Abstract
MicroRNAs (miRNAs) are noncoding RNAs with 18–26 nucleotides; they pair with target mRNAs to regulate gene expression and produce significant changes in various physiological and ...pathological processes. In recent years, the interaction between miRNAs and their target genes has become one of the mainstream directions for drug development. As a large-scale biological database that mainly provides miRNA–target interactions (MTIs) verified by biological experiments, miRTarBase has undergone five revisions and enhancements. The database has accumulated >2 200 449 verified MTIs from 13 389 manually curated articles and CLIP-seq data. An optimized scoring system is adopted to enhance this update’s critical recognition of MTI-related articles and corresponding disease information. In addition, single-nucleotide polymorphisms and disease-related variants related to the binding efficiency of miRNA and target were characterized in miRNAs and gene 3′ untranslated regions. miRNA expression profiles across extracellular vesicles, blood and different tissues, including exosomal miRNAs and tissue-specific miRNAs, were integrated to explore miRNA functions and biomarkers. For the user interface, we have classified attributes, including RNA expression, specific interaction, protein expression and biological function, for various validation experiments related to the role of miRNA. We also used seed sequence information to evaluate the binding sites of miRNA. In summary, these enhancements render miRTarBase as one of the most research-amicable MTI databases that contain comprehensive and experimentally verified annotations. The newly updated version of miRTarBase is now available at https://miRTarBase.cuhk.edu.cn/.
The emergence of sterile individuals in the hybrid backcross progeny of wild and cultivated rice limits the use of wild rice alleles for improving cultivated rice, but the molecular mechanisms ...underlying this sterility remain unclear. Here, we identified the semisterile introgression line YIL42, derived from a cross between the
rice variety Teqing (
) and
accession YJCWR (Yuanjiang common wild rice), which exhibits semisterility. Using positional cloning, we isolated
(
), which encodes a nuclear-membrane localized protein containing an armadillo repeat domain. A mutation in
at position 1819 (
1819
) converts a stop codon into an Arg (R) codon, causing delayed termination of protein translation. Analysis of transgenic lines indicated that the difference in ESA1 protein structure between
-derived
and Teqing-derived
affects female gamete abortion during early mitosis. Fertility investigation and expression analysis indicated that the interaction between
and unknown gene(s) of Teqing affects spikelet fertility of the hybrid backcross progeny. The
allele is present in
but absent in
, suggesting that variation in
may be associated with interspecific hybrid incompatibility between wild and cultivated rice. Our findings provide insight into the molecular mechanism underlying female sterility, which is useful for improving the panicle seed setting rate of rice and for developing a strategy to overcome interspecific hybrid sterility between cultivated rice and wild rice.
Zinc (Zn) deficiency, caused by inadequate Zn intake in the human diet, has serious health implications. Rice (
Oryza sativa
) is the staple food in regions with a high incidence of Zn deficiency, so ...raising Zn levels in rice grain could help alleviate Zn deficiency. The wild relatives of cultivated rice vary widely in grain Zn content and thus are suitable resources for improving this trait. However, few loci underlying grain Zn content have been identified in wild rice relatives. Here, we identified a major quantitative trait locus for grain Zn content,
Grain Zn Content 1
(
qGZnC1
), from Yuanjiang common wild rice (
Oryza rufipogon
Griff.) using map-based cloning. Down-regulating
GZnC1
expression reduced the grain Zn content, whereas the presence of
GZnC1
had the opposite effect, indicating that
GZnC1
is involved in grain Zn content in rice. Notably,
GZnC1
is identical to a previously reported gene,
EMBRYO SAC ABORTION 1
(
ESA1
), involved in seed setting rate. The mutation in
GZnC1/ESA1
at position 1819 (
T
1819
C
) causes delayed termination of protein translation. In addition,
GZnC1
is specifically expressed in developing panicles. Several genes related to Zn-transporter genes were up-regulated in the presence of
GZnC1
. Our results suggest that
GZnC1
activates Zn transporters to promote Zn distribution in panicles. Our work thus sheds light on the genetic mechanism of Zn accumulation in rice grain and provides a new genetic resource for improving Zn content in rice.
Key message
We identified an allele from the rice progenitor
Oryza rufipogon
, GZnC1, that influences grain zinc content. This allele is pleiotropic and is identical to
EMBRYO SAC ABORTION 1
, which is implicated in decreased seed setting rate.
ESA1 is involved in embryo sac abortion in hybrid backcross progeny derived from common wild rice and cultivated rice.
