scholarly journals Transcriptome Atlas of 16 Donkey Tissues

2021 ◽  
Vol 12 ◽  
Author(s):  
Yinan Wang ◽  
Xinyao Miao ◽  
Zicheng Zhao ◽  
Yonghui Wang ◽  
Shuaicheng Li ◽  
...  
Keyword(s):  
Calcium Binding ◽  
Molecular Mechanisms ◽  
Economic Value ◽  
Specific Gene ◽  
Donkey Milk ◽  
Protein Coding ◽  
Tissue Specific ◽  
Lysozyme Gene ◽  
Equus Asinus ◽  
Wide Range

Donkeys (Equus asinus) are important livestock with great economic value in meat, skin, and milk production. However, a lack of knowledge of the transcriptome landscape across a wide range of donkey tissues limits genetic selective breeding and conservation. Here we used transcriptomics to describe the transcriptome landscape, classify the tissue-specific gene expression across all primary donkey tissues, and present supplementary analyses on the protein level of additional donkey milk samples. Overall, 16,013 protein-coding genes and 21,983 transcripts were mapped to the reference genome, including 6,778 ubiquitously expressed genes and 2,601 tissue-enriched genes. Functional analysis revealed that the function of the tissue-enriched genes was highly tissue specific. Tissue-elevated genes that could be associated with unique phenotypes in donkey were analyzed. The results showed that, compared with those in human and other livestock, the lysozyme gene in donkey breast was specifically and highly expressed. The calcium-binding lysozyme, encoded by the lysozyme gene, was also detected in high amounts in donkey milk. Given those intact lysozyme genes that predict potentially functional calcium-binding lysozyme found in only a few species (e.g., donkey and horse), the high expression of the lysozyme gene in donkey breast may contribute to the high lysozyme content in donkey milk. Furthermore, 71% of the proteins in donkey milk overlapped with human milk protein, higher than the overlapping rates of bovine, sheep, and swine with humans. The donkey transcriptomic resource contributes to the available genomic resources to interpret the molecular mechanisms underlying phenotype traits.

scholarly journals Tissue-specific cis-regulatory divergence implicates a fatty acid elongase necessary for inhibiting interspecies mating in Drosophila

2018 ◽  
Author(s):  
Peter A. Combs ◽  
Joshua J. Krupp ◽  
Neil M. Khosla ◽  
Dennis Bua ◽  
Dmitri A. Petrov ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Sister Species ◽  
F1 Hybrids ◽  
Rna Seq ◽  
Fatty Acid Elongase ◽  
Tissue Specific ◽  
Regulatory Changes ◽  
Wide Range

AbstractPheromones known as cuticular hydrocarbons are a major component of reproductive isolation in Drosophila. Individuals from morphologically similar sister species produce different sets of hydrocarbons that allow potential mates to identify them as a suitable partner. In order to explore the molecular mechanisms underlying speciation, we performed RNA-seq in F1 hybrids to measure tissue-specific cis-regulatory divergence between the sister species D. simulans and D. sechellia. By focusing on cis-regulatory changes specific to female oenocytes, we rapidly identified a small number of candidate genes. We found that one of these, the fatty acid elongase eloF, broadly affects both the complement of hydrocarbons present on D. sechellia females and the propensity of D. simulans males to mate with those females. In addition, knockdown of eloF in the more distantly related D. melanogaster led to a similar shift in hydrocarbons as well as lower interspecific mate discrimination by D. simulans males. Thus, cis-regulatory changes in eloF appear to be a major driver in the sexual isolation of D. simulans from multiple other species. More generally, our RNA-seq approach proved to be far more efficient than QTL mapping in identifying candidate genes; the same framework can be used to pinpoint cis-regulatory drivers of divergence in a wide range of traits differing between any interfertile species.

scholarly journals Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses

Planta ◽  
2020 ◽  
Vol 252 (5) ◽  
Author(s):  
Li Chen ◽  
Qian-Hao Zhu ◽  
Kerstin Kaufmann
Keyword(s):  
Stress Responses ◽  
Translational Regulation ◽  
Molecular Mechanisms ◽  
Functional Characterization ◽  
Reproductive Organs ◽  
Gene Activity ◽  
Protein Coding ◽  
Wide Range ◽  
Non Coding Rnas ◽  
Coding Potential

