervous system in patterns similar to those of their vertebrate homologs, suggesting that their functions may be conserved. By contrast, the amphioxus BfAhr and BfNpas4 had expression patterns distinct from those in vertebrates. These results imply that there were changes in gene regulation after the divergence of cephalochordates and vertebrates.ConclusionsWe have identified ten bHLH-PAS genes from the amphioxus genome and determined the embryonic expression profiles for these genes. In addition to the nine currently recognized bHLH-PAS families, our survey suggests that the BfbHLHPAS-orphan gene along with arthropod Met genes and the newly identified spiralian bHLH-PAS-containing sequences represent an ancient group of genes that were lost in the vertebrate lineage. In a comparison with the expression patterns of the vertebrate bHLH-PAS paralogs, which are the result of whole-genome duplication, we found that although several members seem to retain conserved expression patterns during chordate evolution, many duplicated paralogs may have undergone subfunctionalization and neofunctionalization in the vertebrate lineage. In addition, our survey of amphioxus bHLH-PAS gene models from genome browser with experimentally verified cDNA sequences calls into question the accuracy of the current in silico gene annotation of the B. floridae genome.

Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing.

Endosperm is a filial structure resulting from a second fertilization event in angiosperms. As an absorptive storage organ, endosperm plays an essential role in support of embryo development and seedling germination. The accumulation of carbohydrate and protein storage products in cereal endosperm provides humanity with a major portion of its food, feed, and renewable resources. Little is known regarding the regulatory gene networks controlling endosperm proliferation and differentiation. As a first step toward understanding these networks, we profiled all mRNAs in the maize kernel and endosperm at eight successive stages during the first 12 d after pollination. Analysis of these gene sets identified temporal programs of gene expression, including hundreds of transcription-factor genes. We found a close correlation of the sequentially expressed gene sets with distinct cellular and metabolic programs in distinct compartments of the developing endosperm. The results constitute a preliminary atlas of spatiotemporal patterns of endosperm gene expression in support of future efforts for understanding the underlying mechanisms that control seed yield and quality.