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The Shrunken gene, located on the short arm of chromosome 9 of Zea mays, encodes the enzyme sucrose synthase (EC 2.4.1.13). The gene is known to be expressed in the endosperm of the developing maize kernel and seems to be involved in sucrose breakdown prior to starch synthesis. We have analyzed different tissues of the maize plant for transcripts of the Shrunken gene and have found rather high transcription rates in the etiolated shoot and the primary root of the germinating kernel. If the etiolated seedlings are illuminated, the transcript level drops by about 95% in the greening plant parts (1st and 2nd leaves) which are active in photosynthesis. A very low transcript level is found in mature green leaves where sucrose is formed from products of photosynthesis via a separate pathway. Upon anaerobic stress of the young seedling, the level of Shrunken transcripts increases 10 and 20 times in shoot and root tissue respectively. Apparently anaerobic induction supersedes the negative control that is observed after illumination in the 1st and 2nd leaves. From the experiments outlined here we conclude that the anaerobic protein 87 (ANP87, Hake et al. 1985) is encoded by the Shrunken locus. While the expression of the Shrunken gene varies in different tissues and in response to external stimuli, transcription of the second sucrose synthase (B) gene seems to be irresponsive to anaerobic stress and to be expressed at a similar low level in all of the tissues examined.

Isolation of specialized cell types for the analysis of tissue-specific gene function often results in loss of the differentiated phenotype. Examples of this type of phenotypic change following tissue disaggregation are reviewed together with possible explanations. Close similarities between the effects of cell isolation with those of other cellular stresses such as heat or anoxia point to common biochemical mechanisms being involved. This suggests that the study of freshly isolated cells will contribute significantly to out understanding of the nature of cellular stress and its consequences for the maintenance of phenotype and induction of tissue specific gene expression.

The 549 base pairs of the 5' flanking region of a barley seed storage protein (B1 hordein) gene were linked to the reporter gene encoding chloramphenicol acetyl transferase (CAT). The chimaeric gene was transferred into tobacco plants using Agrobacterium tumefaciens. CAT enzyme activity was detected in the seeds, but not in the leaves, of the transgenic plants. Furthermore, enzyme activity was found only in the endosperm, and only from fifteen days after pollination. In contrast, the constitutive 19S promoter from cauliflower mosaic virus (CaMV) directed the expression of the CAT gene in the leaves as well as in both the endosperm and embryo and at all stages in seed development.

Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression to compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy and general robustness to misspecified reference sets. We apply this framework to 44 GTEx tissues and 100+ phenotypes from GWAS and meta-analysis studies, creating a growing public catalog of associations that seeks to capture the effects of gene expression variation on human phenotypes. Replication in an independent cohort is shown. Most of the associations are tissue specific, suggesting context specificity of the trait etiology. Colocalized significant associations in unexpected tissues underscore the need for an agnostic scanning of multiple contexts to improve our ability to detect causal regulatory mechanisms. Monogenic disease genes are enriched among significant associations for related traits, suggesting that smaller alterations of these genes may cause a spectrum of milder phenotypes., Phenotypic variation and diseases are influenced by factors such as genetic variants and gene expression. Here, Barbeira et al. develop S-PrediXcan to compute PrediXcan results using summary data, and investigate the effects of gene expression variation on human phenotypes in 44 GTEx tissues and >100 phenotypes.

Catharanthus roseus produces a wide spectrum of monoterpene indole alkaloids (MIAs). MIA biosynthesis requires a tightly coordinated pathway involving more than 30 enzymatic steps that are spatio-temporally and environmentally regulated so that some MIAs specifically accumulate in restricted plant parts. The first regulatory layer involves a complex network of transcription factors from the basic Helix Loop Helix (bHLH) or AP2 families. In the present manuscript, we investigated whether an additional epigenetic layer could control the organ-, developmental- and environmental-specificity of MIA accumulation. We used Whole-Genome Bisulfite Sequencing (WGBS) together with RNA-seq to identify differentially methylated and expressed genes among nine samples reflecting different plant organs and experimental conditions. Tissue specific gene expression was associated with specific methylation signatures depending on cytosine contexts and gene parts. Some genes encoding key enzymatic steps from the MIA pathway were found to be simultaneously differentially expressed and methylated in agreement with the corresponding MIA accumulation. In addition, we found that transcription factors were strikingly concerned by DNA methylation variations. Altogether, our integrative analysis supports an epigenetic regulation of specialized metabolisms in plants and more likely targeting transcription factors which in turn may control the expression of enzyme-encoding genes.