Abstract Main conclusion Long non-coding RNAs modulate gene activity in plant development and stress responses by various molecular mechanisms. Abstract Long non-coding RNAs (lncRNAs) are transcripts larger than 200 nucleotides without protein coding potential. Computational approaches have identified numerous lncRNAs in different plant species. Research in the past decade has unveiled that plant lncRNAs participate in a wide range of biological processes, including regulation of flowering time and morphogenesis of reproductive organs, as well as abiotic and biotic stress responses. LncRNAs execute their functions by interacting with DNA, RNA and protein molecules, and by modulating the expression level of their targets through epigenetic, transcriptional, post-transcriptional or translational regulation. In this review, we summarize characteristics of plant lncRNAs, discuss recent progress on understanding of lncRNA functions, and propose an experimental framework for functional characterization.

scholarly journals A non-coding genetic variant maximally associated with serum urate levels is functionally linked to HNF4A-dependent PDZK1 expression

2018 ◽  
Author(s):  
Sarada Ketharnathan ◽  
Megan Leask ◽  
James Boocock ◽  
Amanda J. Phipps-Green ◽  
Jisha Antony ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepg2 Cells ◽  
Molecular Mechanisms ◽  
Genetic Variant ◽  
Fluorescent Protein ◽  
Serum Urate ◽  
Specific Gene ◽  
Specific Expression ◽  
Enhancer Activity ◽  
Tissue Specific

ABSTRACTSeveral dozen genetic variants associate with serum urate levels, but the precise molecular mechanisms by which they affect serum urate are unknown. Here we tested for functional linkage of the maximally-associated genetic variant rs1967017 at the PDZK1 locus to elevated PDZK1 expression.We performed expression quantitative trait locus (eQTL) and likelihood analyses followed by gene expression assays. Zebrafish were used to determine the ability of rs1967017 to direct tissue-specific gene expression. Luciferase assays in HEK293 and HepG2 cells measured the effect of rs1967017 on transcription amplitude.PAINTOR analysis revealed rs1967017 as most likely to be causal and rs1967017 was an eQTL for PDZK1 in the intestine. The region harboring rs1967017 was capable of directly driving green fluorescent protein expression in the kidney, liver and intestine of zebrafish embryos, consistent with a conserved ability to confer tissue-specific expression. The urate-increasing T-allele of rs1967017 strengthens a binding site for the transcription factor HNF4A. siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells. Luciferase assays showed that the T-allele of rs1967017 gains enhancer activity relative to the urate-decreasing C-allele, with T-allele enhancer activity abrogated by HNF4A depletion. HNF4A physically binds the rs1967017 region, suggesting direct transcriptional regulation of PDZK1 by HNF4A.With other reports our data predict that the urate-raising T-allele of rs1967017 enhances HNF4A binding to the PDZK1 promoter, thereby increasing PDZK1 expression. As PDZK1 is a scaffold protein for many ion channel transporters, increased expression can be predicted to increase activity of urate transporters and alter excretion of urate.

scholarly journals Network propagation of rare variants in Alzheimer’s disease reveals tissue-specific hub genes and communities

2021 ◽  
Vol 17 (1) ◽  
pp. e1008517
Author(s):  
Marzia Antonella Scelsi ◽  
Valerio Napolioni ◽  
Michael D. Greicius ◽  
Andre Altmann ◽  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Rare Variants ◽  
Late Onset ◽  
Integrative Approach ◽  
Specific Gene ◽  
Tissue Specific ◽  
Association Testing ◽  
Wide Range ◽  
Network Propagation

State-of-the-art rare variant association testing methods aggregate the contribution of rare variants in biologically relevant genomic regions to boost statistical power. However, testing single genes separately does not consider the complex interaction landscape of genes, nor the downstream effects of non-synonymous variants on protein structure and function. Here we present the NETwork Propagation-based Assessment of Genetic Events (NETPAGE), an integrative approach aimed at investigating the biological pathways through which rare variation results in complex disease phenotypes. We applied NETPAGE to sporadic, late-onset Alzheimer’s disease (AD), using whole-genome sequencing from the AD Neuroimaging Initiative (ADNI) cohort, as well as whole-exome sequencing from the AD Sequencing Project (ADSP). NETPAGE is based on network propagation, a framework that models information flow on a graph and simulates the percolation of genetic variation through tissue-specific gene interaction networks. The result of network propagation is a set of smoothed gene scores that can be tested for association with disease status through sparse regression. The application of NETPAGE to AD enabled the identification of a set of connected genes whose smoothed variation profile was robustly associated to case-control status, based on gene interactions in the hippocampus. Additionally, smoothed scores significantly correlated with risk of conversion to AD in Mild Cognitive Impairment (MCI) subjects. Lastly, we investigated tissue-specific transcriptional dysregulation of the core genes in two independent RNA-seq datasets, as well as significant enrichments in terms of gene sets with known connections to AD. We present a framework that enables enhanced genetic association testing for a wide range of traits, diseases, and sample sizes.

