Tissue-Specific and Ubiquitous Expression Patterns from Alternative Promoters of Human Genes

The Syrian golden hamster (Mesocricetus auratus) has recently been demonstrated as a clinically relevant animal model for SARS-CoV-2 infection. However, lack of knowledge about the tissue-specific expression pattern of various proteins in these animals and the unavailability of reagents like antibodies against this species hampers these models’ optimal use. The major objective of our current study was to analyze the tissue-specific expression pattern of angiotensin-converting enzyme 2, a proven functional receptor for SARS-CoV-2 in different organs of the hamster. Using two different antibodies (MA5-32307 and AF933), we have conducted immunoblotting, immunohistochemistry, and immunofluorescence analysis to evaluate the ACE2 expression in different tissues of the hamster. Further, at the mRNA level, the expression of Ace2 in tissues was evaluated through RT-qPCR analysis. Both the antibodies detected expression of ACE2 in kidney, small intestine, tongue, and liver. Epithelium of proximal tubules of kidney and surface epithelium of ileum expresses a very high amount of this protein. Surprisingly, analysis of stained tissue sections showed no detectable expression of ACE2 in the lung or tracheal epithelial cells. Similarly, all parts of the large intestine were negative for ACE2 expression. Analysis of tissues from different age groups and sex didn’t show any obvious difference in ACE2 expression pattern or level. Together, our findings corroborate some of the earlier reports related to ACE2 expression patterns in human tissues and contradict others. We believe that this study’s findings have provided evidence that demands further investigation to understand the predominant respiratory pathology of SARS-CoV-2 infection and disease.

Download Full-text

On the scope and limitations of baker's yeast as a model organism for studying human tissue-specific pathways

10.1101/011858 ◽

2014 ◽

Author(s):

Shahin Mohammadi ◽

Baharak Saberidokht ◽

Shankar Subramaniam ◽

Ananth Grama

Keyword(s):

Drug Targets ◽

Model Organism ◽

Functional Space ◽

Computational Method ◽

Therapeutic Interventions ◽

Human Tissues ◽

Human Interactome ◽

Tissue Specific ◽

Complex Disorders ◽

Human Genes

Budding yeast, S. cerevisiae, has been used extensively as a model organism for studying cellular processes in evolutionarily distant species, including humans. However, different human tissues, while inheriting a similar genetic code, exhibit distinct anatomical and physiological properties. Specific biochemical processes and associated biomolecules that differentiate various tissues are not completely understood, neither is the extent to which a unicellular organism, such as yeast, can be used to model these processes within each tissue. We propose a novel computational and statistical framework to systematically quantify the suitability of yeast as a model organism for different human tissues. We develop a computational method for dissecting the human interactome into tissue-specific cellular networks. Using these networks, we simultaneously partition the functional space of human genes, and their corresponding pathways, based on their conservation both across species and among different tissues. We study these sub-spaces in detail, and relate them to the overall similarity of each tissue with yeast. Many complex disorders are driven by a coupling of housekeeping (universally expressed in all tissues) and tissue-selective (expressed only in specific tissues) dysregulated pathways. We show that human-specific subsets of tissue-selective genes are significantly associated with the onset and development of a number of pathologies. Consequently, they provide excellent candidates as drug targets for therapeutic interventions. We also present a novel tool that can be used to assess the suitability of the yeast model for studying tissue-specific physiology and pathophysiology in humans.

Download Full-text

Development of cDNA normalization system and preliminary transcription analysis of KCS genes in apple tissues

Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis ◽

10.11118/actaun201159030009 ◽

2011 ◽

Vol 59 (3) ◽

pp. 9-12 ◽

Cited By ~ 3

Author(s):

Zsolt Albert ◽

Cs. Deák ◽

A. Miskó ◽

M. Tóth ◽

I. Papp

Keyword(s):

Gene Expression ◽

Expression System ◽

Expression Patterns ◽

Housekeeping Genes ◽

Apple Fruit ◽

Rt Pcr ◽

Specific Primers ◽

Specific Expression ◽

Transcription Analysis ◽

Tissue Specific

Wax production is an important aspect of apple (Malus domestica Borkh.) fruit development from both theoretical and practical point of views. The complex molecular mechanism that controls wax biosynthesis is still widely unknown but many studies focused on this topic. We aimed to develop further the experimental framework of these efforts with a description of an improved reference genes expression system. Results in the literature show that similarities exist among the expression of some housekeeping genes of different plant species. Based on these considerations and on gene expression data from Arabidopsis thaliana, some genes in apple were assigned for analysis. EST sequences of apple were used to design specific primers for RT-PCR experiments. Isolation of intact RNA from different apple tissues and performing RT-PCR reaction were also key point in obtaining expression patterns. To monitor DNA contamination of the RNA samples, specific primers were used that amplify intron-containing sequences from the cDNA. We found that actin primers can be used for the detection of intron containing genomic DNA, and tubulin primers are good internal controls in RT-PCR experiments. We were able to make a difference between tissue-specific and tissue-independent gene-expression, furthermore we found tissue specific differences between the expression patterns of candidate genes, that are potentially involved in wax-biosynthesis. Our results show that KCS1 and KCS4 are overexpressed in the skin tissue, this could mean that these genes have skin-specific expression in apple fruit.

