Function of Circular RNAs in Fish and Their Potential Application as Biomarkers

Circular RNAs (circRNAs) are an emerging class of regulatory RNAs with a covalently closed-loop structure formed during pre-mRNA splicing. Recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of novel approaches to their identification and functional characterization. CircRNAs are stable, developmentally regulated, and show tissue- and cell-type-specific expression across different taxonomic groups. They play a crucial role in regulating various biological processes at post-transcriptional and translational levels. However, the involvement of circRNAs in fish immunity has only recently been recognized. There is also broad evidence in mammals that the timely expression of circRNAs in muscle plays an essential role in growth regulation but our understanding of their expression and function in teleosts is still very limited. Here, we discuss the available knowledge about circRNAs and their role in growth and immunity in vertebrates from a comparative perspective, with emphasis on cultured teleost fish. We expect that the interest in teleost circRNAs will increase substantially soon, and we propose that they may be used as biomarkers for selective breeding of farmed fish, thus contributing to the sustainability of the aquaculture sector.

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Cell Type-specific Expression and Function of Toll-like Receptors 2 and 4 in Human Placenta: Implications in Fetal Infection

Placenta ◽

10.1016/j.placenta.2007.05.003 ◽

2007 ◽

Vol 28 (10) ◽

pp. 1024-1031 ◽

Cited By ~ 55

Author(s):

Y. Ma ◽

G. Krikun ◽

V.M. Abrahams ◽

G. Mor ◽

S. Guller

Keyword(s):

Human Placenta ◽

Toll Like Receptors ◽

Cell Type ◽

Specific Expression ◽

Fetal Infection ◽

Cell Type Specific Expression ◽

Cell Type Specific ◽

And Function

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Adeno-Associated Virus Technologies and Methods for Targeted Neuronal Manipulation

10.1101/759936 ◽

2019 ◽

Author(s):

Leila Haery ◽

Benjamin E. Deverman ◽

Katherine Matho ◽

Ali Cetin ◽

Kenton Woodard ◽

...

Keyword(s):

Viral Vectors ◽

Cell Types ◽

Regulatory Elements ◽

Specific Cell ◽

Specific Expression ◽

Adeno Associated Virus ◽

Cell Type Specific Expression ◽

Cell Type Specific ◽

And Function ◽

Novel Applications

AbstractCell-type-specific expression of molecular tools and sensors is critical to construct circuit diagrams and to investigate the activity and function of neurons within the nervous system. Strategies for targeted manipulation include combinations of classical genetic tools such as Cre/loxP and Flp/FRT, use of cis-regulatory elements, targeted knock-in transgenic mice, and gene delivery by AAV and other viral vectors. The combination of these complex technologies with the goal of precise neuronal targeting is a challenge in the lab. This report will discuss the theoretical and practical aspects of combining current technologies and establish best practices for achieving targeted manipulation of specific cell types. Novel applications and tools, as well as areas for development, will be envisioned and discussed.

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Cell Type-specific Expression of the Mas Proto-oncogene in Testis

Journal of Histochemistry & Cytochemistry ◽

10.1177/002215540205000510 ◽

2002 ◽

Vol 50 (5) ◽

pp. 691-695 ◽

Cited By ~ 30

Author(s):

Natalia Alenina ◽

Tatjana Baranova ◽

Eugene Smirnow ◽

Michael Bader ◽

Andrea Lippoldt ◽

...

Keyword(s):

Leydig Cells ◽

Rnase Protection Assay ◽

Cell Type ◽

Cell Type Specificity ◽

Specific Expression ◽

Rnase Protection ◽

Cell Type Specific Expression ◽

Cell Type Specific ◽

And Function ◽

Old Mice

The Mas proto-oncogene encodes a G-protein-coupled receptor with the common seven transmembrane domains and may be involved in the actions of angiotensins. Because Mas is highly expressed in testis, we investigated the cell type-specificity and the onset of expression of the gene in this organ. Using an RNase protection assay, it could be shown that neither whole testes nor cultured Sertoli and Leydig cells of 12-day-old mice express Mas mRNA. Mas expression is first detected in 18-day-old mice and thereafter increases continuously until 6 months of age. By in situ hybridization, the expression could be localized to Leydig cells and Sertoli cells, the signals being much more pronounced in the former. A weak signal was detected in primary spermatocytes. The strong ontogenetically controlled and cell type-specific expression of this membrane-bound receptor in testis implicates a role for the Mas proto-oncogene in testis maturation and function.

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Tissue- and Cell Type-Specific Expression of the Long Noncoding RNA Klhl14-AS in Mouse

International Journal of Genomics ◽

10.1155/2017/9769171 ◽

2017 ◽

Vol 2017 ◽

pp. 1-7 ◽

Cited By ~ 6

Author(s):

Sara Carmela Credendino ◽

Nicole Lewin ◽

Miriane de Oliveira ◽

Swaraj Basu ◽

Barbara D’Andrea ◽

...

