Expression and Regulation Profile of Mature MicroRNA in the Pig: Relevance to Xenotransplantation

The pig is an important source of meat production and provides a valuable model for certain human diseases. MicroRNA (miRNA), which is non-coding RNA and regulates gene expression at the posttranscriptional level, plays a critical role in various biological processes. Studies on identification and function of mature miRNAs in multiple pig tissues are increasing, yet the literature is limited. Therefore, we reviewed current research to determine the miRNAs expressed in specific pig tissues that are involved in carcass values (including muscle and adipocytes), reproduction (including pituitary, testis, and ovary), and development of some solid organs (e.g., brain, lung, kidney, and liver). We also discuss the possible regulating mechanisms of miRNA. Finally, as pig organs are suitable candidates for xenotransplantation, biomarkers of their miRNA in xenotransplantation were evaluated.

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Expression and Regulation Profile of Mature MicroRNA in the Pig: Relevance to Xenotransplantation

BioMed Research International ◽

10.1155/2018/2983908 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 4

Author(s):

Zongpei Song ◽

David K. C. Cooper ◽

Zhiming Cai ◽

Lisha Mou

Keyword(s):

Gene Expression ◽

Noncoding Rna ◽

Critical Role ◽

Mature Mirnas ◽

Human Diseases ◽

Meat Production ◽

Biological Processes ◽

Mature Microrna ◽

And Function ◽

Posttranscriptional Level

The pig is an important source of meat production and provides a valuable model for certain human diseases. MicroRNA (miRNA), which is noncoding RNA and regulates gene expression at the posttranscriptional level, plays a critical role in various biological processes. Studies on identification and function of mature miRNAs in multiple pig tissues are increasing, yet the literature is limited. Therefore, we reviewed current research to determine the miRNAs expressed in specific pig tissues that are involved in carcass values (including muscle and adipocytes), reproduction (including pituitary, testis, and ovary), and development of some solid organs (e.g., brain, lung, kidney, and liver). We also discuss the possible regulating mechanisms of miRNA. Finally, as pig organs are suitable candidates for xenotransplantation, biomarkers of their miRNA in xenotransplantation were evaluated.

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HOTAIR: An Oncogenic Long Non-Coding RNA in Human Cancer

Cellular Physiology and Biochemistry ◽

10.1159/000490131 ◽

2018 ◽

Vol 47 (3) ◽

pp. 893-913 ◽

Cited By ~ 87

Author(s):

Qing Tang ◽

Swei Sunny Hann

Keyword(s):

Drug Resistance ◽

Human Cancer ◽

Critical Role ◽

Stem Cell Differentiation ◽

Human Diseases ◽

Biological Functions ◽

Protein Coding ◽

Non Coding Rna ◽

And Function ◽

Long Non Coding Rna

Long non-coding RNAs (LncRNAs) represent a novel class of noncoding RNAs that are longer than 200 nucleotides without protein-coding potential and function as novel master regulators in various human diseases, including cancer. Accumulating evidence shows that lncRNAs are dysregulated and implicated in various aspects of cellular homeostasis, such as proliferation, apoptosis, mobility, invasion, metastasis, chromatin remodeling, gene transcription, and post-transcriptional processing. However, the mechanisms by which lncRNAs regulate various biological functions in human diseases have yet to be determined. HOX antisense intergenic RNA (HOTAIR) is a recently discovered lncRNA and plays a critical role in various areas of cancer, such as proliferation, survival, migration, drug resistance, and genomic stability. In this review, we briefly introduce the concept, identification, and biological functions of HOTAIR. We then describe the involvement of HOTAIR that has been associated with tumorigenesis, growth, invasion, cancer stem cell differentiation, metastasis, and drug resistance in cancer. We also discuss emerging insights into the role of HOTAIR as potential biomarkers and therapeutic targets for novel treatment paradigms in cancer.