Despite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris across five tissues: embryo, megagametophyte, needle, phloem and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.

Transgenic mice have offered a unique opportunity for molecular biologists to study DNA sequences involved in controlling tissue specific gene expression in the intact animal. The knowledge gained from such studies is now being used to the benefit of mammalian developmental biologists. Or at least, this is the claim in two recent papers using transgenics to annihilate particular cell populations l'z. Both demonstrate that it is possible to ablate, or anyway parfi'ally destroy, certain tissues which express a common marker gene, and this is seen as a prelude to being able to effect specific cell lineage ablation. The basic strategy behind both these studies is the fusion of part of the diphtheria toxin gene to a tissue spec~Jic promoter or enhancer. The diphtheria toxin gene, from C o ~ e bacterium diphtheriae, codes for a polypeptide which is cleaved into two subunits. Subunit A comprises an ADP-ribosyltransferase which catalyses the transfer of ADP-ribose from NAD to elongation factor 2, thus inhibiting protein synthesis and eventually killing the celP. So effective is this enzyme that it is estimated that a single molecule in the cytoplasm can prove fatal to a cell 4. Subunit B, on the other hand, binds to the cell surface and is instrumental in ensuring that the toxin is taken into cells by endocytosis. Without subunit B the ADP-ribosyltransferase cannot get into cells and is essentially harmless. Fusing the sequence encoding subunit A (DT-A) to a tissue specific promoter should, therefore, produce cell autonomous death in all cells in which that promoter is active. There is undoubtedly something very attractive about such nicely directed proscription. The two tissues which have been used to demonstrate that the strategy does indeed work are the pancreas and the lens. The rat e!~stase gene codes for a serine protease which is expressed almost exclusively in the exocrine acinar cell population of the pancreas. The enhancer/promoter of this gene lies in a 133 bp region 5' to the gene and has been shown to be capable of directing the expression of human growth hormone (hGH) exclusively to the exocrine pancreas s. SimiI~rly, the mouse yz-crystallin promoter is active only in lens fibre cells and the /ac Z gene fused to this promoter is expressed only in these cells in transgenic mice e. Thus, fusion of DT-A to the elastase enhancer should delete, at the very least, the acinar cell population of the pancreas, while Yzcrystallin-DT-A constructs should destroy the lens fibre cells. Some transgenlcs carrying the DT-A sequence (which, for reasons that are not clear, was only expressed when incorporated into the original rat elastase-hGH construct) did bck a normal pancreas. However, the frequency of this abnormality, presumably coincident with expression of the construct, was less than half that expected from the expression of hGH in transgenics without the DT-A insert (and this did not seem to be due to specific selection of wild-type pancreatic cells in otherwise mosaic founder animals). In affected transgenics, pancreatic development seemed to be arrested either at the embryonic rudiment stage, or during the early stages of differentiation when it is composed only of duct-like structures or, in one animal, had formed a few acinar-like cells. Lmmunocytochemistry demonstrated that amylase, a major exocrine product, was greatly reduced in the most advanced of these pancreatic structures and that there was a deficiency in endocrine products, such as insulin, compared with controls. All in all, the genetic ablation seems to have achieved a 10--100-fold reduction in islet and duct cells and almost complete depletion of exocrine cells I. In the absence of mosaic founder transgenics it is not possible to test the inheritance of this trait and to examine its pheno