scholarly journals Tissue-specific gene expression in the pituitary: the glycoprotein hormone alpha-subunit gene is regulated by a gonadotrope-specific protein.

1992 ◽  
Vol 12 (5) ◽  
pp. 2143-2153 ◽  
Author(s):  
F Horn ◽  
J J Windle ◽  
K M Barnhart ◽  
P L Mellon
Keyword(s):  
Molecular Mechanisms ◽  
Regulatory Element ◽  
Alpha Subunit ◽  
Specific Factor ◽  
Specific Gene ◽  
Homeodomain Protein ◽  
Subunit Gene ◽  
Glycoprotein Hormone ◽  
Specific Expression ◽  
Tissue Specific

The molecular mechanisms for the development of multiple distinct endocrine cell types in the anterior pituitary have been an area of intensive investigation. Though the homeodomain protein Pit-1/GHF-1 is known to be involved in differentiation of the somatotrope and lactotrope lineages, which produce growth hormone and prolactin, respectively, little is known of the transcriptional regulators important for the gonadotrope cell lineage, which produces the glycoprotein hormones luteinizing hormone and follicle-stimulating hormone. Using transgenic mice and transfection into a novel gonadotrope lineage cell line, we have identified a regulatory element that confers gonadotrope-specific expression to the glycoprotein hormone alpha-subunit gene. A tissue-specific factor that binds to this element is purified and characterized as a 54-kDa protein which is present uniquely in cells of the gonadotrope lineage and is not Pit-1/GHF-1. The human and equine alpha-subunit genes are also expressed in placental cells. However, the previously characterized placental transcription factors designated TSEB and alpha-ACT are not found in the pituitary gonadotrope cells, indicating that independent mechanisms confer expression of these genes in the two different tissues.

scholarly journals Tissue-Specific Profiling of Oxidative Stress-Associated Transcriptome in a Healthy Mouse Model

2018 ◽  
Vol 19 (10) ◽  
pp. 3174 ◽  
Author(s):  
Jung Kim ◽  
Hyeong Kim ◽  
Chang Son
Keyword(s):  
Oxidative Stress ◽  
Quantitative Polymerase Chain Reaction ◽  
Specific Gene ◽  
Tissue Specific ◽  
Age Related ◽  
Wide Range ◽  
Liver And Kidney ◽  
Specific Variation ◽  
Polymerase Chain ◽  
Lung And Kidney

Oxidative stress is a common phenomenon and is linked to a wide range of diseases and pathological processes including aging. Tissue-specific variation in redox signaling and cellular responses to oxidative stress may be associated with vulnerability especially to age-related and chronic diseases. In order to provide a basis for tissue-specific difference, we examined the tissue-specific transcriptional features of 101 oxidative stress-associated genes in 10 different tissues and organs of healthy mice under physiological conditions. Microarray analysis results, which were consistent with quantitative polymerase chain reaction (qPCR) results, showed that catalase, Gpx3, and Gpx4 were most highly regulated in the liver, kidney, and testes. We also found the tissue-specific gene expression of SOD1 (liver and kidney), SOD2 (heart and muscle), and SOD3 (lung and kidney). The current results will serve as a reference for animal models and help advance our understanding of tissue-specific variability in oxidative stress-associated pathogenesis.

scholarly journals Microalgae: New Source of Plant Biostimulants

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1240 ◽  
Author(s):  
Giuseppe Colla ◽  
Youssef Rouphael
Keyword(s):  
Green Algae ◽  
Molecular Mechanisms ◽  
Nutrient Use Efficiency ◽  
Economic Value ◽  
Biofuel Production ◽  
Blue Green Algae ◽  
Agronomic Crops ◽  
Nutrient Use ◽  
Wide Range ◽  
Innovative Products