The emergence of sterile individuals in the hybrid backcross progeny of wild and ...cultivated rice limits the use of wild rice alleles for improving cultivated rice, but the molecular mechanisms underlying this sterility remain unclear. Here, we identified the semisterile introgression line YIL42, derived from a cross between the
indica
rice variety Teqing (
Oryza sativa
) and
Oryza rufipogon
accession YJCWR (Yuanjiang common wild rice), which exhibits semisterility. Using positional cloning, we isolated
EMBRYO SAC ABORTION 1
(
ESA1
), which encodes a nuclear-membrane localized protein containing an armadillo repeat domain. A mutation in
ESA1
at position 1819 (
T
1819
C
) converts a stop codon into an Arg (R) codon, causing delayed termination of protein translation. Analysis of transgenic lines indicated that the difference in ESA1 protein structure between
O. rufipogon
–derived
ESA1
and Teqing-derived
esa1
affects female gamete abortion during early mitosis. Fertility investigation and expression analysis indicated that the interaction between
ESA1
T1819
and unknown gene(s) of Teqing affects spikelet fertility of the hybrid backcross progeny. The
ESA1
T1819
allele is present in
O. rufipogon
but absent in
O. sativa
, suggesting that variation in
ESA1
may be associated with interspecific hybrid incompatibility between wild and cultivated rice. Our findings provide insight into the molecular mechanism underlying female sterility, which is useful for improving the panicle seed setting rate of rice and for developing a strategy to overcome interspecific hybrid sterility between cultivated rice and wild rice.
Carassius auratus gibelio has been widely cultivated in fish farms in China, with avermectin (AVM) being used to prevent parasite infection. Recently, AVM was found to pass through the Carassius ...auratus gibelio blood-brain barrier (BBB). Although AVM acts mainly through a GABA receptor and specifically the alpha 1 subunit gene, the most common isoform of the GABA A receptor, which is widely expressed in brain neurons and has been studied in other fish, Carassius auratus gibelio GABA A receptor alpha 1 subunit gene cloning, and whether AVM passes through the BBB to induce Carassius auratus gibelio GABA A receptor alpha 1 subunit gene expression have not been studied. The aim of this study was to clone, sequence, and phylogenetically analyze the GABA A receptor alpha 1 subunit gene and to investigate the correlation of its expression with neurotoxicity in brain, liver, and kidney after AVM treatment by quantitative real-time reverse transcription polymerase chain reaction. The alpha 1 subunit gene was 1550 bp in length with an open reading frame of 1380 bp encoding a predicted protein with 459 amino acid residues. The gene contained 128 bp of 5' terminal untranslated region (URT) and 72 bp of 3' terminal UTR. The alpha 1 subunit structural features conformed to the Cys-loop ligand-gated ion channels family, which includes a signal peptide, an extracellular domain at the N-terminal, and four transmembrane domains. The established phylogenetic tree indicated that the alpha 1 subunits of Carassius auratus gibelio and Danio rerio were the most closely related to each other. The alpha 1 subunit was found to be highly expressed in brain and ovary, and the alpha 1 mRNA transcription level increased significantly in brain. Moreover, the higher the concentration of AVM was, the higher the GABA A receptor expression was, indicating that AVM can induce significant neurotoxicity to Carassius auratus gibelio. Therefore, the alpha 1 subunit mRNA expression was positively correlated with the neurotoxicity of AVM in Carassius auratus gibelio. Our findings suggest that AVM should be used carefully in Carassius auratus gibelio farming, and other alternate antibiotics with lower toxicity should be investigated with respect to toxicity via the induction of GABA A receptor expression for fish farming.
Carassius auratus gibelio has been widely cultivated in fish farms in China, with avermectin (AVM) being used to prevent parasite infection. Recently, AVM was found to pass through the Carassius ...auratus gibelio blood–brain barrier (BBB). Although AVM acts mainly through a GABA receptor and specifically the α1 subunit gene, the most common isoform of the GABA A receptor, which is widely expressed in brain neurons and has been studied in other fish, Carassius auratus gibelio GABA A receptor α1 subunit gene cloning, and whether AVM passes through the BBB to induce Carassius auratus gibelio GABA A receptor α1 subunit gene expression have not been studied. The aim of this study was to clone, sequence, and phylogenetically analyze the GABA A receptor α1 subunit gene and to investigate the correlation of its expression with neurotoxicity in brain, liver, and kidney after AVM treatment by quantitative real-time reverse transcription polymerase chain reaction. The α1 subunit gene was 1550 bp in length with an open reading frame of 1380 bp encoding a predicted protein with 459 amino acid residues. The gene contained 128 bp of 5′ terminal untranslated region (URT) and 72 bp of 3′ terminal UTR. The α1 subunit structural features conformed to the Cys-loop ligand-gated ion channels family, which includes a signal peptide, an extracellular domain at the N-terminal, and four transmembrane domains. The established phylogenetic tree indicated that the α1 subunits of Carassius auratus gibelio and Danio rerio were the most closely related to each other. The α1 subunit was found to be highly expressed in brain and ovary, and the α1 mRNA transcription level increased significantly in brain. Moreover, the higher the concentration of AVM was, the higher the GABA A receptor expression was, indicating that AVM can induce significant neurotoxicity to Carassius auratus gibelio. Therefore, the α1 subunit mRNA expression was positively correlated with the neurotoxicity of AVM in Carassius auratus gibelio. Our findings suggest that AVM should be used carefully in Carassius auratus gibelio farming, and other alternate antibiotics with lower toxicity should be investigated with respect to toxicity via the induction of GABA A receptor expression for fish farming.