Background Meiotic sex chromosome inactivation (MSCI) during spermatogenesis has been proposed as one of the evolutionary driving forces behind both the under-representation of male-biased genes on, and the gene movement out of, the X chromosome in Drosophila. However, the relevance of MSCI in shaping sex chromosome evolution is controversial. Here we examine two aspects of a recent study on testis gene expression (Mikhaylova and Nurminsky, BMC Biol 2011, 9:29) that failed to support the MSCI in Drosophila. First, Mikhaylova and Nurminsky found no differences between X-linked and autosomal genes based on the transcriptional profiling of the early testis development, and thus concluded that MSCI does not occur in D. melanogaster. Second, they also analyzed expression data from several D. melanogaster tissues and concluded that under-representation on the X chromosome is not an exclusive property of testis-biased genes, but instead, a general property of tissue-specific genes. Results By re-analyzing the Mikhaylova and Nurminsky's testis data and the expression data on several D. melanogaster tissues, we made two major findings that refuted their original claims. First, the developmental testis data has generally greater experimental error than conventional analyses, which reduced significantly the power to detect chromosomal differences in expression. Nevertheless, our re-analysis observed significantly lower expression of the X chromosome in the genomic transcriptomes of later development stages of the testis, which is consistent with the MSCI hypothesis. Second, tissue-specific genes are also in general enriched with genes more expressed in testes than in ovaries, that is testis-biased genes. By completely excluding from the analyses the testis-biased genes, which are known to be under-represented in the X, we found that all the other tissue-specific genes are randomly distributed between the X chromosome and the autosomes. Conclusions Our findings negate the original study of Mikhaylova and Nurminsky, which concluded a lack of MSCI and generalized the pattern of paucity in the X chromosome for tissue-specific genes in Drosophila. Therefore, MSCI and other selection-based models such as sexual antagonism, dosage compensation, and meiotic-drive continue to be viable models as driving forces shaping the genomic distribution of male-related genes in Drosophila.

Background The discovery of gene body methylation, which refers to DNA methylation within gene coding region, suggests an as yet unknown role of DNA methylation at actively transcribed genes. In invertebrates, gene bodies are the primary targets of DNA methylation, and only a subset of expressed genes is modified. Results Here we investigate the tissue variability of both the global levels and distribution of 5-methylcytosine (5mC) in the sea squirt Ciona intestinalis. We find that global 5mC content of early developmental embryos is high, but is strikingly reduced in body wall tissues. We chose sperm and adult muscle cells, with high and reduced levels of global 5mC respectively, for genome-wide analysis of 5mC targets. By means of CXXC-affinity purification followed by deep sequencing (CAP-seq), and genome-wide bisulfite sequencing (BS-seq), we designated body-methylated and unmethylated genes in each tissue. Surprisingly, body-methylated and unmethylated gene groups are identical in the sperm and muscle cells. Our analysis of microarray expression data shows that gene body methylation is associated with broad expression throughout development. Moreover, transgenic analysis reveals contrasting gene body methylation at an identical gene-promoter combination when integrated at different genomic sites. Conclusions We conclude that gene body methylation is not a direct regulator of tissue specific gene expression in C. intestinalis. Our findings reveal constant targeting of gene body methylation irrespective of cell type, and they emphasize a correlation between gene body methylation and ubiquitously expressed genes. Our transgenic experiments suggest that the promoter does not determine the methylation status of the associated gene body.

Congenital heart defects (CHD) are the most common cause of death in children under the age of 1. Tetralogy of Fallot (TOF) is a severe CHD that results from developmental defects in the conotruncal outflow tract. Recently, a tissue-specific gene expression template (GET) was derived from microarray data that accurately characterized multiple normal human tissues. We used the GET to examine spatial, temporal, and a pathological condition (TOF) within a single organ, the heart. The GET, as previously defined, generally identified temporal and spatial differences in the cardiac tissue. Differences in the stoichiometry of the GET reflected the severe developmental disturbance associated with TOF. Our analysis suggests that the homoeostatic equilibrium assessed by the GET at the inter-organ level is generally maintained at the intra-organ level as well.