scholarly journals miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish

2018 ◽  
Author(s):  
Thomas Desvignes ◽  
Peter Batzel ◽  
Jason Sydes ◽  
B. Frank Eames ◽  
John Postlethwait
Keyword(s):  
Gasterosteus Aculeatus ◽  
Mature Mirnas ◽  
Evolutionary Conservation ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Specific Expression ◽  
Tissue Specific ◽  
Mirna Genes ◽  
Evolutionarily Conserved ◽  
Organ Specific

AbstractMicroRNAs (miRNAs) can have tissue-specific expression and functions; they can originate from dedicated miRNA genes, from non-canonical miRNA genes, or from mirror-miRNA genes and can also experience post-transcriptional variations. It remains unclear, however, which mechanisms of miRNA production or modification are tissue-specific and the extent of their evolutionary conservation. To address these issues, we developed the software Prost! (PRocessing Of Short Transcripts), which, among other features, allows accurate quantification of mature miRNAs, takes into account post-transcriptional processing, such as nucleotide editing, and helps identify mirror-miRNAs. Here, we applied Prost! to annotate and analyze miRNAs in three-spined stickleback (Gasterosteus aculeatus), a model fish for evolutionary biology reported to have a miRNome larger than most teleost fish. Zebrafish (Danio rerio), a distantly related teleost with a well-known miRNome, served as comparator. Despite reports suggesting that stickleback had a large miRNome, results showed that stickleback has 277 evolutionary-conserved mir genes and 366 unique mature miRNAs (excluding mir430 gene replicates and the vaultRNA-derived mir733), similar to zebrafish. In addition, small RNA sequencing data from brain, heart, testis, and ovary in both stickleback and zebrafish identified suites of mature miRNAs that display organ-specific enrichment, which is, for many miRNAs, evolutionarily-conserved. These data also supported the hypothesis that evolutionarily-conserved, organ-specific mechanisms regulate miRNA post-transcriptional variations. In both stickleback and zebrafish, miR2188-5p was edited frequently with similar nucleotide editing patterns in the seed sequence in various tissues, and the editing rate was organ-specific with higher editing in the brain. In summary, Prost! is a critical new tool to identify and understand small RNAs and can help clarify a species’ miRNA biology, as shown here for an important fish model for the evolution of developmental mechanisms, and can provide insight into organ-specific expression and evolutionary-conserved miRNA post-transcriptional mechanisms.

scholarly journals Upgrading the Repertoire of miRNAs in Gastric Adenocarcinoma to Provide a New Resource for Biomarker Discovery

2019 ◽  
Vol 20 (22) ◽  
pp. 5697 ◽  
Author(s):  
Michelle E. Pewarchuk ◽  
Mateus C. Barros-Filho ◽  
Brenda C. Minatel ◽  
David E. Cohn ◽  
Florian Guisier ◽  
...  
Keyword(s):  
Gastric Adenocarcinoma ◽  
Biomarker Discovery ◽  
The Cancer Genome Atlas ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Specific Expression ◽  
Novel Mirna ◽  
Cancer Genome Atlas ◽  
Context Specific ◽  
Independent Cohort

Recent studies have uncovered microRNAs (miRNAs) that have been overlooked in early genomic explorations, which show remarkable tissue- and context-specific expression. Here, we aim to identify and characterize previously unannotated miRNAs expressed in gastric adenocarcinoma (GA). Raw small RNA-sequencing data were analyzed using the miRMaster platform to predict and quantify previously unannotated miRNAs. A discovery cohort of 475 gastric samples (434 GA and 41 adjacent nonmalignant samples), collected by The Cancer Genome Atlas (TCGA), were evaluated. Candidate miRNAs were similarly assessed in an independent cohort of 25 gastric samples. We discovered 170 previously unannotated miRNA candidates expressed in gastric tissues. The expression of these novel miRNAs was highly specific to the gastric samples, 143 of which were significantly deregulated between tumor and nonmalignant contexts (p-adjusted < 0.05; fold change > 1.5). Multivariate survival analyses showed that the combined expression of one previously annotated miRNA and two novel miRNA candidates was significantly predictive of patient outcome. Further, the expression of these three miRNAs was able to stratify patients into three distinct prognostic groups (p = 0.00003). These novel miRNAs were also present in the independent cohort (43 sequences detected in both cohorts). Our findings uncover novel miRNA transcripts in gastric tissues that may have implications in the biology and management of gastric adenocarcinoma.