Download Full-text

Translation elongation factor 1A2 is encoded by one of four closely related eef1a genes and is dispensable for survival in zebrafish

Bioscience Reports ◽

10.1042/bsr20194191 ◽

2020 ◽

Vol 40 (1) ◽

Author(s):

Nwamaka J. Idigo ◽

Dinesh C. Soares ◽

Catherine M. Abbott

Keyword(s):

De Novo ◽

Single Gene ◽

Expression Patterns ◽

Elongation Factor ◽

Model Organisms ◽

Translation Elongation Factor ◽

Translation Elongation ◽

Tissue Specific ◽

Elongation Factor 1A2 ◽

Mutant Lines

Abstract Zebrafish are valuable model organisms for the study of human single-gene disorders: they are genetically manipulable, their development is well understood, and mutant lines with measurable, disease-appropriate phenotypic abnormalities can be used for high throughput drug screening approaches. However, gene duplication events in zebrafish can result in redundancy of gene function, masking loss-of-function phenotypes and thus confounding this approach to disease modelling. Furthermore, recent studies have yielded contrasting results depending on whether specific genes are targeted using genome editing to make mutant lines, or whether morpholinos are used (morphants). De novo missense mutations in the human gene EEF1A2, encoding a tissue-specific translation elongation factor, cause severe neurodevelopmental disorders; there is a real need for a model system to study these disorders and we wanted to explore the possibility of a zebrafish model. We identified four eef1a genes and examined their developmental and tissue-specific expression patterns: eef1a1l1 is first to be expressed while eef1a2 is only detected later during development. We then determined the effects of introducing null mutations into translation elongation factor 1A2 (eEF1A2) in zebrafish using CRISPR/Cas9 gene editing, in order to compare the results with previously described morphants, and with severe neurodegenerative lethal phenotype of eEF1A2-null mice. In contrast with both earlier analyses in zebrafish using morpholinos and with the mouse eEF1A2-null mice, disruption of the eef1a2 gene in zebrafish is compatible with normal lifespan. The resulting lines, however, may provide a valuable platform for studying the effects of expression of mutant human eEF1A2 mRNA.

Download Full-text

Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data

PLoS ONE ◽

10.1371/journal.pone.0166978 ◽

2016 ◽

Vol 11 (11) ◽

pp. e0166978 ◽

Cited By ~ 9

Author(s):

Eman Badr ◽

Mahmoud ElHefnawi ◽

Lenwood S. Heath

Keyword(s):

Regulatory Elements ◽

Rna Seq ◽

Tissue Specific ◽

Human Genes ◽

Splicing Regulatory Elements ◽

Computational Identification

Download Full-text

Differential expression of Broad-Complex transcription factors may forecast tissue-specific developmental fates during Drosophila metamorphosis

Development ◽

10.1242/dev.120.11.3275 ◽

1994 ◽

Vol 120 (11) ◽

pp. 3275-3287 ◽

Cited By ~ 20

Author(s):

I.F. Emery ◽

V. Bedian ◽

G.M. Guild

Keyword(s):

Western Blot ◽

Expression Patterns ◽

Primary Response ◽

Protein Isoforms ◽

Secondary Response ◽

C Protein ◽

Tissue Specific ◽

Specific Outcome ◽

C Proteins ◽

Broad Complex

The steroid hormone ecdysone initiates metamorphosis in Drosophila melanogaster by activating a cascade of gene activity that includes primary response transcriptional regulators and secondary response structural genes. The Broad-Complex (BR-C) primary response gene is composed of several distinct genetic functions and encodes a family of related transcription factor isoforms. Our objective was to determine whether BR-C isoforms were components of the primary ecdysone response in all tissues and whether tissue-specific isoform expression is associated with tissue-specific metamorphic outcomes. We used specific antibody reagents that recognize and distinguish among the Z1, Z2 and Z3 BR-C protein isoforms to study protein expression patterns during the initial stages of metamorphosis. Western blot analyses demonstrated that BR-C isoforms are induced at the onset of metamorphosis, each with unique kinetics of induction and repression. Whole-mount immunostaining showed that the BR-C proteins accumulate in the nuclei of all larval and imaginal tissues indicating that the BR-C is induced as a primary response in many tissues. Several tissues express different levels and combinations of the BR-C isoforms suggesting that the BR-C is important in determining the tissue-specific outcome of many parallel ecdysone response cascades. For example, prepupal salivary glands (destined for histolysis during metamorphosis) express Z1 isoforms while imaginal discs (destined for cell differentiation and morphogenesis) shift from the synthesis of Z2 isoforms to the synthesis of Z1 isoforms. The prepupal central nervous system (destined for tissue remodeling) expresses all isoforms, with Z3 predominating. Salivary gland chromosome immunostaining indicated that BR-C proteins interact directly with numerous loci in the polytene genome. Finally, western blot analyses showed that distinct BR-C genetic functions can be correlated with single and specific BR-C protein isoforms.