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The role of m6A, m5C and Ψ RNA modifications in cancer: Novel therapeutic opportunities

Molecular Cancer ◽

10.1186/s12943-020-01263-w ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Paz Nombela ◽

Borja Miguel-López ◽

Sandra Blanco

Keyword(s):

Gene Expression ◽

Rna Processing ◽

Therapeutic Potential ◽

Biological Processes ◽

Rna Modifications ◽

Non Coding Rna ◽

Non Coding Rnas ◽

And Function ◽

Made In

AbstractRNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programmes. Significant advances have been made in understanding the functional role of RNA modifications in regulating coding and non-coding RNA processing and function, which in turn thoroughly shape distinct gene expression programmes. They affect diverse biological processes, and the correct deposition of many of these modifications is required for normal development. Alterations of their deposition are implicated in several diseases, including cancer. In this Review, we focus on the occurrence of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) in coding and non-coding RNAs and describe their physiopathological role in cancer. We will highlight the latest insights into the mechanisms of how these posttranscriptional modifications influence tumour development, maintenance, and progression. Finally, we will summarize the latest advances on the development of small molecule inhibitors that target specific writers or erasers to rewind the epitranscriptome of a cancer cell and their therapeutic potential.

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The physiological and pathophysiological roles of adipocyte miRNAs

Biochemistry and Cell Biology ◽

10.1139/bcb-2012-0053 ◽

2013 ◽

Vol 91 (4) ◽

pp. 195-202 ◽

Cited By ~ 11

Author(s):

Hongyan Ling ◽

Xing Li ◽

Chao Hua Yao ◽

Bi Hu ◽

Duanfang Liao ◽

...

Keyword(s):

Gene Expression ◽

Adipocyte Differentiation ◽

Noncoding Rnas ◽

Biological Processes ◽

Insulin Production ◽

Regulate Gene Expression ◽

Small Noncoding Rnas ◽

And Function ◽

Posttranscriptional Level ◽

Regulate Gene

MicroRNAs (miRNAs) are highly conserved, small, noncoding RNAs that regulate gene expression at the posttranscriptional level. Their actions affect numerous important biological processes, including adipocyte differentiation and function, sugar and lipid metabolism, and insulin production and secretion. Recent reports suggest miRNAs may also be involved in the pathogenic processes of obesity, diabetes, and insulin resistance. In this review, we summarize research progresses on adipocyte miRNAs and their physiological and pathological implications.

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Commuting to Work: Nucleolar Long Non-Coding RNA Control Ribosome Biogenesis from Near and Far

Non-Coding RNA ◽

10.3390/ncrna7030042 ◽

2021 ◽

Vol 7 (3) ◽

pp. 42

Author(s):

Victoria Mamontova ◽

Barbara Trifault ◽

Lea Boten ◽

Kaspar Burger

Keyword(s):

Gene Expression ◽

Rna Polymerase Ii ◽

Ribosome Biogenesis ◽

Intergenic Spacer ◽

Cellular Growth ◽

Rrna Synthesis ◽

Protein Coding ◽

Non Coding Rna ◽

And Function ◽

In Cis

Gene expression is an essential process for cellular growth, proliferation, and differentiation. The transcription of protein-coding genes and non-coding loci depends on RNA polymerases. Interestingly, numerous loci encode long non-coding (lnc)RNA transcripts that are transcribed by RNA polymerase II (RNAPII) and fine-tune the RNA metabolism. The nucleolus is a prime example of how different lncRNA species concomitantly regulate gene expression by facilitating the production and processing of ribosomal (r)RNA for ribosome biogenesis. Here, we summarise the current findings on how RNAPII influences nucleolar structure and function. We describe how RNAPII-dependent lncRNA can both promote nucleolar integrity and inhibit ribosomal (r)RNA synthesis by modulating the availability of rRNA synthesis factors in trans. Surprisingly, some lncRNA transcripts can directly originate from nucleolar loci and function in cis. The nucleolar intergenic spacer (IGS), for example, encodes nucleolar transcripts that counteract spurious rRNA synthesis in unperturbed cells. In response to DNA damage, RNAPII-dependent lncRNA originates directly at broken ribosomal (r)DNA loci and is processed into small ncRNA, possibly to modulate DNA repair. Thus, lncRNA-mediated regulation of nucleolar biology occurs by several modes of action and is more direct than anticipated, pointing to an intimate crosstalk of RNA metabolic events.