scholarly journals AEBP1 is Upregulated in Diabetic Nephropathy Biopsies

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Benjamin Freije ◽  
Ricardo Melo Ferreira ◽  
Ying-Hua Cheng ◽  
Samir Parikh ◽  
Michael Eadon
Keyword(s):  
Diabetic Nephropathy ◽  
Kidney Disease ◽  
Interstitial Fibrosis ◽  
Treatment Strategies ◽  
Human Kidney ◽  
Sequencing Data ◽  
Specific Expression ◽  
Enhancer Binding Protein ◽  
Organ Specific ◽  
Matrix Organization

Background: Worldwide, one in eleven adults have diabetes mellitus and 30% to 40% will develop diabetic kidney disease (DKD). A mechanistic understanding of DKD is crucial to develop treatment strategies. To unravel DKD’s pathogenesis, single cell (scRNA) sequencing has proven a powerful tool, but is limited by a lack of localization. Spatial transcriptomics allows the mapping of scRNA sequencing data back to histology. Methods: Frozen human nephrectomy and biopsy samples were processed according to Visium spatial gene expression protocols, stained with H&E, and imaged. Samples were permeabilized for RNA capture, reverse transcribed and sequenced on an Illumina NovaSeq 6000. Mapping and counting were completed in Space Ranger and data was processed in Seurat. Samples were laser microdissected, protein was isolated, and protein was quantified by HPLC-MS. Results: Clusters from scRNAseq were mapped upon reference and DKD spatial transcriptomic images (N=4 reference, 2 DKD). Differentially expressed genes were identified in diabetic kidneys, including the upregulation of Adipocyte Enhancer Binding Protein (AEBP1).  Pathway analysis revealed enrichment of extracellular matrix organization and immune process pathways. To increase the confidence of these findings, glomeruli and the tubulointerstitium were laser microdissected (N=7 diseased, 4 reference) for proteomic analysis. AEBP1 was upregulated in the tubular interstitium of diseased kidneys and selectively upregulated in the glomeruli of Diabetic Nephropathy samples (N=2). AEBP1 localized to the interstitium by spatial transcriptomics and was expressed in highly fibrotic regions. Glomerular expression was not observed due to glomerulosclerosis. Conclusion: AEBP1 upregulation is a marker of interstitial fibrosis, with specific expression in the glomeruli of diabetic nephropathy specimens with glomerulosclerosis. Impact: This is the first study utilizing spatial transcriptomics to define and localize markers of human kidney disease. Confirmatory studies are required in larger sample sizes. AEBP1 is a previously unidentified marker of DKD previously associated with fibrosis in other organ-specific diseases.

Tissue-Specific and Organ-Specific Expression of Soybean Auxin-Responsive Transcripts GH3 and SAURs

1991 ◽  
Vol 3 (4) ◽  
pp. 419 ◽  
Author(s):  
Melissa A. Gee ◽  
Gretchen Hagen ◽  
Tom J. Guilfoyle
Keyword(s):  
Specific Expression ◽  
Tissue Specific ◽  
Organ Specific ◽  
Organ Specific Expression

scholarly journals Tissue-specific expression of two Artemia franciscana sarco/endoplasmic reticulum Ca-ATPase isoforms.

1996 ◽  
Vol 44 (4) ◽  
pp. 321-325 ◽  
Author(s):  
R Escalante ◽  
L Sastre
Keyword(s):  
Endoplasmic Reticulum ◽  
Artemia Franciscana ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Tissue Sections ◽  
Evolutionarily Conserved ◽  
Enzyme Isoforms ◽  
The One

The sarco/endoplasmic reticulum Ca-ATPase (SERCA) gene from Artemia franciscana is transcribed into two mRNAs that code for two different enzyme isoforms. We investigated the tissue-specific expression of each mRNA by in situ hybridization of larval tissue sections. One of the isoforms is expressed in the muscle fibers of the appendages. The other isoform is generally expressed throughout all tissues of the larvae. The tissue distribution of these two isoforms is very similar to the one described for the two homologous isoforms generated from the vertebrate SERCA 2 gene, and shows the evolutionarily conserved nature of their tissue-specific expression.