Biostimulant manufacturers have developed innovative products targeting specific agronomic needs, hence attracting the attention of the scientific community, extension specialists, and industry stakeholders including policymakers and crop producers. Microalgae acquire a broad economic value in the production of nutrient dense food and supplementary diet produce, in addition to their high importance in biofuel production and wastewater bioremediation. Recently, microalgae, which comprise blue-green algae (eukaryotic and prokaryotic cyanobacteria), have gained prominence as biostimulant products due to their potential to increase germination, seedling growth, plant growth, productivity, nutrient use efficiency, as well as tolerance to a wide range of abiotic stresses (salinity, drought, sub- and supra-optimal temperatures, and heavy metals contamination). Although it is well established that green and blue-green algae produce several bioactive and signaling molecules active on horticultural and agronomic crops, their targeted applications in plant science are still in their infancy stage. The aim of this editorial paper is to provide an updated overview of this far-reaching new category of plant biostimulants and the possible physiological and molecular mechanisms behind the biostimulatory action based on the recent scientific literature. Finally, this editorial paper identifies the main bottlenecks that hamper market introduction and farmers from reaping the full benefit of microalgae-based biostimulants; it also pinpoints the future relevant areas of microalgae research to enhance the biostimulant action of microalgal extracts in agriculture.

scholarly journals Comparative Transcriptome Analysis of Alpinia oxyphylla reveals Tissue-specific Expression of Flavonoid Biosynthesis Genes

2020 ◽  
Author(s):  
Bingmiao Gao
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Genetically Engineered ◽  
Flavonoid Biosynthesis ◽  
Specific Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Alpinia Oxyphylla

Abstract Background: Alpinia oxyphylla is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla ; however, the genetic and molecular mechanisms of flavonoid biosynthesis are not well understood. Methods: We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant. Results: In all, 8.85, 10.10, 8.68, 6.89, and 8.51 Gb clean data were obtained for early-, middle-, and late-stage fruits, leaves, and roots, respectively. Furthermore, 50,401 unigenes were grouped into functional categories based on four databases, namely Nr (47,745 unigenes), Uniprot (49,685 unigenes), KOG (20,153 unigenes), and KEGG (27,285 unigenes). A total of 3,110 differentially expressed genes and five distinct clusters with similar expression patterns were obtained, in which 27 unigenes encoded 13 key enzymes (such as CHS, CHI, F3H, FLS, ANS ) associated with flavonoid biosynthesis. Conclusion: The tissue-specific expression of the genes corresponds to accumulation of flavonoids in these tissues.These results provide insights into the molecular mechanism of flavonoid biosynthesis in A. oxyphylla and application of genetically engineered varieties of A. oxyphylla .

Tissue-specific gene expression in the pituitary: the glycoprotein hormone alpha-subunit gene is regulated by a gonadotrope-specific protein

1992 ◽  
Vol 12 (5) ◽  
pp. 2143-2153
Author(s):  
F Horn ◽  
J J Windle ◽  
K M Barnhart ◽  
P L Mellon
Keyword(s):  
Molecular Mechanisms ◽  
Regulatory Element ◽  
Alpha Subunit ◽  
Specific Factor ◽  
Specific Gene ◽  
Homeodomain Protein ◽  
Subunit Gene ◽  
Glycoprotein Hormone ◽  
Specific Expression ◽  
Tissue Specific

The molecular mechanisms for the development of multiple distinct endocrine cell types in the anterior pituitary have been an area of intensive investigation. Though the homeodomain protein Pit-1/GHF-1 is known to be involved in differentiation of the somatotrope and lactotrope lineages, which produce growth hormone and prolactin, respectively, little is known of the transcriptional regulators important for the gonadotrope cell lineage, which produces the glycoprotein hormones luteinizing hormone and follicle-stimulating hormone. Using transgenic mice and transfection into a novel gonadotrope lineage cell line, we have identified a regulatory element that confers gonadotrope-specific expression to the glycoprotein hormone alpha-subunit gene. A tissue-specific factor that binds to this element is purified and characterized as a 54-kDa protein which is present uniquely in cells of the gonadotrope lineage and is not Pit-1/GHF-1. The human and equine alpha-subunit genes are also expressed in placental cells. However, the previously characterized placental transcription factors designated TSEB and alpha-ACT are not found in the pituitary gonadotrope cells, indicating that independent mechanisms confer expression of these genes in the two different tissues.

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