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miRNAome expression profiles in the gonads of adultMelopsittacus undulatus

PeerJ ◽

10.7717/peerj.4615 ◽

2018 ◽

Vol 6 ◽

pp. e4615 ◽

Cited By ~ 5

Author(s):

Lan Jiang ◽

Qingqing Wang ◽

Jue Yu ◽

Vinita Gowda ◽

Gabriel Johnson ◽

...

Keyword(s):

Gene Expression ◽

Early Development ◽

Expression Profiles ◽

Critical Role ◽

Genomic Research ◽

Go Annotation ◽

Rna Molecules ◽

Non Coding Rna ◽

Mirnas Expression ◽

Paired End Sequencing

The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. However, very little is known about the role gonadal miRNAs play in the early development of birds. Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known aboutM. undulatus. In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. We obtained 254 known and 141 novel miRNAs, and randomly validated five miRNAs. Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research.

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miRSwitch: Detecting microRNA arm shift and switch events

10.1101/2020.03.25.007351 ◽

2020 ◽

Author(s):

Fabian Kern ◽

Jeremy Amand ◽

Ilya Senatorov ◽

Alina Isakova ◽

Christina Backes ◽

...

Keyword(s):

Homo Sapiens ◽

Mature Mirnas ◽

Process Time ◽

Data Set ◽

Preferential Expression ◽

Disease States ◽

Non Coding Rna ◽

Mature Microrna ◽

Reference Map ◽

Sensitive Parameters

AbstractArm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30,521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customised arm switch analyses along with comprehensive visualisations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.

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Critical Role of Types 2 and 3 Deiodinases in the Negative Regulation of Gene Expression by T3 in the Mouse Cerebral Cortex

Endocrinology ◽

10.1210/en.2011-1905 ◽

2012 ◽

Vol 153 (6) ◽

pp. 2919-2928 ◽

Cited By ~ 47

Author(s):

Arturo Hernandez ◽

Beatriz Morte ◽

Mónica M. Belinchón ◽

Ainhoa Ceballos ◽

Juan Bernal

Keyword(s):

Gene Expression ◽

Cerebral Cortex ◽

Thyroid Hormone ◽

Critical Role ◽

Regulation Of Gene Expression ◽

Control Of Gene Expression ◽

High Doses ◽

And Function ◽

Type 3

Thyroid hormones regulate brain development and function through the control of gene expression, mediated by binding of T3 to nuclear receptors. Brain T3 concentration is tightly controlled by homeostatic mechanisms regulating transport and metabolism of T4 and T3. We have examined the role of the inactivating enzyme type 3 deiodinase (D3) in the regulation of 43 thyroid hormone-dependent genes in the cerebral cortex of 30-d-old mice. D3 inactivation increased slightly the expression of two of 22 positively regulated genes and significantly decreased the expression of seven of 21 negatively regulated genes. Administration of high doses of T3 led to significant changes in the expression of 12 positive genes and three negative genes in wild-type mice. The response to T3 treatment was enhanced in D3-deficient mice, both in the number of genes and in the amplitude of the response, demonstrating the role of D3 in modulating T3 action. Comparison of the effects on gene expression observed in D3 deficiency with those in hypothyroidism, hyperthyroidism, and type 2 deiodinase (D2) deficiency revealed that the negative genes are more sensitive to D2 and D3 deficiencies than the positive genes. This observation indicates that, in normal physiological conditions, D2 and D3 play critical roles in maintaining local T3 concentrations within a very narrow range. It also suggests that negatively and positively regulated genes do not have the same physiological significance or that their regulation by thyroid hormone obeys different paradigms at the molecular or cellular levels.

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miRSwitch: detecting microRNA arm shift and switch events

Nucleic Acids Research ◽

10.1093/nar/gkaa323 ◽

2020 ◽

Vol 48 (W1) ◽

pp. W268-W274 ◽

Cited By ~ 4

Author(s):

Fabian Kern ◽

Jeremy Amand ◽

Ilya Senatorov ◽

Alina Isakova ◽

Christina Backes ◽

...

Keyword(s):

Homo Sapiens ◽

Mature Mirnas ◽

Process Time ◽

Data Set ◽

Preferential Expression ◽

Disease States ◽

Non Coding Rna ◽

Mature Microrna ◽

Reference Map ◽

Sensitive Parameters

Abstract Arm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30 521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customized arm switch analyses along with comprehensive visualizations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.

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