Transcriptional control of Ca(2+)-activated K(+) channel expression: identification of a second, evolutionarily conserved, neuronal promoter

2000 ◽  
Vol 203 (4) ◽  
pp. 693-704
Author(s):  
R.A. Bohm ◽  
B. Wang ◽  
R. Brenner ◽  
N.S. Atkinson
Keyword(s):  
Transcriptional Control ◽  
Evolutionary Conservation ◽  
K Channel ◽  
Transcription Start ◽  
Specific Expression ◽  
Channel Density ◽  
Transcriptional Control Region ◽  
Evolutionarily Conserved ◽  
Polypeptide Sequence ◽  
Channel Expression

Neuronal signaling properties are largely determined by the quantity and combination of ion channels expressed. The Drosophila slowpoke gene encodes a Ca(2+)-activated K(+) channel used throughout the nervous system. The slowpoke transcriptional control region is large and complex. To simplify the search for sequences responsible for tissue-specific expression, we relied on evolutionary conservation of functionally important sequences. A number of conserved segments were found between two Drosophila species. One led us to a new 5′ exon and a new transcriptional promoter: Promoter C0. In larvae and adults, Promoter C0 was demonstrated to be neural-specific using flies transformed with reporter genes that either contain or lack the promoter. The transcription start site of Promoter C0 was mapped, and the exon it appends to the 5′ end of the mRNA was sequenced. This is the second neural-specific slowpoke promoter to be identified, the first being Promoter C1. Promoter choice does not alter the encoded polypeptide sequence. RNAase protection assays indicate that Promoter C0 transcripts are approximately 12 times more abundant that Promoter C1 transcripts. Taken together, these facts suggest that promoter choice may be a means for cells to control channel density.

scholarly journals Revised annotation and characterization of novel Aedes albopictus miRNAs and their potential functions in dengue virus infection

2020 ◽  
Author(s):  
Azali Azlan ◽  
Muhammad Amir Yunus ◽  
Ghows Azzam
Keyword(s):  
Aedes Albopictus ◽  
Target Genes ◽  
Sequence Data ◽  
Target Prediction ◽  
Mature Mirnas ◽  
Denv Infection ◽  
Future Research ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Public Datasets

AbstractThe Asian tiger mosquito, Aedes albopictus (Ae. albopictus), is a highly invasive species that transmit several arboviruses including dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV). Although several studies have identified microRNAs (miRNAs) in Ae. albopictus, it is crucial to extend and improve current annotations with the newly improved genome assembly, and the increase number of small RNA-sequencing data. We combined our high-depth sequence data and 26 public datasets to re-annotate Ae. albopictus miRNAs, and found a total of 110 novel mature miRNAs. We discovered that the expression of novel miRNAs was lower than known miRNAs. Furthermore, compared to known miRNAs, novel miRNAs are prone to be expressed in stage-specific manner. Upon DENV infection, a total of 59 novel miRNAs were differentially expressed, and target prediction analysis revealed that miRNA-target genes were involved in lipid metabolism and protein processing in endoplasmic reticulum. Taken together, miRNA annotation profile provided here is the most comprehensive to date, and we believed that this will facilitate future research in understanding virus-host interactions particularly on the role of miRNAs.

scholarly journals Between Stress and Response: Function and Localization of Mechanosensitive Ca2+ Channels in Herbaceous and Perennial Plants

2021 ◽  
Vol 22 (20) ◽  
pp. 11043
Author(s):  
Félix P. Hartmann ◽  
Erwan Tinturier ◽  
Jean-Louis Julien ◽  
Nathalie Leblanc-Fournier
Keyword(s):  
Mechanical Stress ◽  
Regulatory Networks ◽  
Root Apex ◽  
Sequencing Data ◽  
Specific Expression ◽  
Tissue Specific ◽  
Practical Applications ◽  
Tissue Specific Expression ◽  
Expression Studies ◽  
Sense And Respond

Over the past three decades, how plants sense and respond to mechanical stress has become a flourishing field of research. The pivotal role of mechanosensing in organogenesis and acclimation was demonstrated in various plants, and links are emerging between gene regulatory networks and physical forces exerted on tissues. However, how plant cells convert physical signals into chemical signals remains unclear. Numerous studies have focused on the role played by mechanosensitive (MS) calcium ion channels MCA, Piezo and OSCA. To complement these data, we combined data mining and visualization approaches to compare the tissue-specific expression of these genes, taking advantage of recent single-cell RNA-sequencing data obtained in the root apex and the stem of Arabidopsis and the Populus stem. These analyses raise questions about the relationships between the localization of MS channels and the localization of stress and responses. Such tissue-specific expression studies could help to elucidate the functions of MS channels. Finally, we stress the need for a better understanding of such mechanisms in trees, which are facing mechanical challenges of much higher magnitudes and over much longer time scales than herbaceous plants, and we mention practical applications of plant responsiveness to mechanical stress in agriculture and forestry.

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