Keyword(s):

Noncoding Rna ◽

Wide Spectrum ◽

Functional Characterization ◽

Cell Type ◽

Specific Expression ◽

Similar Expression Profile ◽

Mouse Tissues ◽

Cell Type Specific Expression ◽

A Cell ◽

Cell Type Specific

lncRNAs are acquiring increasing relevance as regulators in a wide spectrum of biological processes. The extreme heterogeneity in the mechanisms of action of these molecules, however, makes them very difficult to study, especially regarding their molecular function. A novel lncRNA has been recently identified as the most enriched transcript in mouse developing thyroid. Due to its genomic localization antisense to the protein-encoding Klhl14 gene, we named it Klhl14-AS. In this paper, we highlight that mouse Klhl14-AS produces at least five splicing variants, some of which have not been previously described. Klhl14-AS is expressed with a peculiar pattern, characterized by diverse relative abundance of its isoforms in different mouse tissues. We examine the whole expression level of Klhl14-AS in a panel of adult mouse tissues, showing that it is expressed in the thyroid, lung, kidney, testis, ovary, brain, and spleen, although at different levels. In situ hybridization analysis reveals that, in the context of each organ, Klhl14-AS shows a cell type-specific expression. Interestingly, databases report a similar expression profile for human Klhl14-AS. Our observations suggest that this lncRNA could play cell type-specific roles in several organs and pave the way for functional characterization of this gene in appropriate biological contexts.

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Changing Patterns of Gene Expression in Dictyostelium Prestalk Cell Subtypes Recognized by In Situ Hybridization with Genes from Microarray Analyses

Eukaryotic Cell ◽

10.1128/ec.2.3.627-637.2003 ◽

2003 ◽

Vol 2 (3) ◽

pp. 627-637 ◽

Cited By ~ 57

Author(s):

Mineko Maeda ◽

Haruyo Sakamoto ◽

Negin Iranfar ◽

Danny Fuller ◽

Toshinari Maruo ◽

...

Keyword(s):

Gene Expression ◽

In Situ Hybridization ◽

Cell Types ◽

Cell Type ◽

Developmentally Regulated ◽

Specific Expression ◽

Cell Type Specific Expression ◽

Changing Patterns ◽

Cell Type Specific

ABSTRACT We used microarrays carrying most of the genes that are developmentally regulated in Dictyostelium to discover those that are preferentially expressed in prestalk cells. Prestalk cells are localized at the front of slugs and play crucial roles in morphogenesis and slug migration. Using whole-mount in situ hybridization, we were able to verify 104 prestalk genes. Three of these were found to be expressed only in cells at the very front of slugs, the PstA cell type. Another 10 genes were found to be expressed in the small number of cells that form a central core at the anterior, the PstAB cell type. The rest of the prestalk-specific genes are expressed in PstO cells, which are found immediately posterior to PstA cells but anterior to 80% of the slug that consists of prespore cells. Half of these are also expressed in PstA cells. At later stages of development, the patterns of expression of a considerable number of these prestalk genes changes significantly, allowing us to further subdivide them. Some are expressed at much higher levels during culmination, while others are repressed. These results demonstrate the extremely dynamic nature of cell-type-specific expression in Dictyostelium and further define the changing physiology of the cell types. One of the signals that affect gene expression in PstO cells is the hexaphenone DIF-1. We found that expression of about half of the PstO-specific genes were affected in a mutant that is unable to synthesize DIF-1, while the rest appeared to be DIF independent. These results indicate that differentiation of some aspects of PstO cells can occur in the absence of DIF-1.

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A cell type‐specific expression map of NCoR1 and SMRT transcriptional co‐repressors in the mouse brain

The Journal of Comparative Neurology ◽

10.1002/cne.24886 ◽

2020 ◽

Vol 528 (13) ◽

pp. 2218-2238 ◽

Cited By ~ 2

Author(s):

Attilio Iemolo ◽

Patricia Montilla‐Perez ◽

I‐Chi Lai ◽

Yinuo Meng ◽

Syreeta Nolan ◽

...

Keyword(s):

Mouse Brain ◽

Cell Type ◽

Specific Expression ◽

Cell Type Specific Expression ◽

A Cell ◽

Cell Type Specific

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Cell‐type specific expression and behavioral impact of galanin and GalR1 in the locus coeruleus during opioid withdrawal

Addiction Biology ◽

10.1111/adb.13037 ◽

2021 ◽

Author(s):

Stephanie L. Foster ◽

Ewa Galaj ◽

Saumya L. Karne ◽

Sergi Ferré ◽

David Weinshenker

Keyword(s):

Locus Coeruleus ◽

Opioid Withdrawal ◽

Cell Type ◽

Specific Expression ◽

Cell Type Specific Expression ◽

Cell Type Specific ◽

Behavioral Impact

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Olfactory expression of trace amine-associated receptors requires cooperative cis-acting enhancers

Nature Communications ◽

10.1038/s41467-021-23824-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ami Shah ◽

Madison Ratkowski ◽

Alessandro Rosa ◽

Paul Feinstein ◽

Thomas Bozza

Keyword(s):

Gene Expression ◽

Large Family ◽

Sequence Motifs ◽

Specific Expression ◽

Cis Acting ◽

Conserved Sequence ◽

Trace Amine ◽

Sequence Elements ◽

Cell Type Specific Expression ◽

Cell Type Specific

AbstractOlfactory sensory neurons express a large family of odorant receptors (ORs) and a small family of trace amine-associated receptors (TAARs). While both families are subject to so-called singular expression (expression of one allele of one gene), the mechanisms underlying TAAR gene choice remain obscure. Here, we report the identification of two conserved sequence elements in the mouse TAAR cluster (T-elements) that are required for TAAR gene expression. We observed that cell-type-specific expression of a TAAR-derived transgene required either T-element. Moreover, deleting either element reduced or abolished expression of a subset of TAAR genes, while deleting both elements abolished olfactory expression of all TAARs in cis with the mutation. The T-elements exhibit several features of known OR enhancers but also contain highly conserved, unique sequence motifs. Our data demonstrate that TAAR gene expression requires two cooperative cis-acting enhancers and suggest that ORs and TAARs share similar mechanisms of singular expression.

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