Download Full-text

Single-Cell RNA Sequencing Unveils Unique Transcriptomic Signatures of Organ-Specific Endothelial Cells

Circulation ◽

10.1161/circulationaha.119.041433 ◽

2020 ◽

Vol 142 (19) ◽

pp. 1848-1862 ◽

Cited By ~ 1

Author(s):

David T. Paik ◽

Lei Tian ◽

Ian M. Williams ◽

Siyeon Rhee ◽

Hao Zhang ◽

...

Keyword(s):

Endothelial Cells ◽

Single Cell ◽

Rna Sequencing ◽

Expression Patterns ◽

Receptor Expression ◽

Transcriptional Networks ◽

Sequencing Data ◽

Tissue Specific ◽

Functional Relationships ◽

Single Cell Rna Sequencing

Background: Endothelial cells (ECs) display considerable functional heterogeneity depending on the vessel and tissue in which they are located. Whereas these functional differences are presumably imprinted in the transcriptome, the pathways and networks that sustain EC heterogeneity have not been fully delineated. Methods: To investigate the transcriptomic basis of EC specificity, we analyzed single-cell RNA sequencing data from tissue-specific mouse ECs generated by the Tabula Muris consortium. We used a number of bioinformatics tools to uncover markers and sources of EC heterogeneity from single-cell RNA sequencing data. Results: We found a strong correlation between tissue-specific EC transcriptomic measurements generated by either single-cell RNA sequencing or bulk RNA sequencing, thus validating the approach. Using a graph-based clustering algorithm, we found that certain tissue-specific ECs cluster strongly by tissue (eg, liver, brain), whereas others (ie, adipose, heart) have considerable transcriptomic overlap with ECs from other tissues. We identified novel markers of tissue-specific ECs and signaling pathways that may be involved in maintaining their identity. Sex was a considerable source of heterogeneity in the endothelial transcriptome and we discovered Lars2 to be a gene that is highly enriched in ECs from male mice. We found that markers of heart and lung ECs in mice were conserved in human fetal heart and lung ECs. We identified potential angiocrine interactions between tissue-specific ECs and other cell types by analyzing ligand and receptor expression patterns. Conclusions: We used single-cell RNA sequencing data generated by the Tabula Muris consortium to uncover transcriptional networks that maintain tissue-specific EC identity and to identify novel angiocrine and functional relationships between tissue-specific ECs.

Download Full-text

Transcription Profiles of Age-at-Maturity-Associated Genes Suggest Cell Fate Commitment Regulation as a Key Factor in the Atlantic Salmon Maturation Process

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400882 ◽

2019 ◽

Vol 10 (1) ◽

pp. 235-246 ◽

Cited By ~ 3

Author(s):

Johanna Kurko ◽

Paul V. Debes ◽

Andrew H. House ◽

Tutku Aykanat ◽

Jaakko Erkinaro ◽

...

Keyword(s):

Atlantic Salmon ◽

Cell Fate ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Expression Patterns ◽

Hippo Signaling ◽

Age At Maturity ◽

Specific Expression ◽

Hpg Axis ◽

Tissue Specific

Despite recent taxonomic diversification in studies linking genotype with phenotype, follow-up studies aimed at understanding the molecular processes of such genotype-phenotype associations remain rare. The age at which an individual reaches sexual maturity is an important fitness trait in many wild species. However, the molecular mechanisms regulating maturation timing processes remain obscure. A recent genome-wide association study in Atlantic salmon (Salmo salar) identified large-effect age-at-maturity-associated chromosomal regions including genes vgll3, akap11 and six6, which have roles in adipogenesis, spermatogenesis and the hypothalamic-pituitary-gonadal (HPG) axis, respectively. Here, we determine expression patterns of these genes during salmon development and their potential molecular partners and pathways. Using Nanostring transcription profiling technology, we show development- and tissue-specific mRNA expression patterns for vgll3, akap11 and six6. Correlated expression levels of vgll3 and akap11, which have adjacent chromosomal location, suggests they may have shared regulation. Further, vgll3 correlating with arhgap6 and yap1, and akap11 with lats1 and yap1 suggests that Vgll3 and Akap11 take part in actin cytoskeleton regulation. Tissue-specific expression results indicate that vgll3 and akap11 paralogs have sex-dependent expression patterns in gonads. Moreover, six6 correlating with slc38a6 and rtn1, and Hippo signaling genes suggests that Six6 could have a broader role in the HPG neuroendrocrine and cell fate commitment regulation, respectively. We conclude that Vgll3, Akap11 and Six6 may influence Atlantic salmon maturation timing via affecting adipogenesis and gametogenesis by regulating cell fate commitment and the HPG axis. These results may help to unravel general molecular mechanisms behind maturation.

Download Full-text