Carassius auratus gibelio has been widely cultivated in fish farms in China, with avermectin (AVM) being used to prevent parasite infection. Recently, AVM was found to pass through the Carassius ...auratus gibelio blood-brain barrier (BBB). Although AVM acts mainly through a GABA receptor and specifically the alpha1 subunit gene, the most common isoform of the GABA A receptor, which is widely expressed in brain neurons and has been studied in other fish, Carassius auratus gibelio GABA A receptor alpha1 subunit gene cloning, and whether AVM passes through the BBB to induce Carassius auratus gibelio GABA A receptor alpha1 subunit gene expression have not been studied. The aim of this study was to clone, sequence, and phylogenetically analyze the GABA A receptor alpha1 subunit gene and to investigate the correlation of its expression with neurotoxicity in brain, liver, and kidney after AVM treatment by quantitative real-time reverse transcription polymerase chain reaction. The alpha1 subunit gene was 1550 bp in length with an open reading frame of 1380 bp encoding a predicted protein with 459 amino acid residues. The gene contained 128 bp of 5' terminal untranslated region (URT) and 72 bp of 3' terminal UTR. The alpha1 subunit structural features conformed to the Cys-loop ligand-gated ion channels family, which includes a signal peptide, an extracellular domain at the N-terminal, and four transmembrane domains. The established phylogenetic tree indicated that the alpha1 subunits of Carassius auratus gibelio and Danio rerio were the most closely related to each other. The alpha1 subunit was found to be highly expressed in brain and ovary, and the alpha1 mRNA transcription level increased significantly in brain. Moreover, the higher the concentration of AVM was, the higher the GABA A receptor expression was, indicating that AVM can induce significant neurotoxicity to Carassius auratus gibelio. Therefore, the alpha1 subunit mRNA expression was positively correlated with the neurotoxicity of AVM in Carassius auratus gibelio. Our findings suggest that AVM should be used carefully in Carassius auratus gibelio farming, and other alternate antibiotics with lower toxicity should be investigated with respect to toxicity via the induction of GABA A receptor expression for fish farming.
Gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in brain, is synthesized from glutamate and metabolized to succinic semialdehyde by glutamic acid decarboxylase (GAD) and GABA ...transaminase (GABA-T), respectively. The fast inhibitory effect of GABA is mediated by GABA type A (GABAA) receptors that are associated with several neurological disorders, and GABAA receptors are targets of several therapeutic agents. To date, information on the distribution and quantity of GABAA receptors in Carassius auratus gibelio is still limited. We investigated for the first time, the tissue-specific distribution of GABAARβ2a and GABAARβ2b, the two subunits of the predominant GABAA receptor subtype (α1β2γ2), and then, the expression of GABAARβ2a, GABAARβ2b, GAD, and quantified GABA-T genes in different tissues by quantitative real-time PCR method and compared different expressions between two developmental stages of C. auratus gibelio. Results showed that GABAARβ2a and GABAARβ2b genes expressed in both brain and peripheral organs using reverse transcription-polymerase chain reaction. In addition, the majority of GABAARβ2a, GABAARβ2b, GAD, and GABA-T were mainly synthesized in brain; however, a considerable amount of GABA-T was secreted from the peripheral tissues, especially in the liver. Moreover, the expression of GABAARβ2a and GABAARβ2b genes in different tissues varied with body weight change. This study provides a reference for further studies on GABA and GABAA receptors subunits and an insight on the possible pharmacological properties of the GABAA receptor in C. auratus gibelio.
Gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in brain, is synthesized from glutamate and metabolized to succinic semialdehyde by glutamic acid decarboxylase (GAD) and GABA ...transaminase (GABA-T), respectively. The fast inhibitory effect of GABA is mediated by GABA type A (GABA^sub A^) receptors that are associated with several neurological disorders, and GABA^sub A^ receptors are targets of several therapeutic agents. To date, information on the distribution and quantity of GABA^sub A^ receptors in Carassius auratus gibelio is still limited. We investigated for the first time, the tissue-specific distribution of GABA^sub A^Rbeta2a and GABA^sub A^Rbeta2b, the two subunits of the predominant GABA^sub A^ receptor subtype (alpha1beta2γ2), and then, the expression of GABA^sub A^Rbeta2a, GABA^sub A^Rbeta2b, GAD, and quantified GABA-T genes in different tissues by quantitative real-time PCR method and compared different expressions between two developmental stages of C. auratus gibelio. Results showed that GABA^sub A^Rbeta2a and GABA^sub A^Rbeta2b genes expressed in both brain and peripheral organs using reverse transcription-polymerase chain reaction. In addition, the majority of GABA^sub A^Rbeta2a, GABA^sub A^Rbeta2b, GAD, and GABA-T were mainly synthesized in brain; however, a considerable amount of GABA-T was secreted from the peripheral tissues, especially in the liver. Moreover, the expression of GABA^sub A^Rbeta2a and GABA^sub A^Rbeta2b genes in different tissues varied with body weight change. This study provides a reference for further studies on GABA and GABA^sub A^ receptors subunits and an insight on the possible pharmacological properties of the GABA^sub A^ receptor in C. auratus gibelio. PUBLICATION ABSTRACT
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