Cytoplasmic HYL1 modulates miRNA-mediated translational repression

2021 ◽  
Author(s):  
Xi Yang ◽  
Weiguo Dong ◽  
Wenqing Ren ◽  
Qiuxia Zhao ◽  
Feijie Wu ◽  
...  
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Mrna Translation ◽  
Gene Repression ◽  
Translational Repression ◽  
Mirna Biogenesis ◽  
Biological Processes ◽  
Core Component ◽  
Plant Gene Regulation ◽  
Insight Into

Abstract MicroRNAs (miRNAs) control various biological processes by repressing target mRNAs. In plants, miRNAs mediate target gene repression via both mRNA cleavage and translational repression. However, the mechanism underlying this translational repression is poorly understood. Here, we found that Arabidopsis thaliana HYPONASTIC LEAVES1 (HYL1), a core component of the miRNA processing machinery, regulates miRNA-mediated mRNA translation but not miRNA biogenesis when it localized in the cytoplasm. Cytoplasmic HYL1 localizes to the endoplasmic reticulum and associates with ARGONAUTE1 (AGO1) and ALTERED MERISTEM PROGRAM1 (AMP1). In the cytoplasm, HYL1 monitors the distribution of AGO1 onto polysomes, binds to the mRNAs of target genes, represses their translation, and partially rescues the phenotype of the hyl1 null mutant. This study uncovered another function of HYL1 and provides insight into the mechanism of plant gene regulation.

M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers

2020 ◽  
Author(s):  
Shuang Deng ◽  
Hongwan Zhang ◽  
Kaiyu Zhu ◽  
Xingyang Li ◽  
Ying Ye ◽  
...  
Keyword(s):  
High Throughput ◽  
Target Gene ◽  
Target Genes ◽  
Biological Processes ◽  
Public Repository ◽  
Reversible Process ◽  
Comprehensive Database ◽  
Dynamic Modification ◽  
Gene Database ◽  
User Friendly

Abstract N6-methyladenosine (m6A) is the most abundant posttranscriptional modification in mammalian mRNA molecules and has a crucial function in the regulation of many fundamental biological processes. The m6A modification is a dynamic and reversible process regulated by a series of writers, erasers and readers (WERs). Different WERs might have different functions, and even the same WER might function differently in different conditions, which are mostly due to different downstream genes being targeted by the WERs. Therefore, identification of the targets of WERs is particularly important for elucidating this dynamic modification. However, there is still no public repository to host the known targets of WERs. Therefore, we developed the m6A WER target gene database (m6A2Target) to provide a comprehensive resource of the targets of m6A WERs. M6A2Target provides a user-friendly interface to present WER targets in two different modules: ‘Validated Targets’, referred to as WER targets identified from low-throughput studies, and ‘Potential Targets’, including WER targets analyzed from high-throughput studies. Compared to other existing m6A-associated databases, m6A2Target is the first specific resource for m6A WER target genes. M6A2Target is freely accessible at http://m6a2target.canceromics.org.

scholarly journals Network Properties for Ranking Predicted miRNA Targets in Breast Cancer

2009 ◽  
Vol 2009 ◽  
pp. 1-7 ◽  
Author(s):  
Jörg Linde ◽  
Björn Olsson ◽  
Zelmina Lubovac
Keyword(s):  
Breast Cancer ◽  
Target Genes ◽  
State Of The Art ◽  
Translational Repression ◽  
Prediction Methods ◽  
Biological Processes ◽  
Computer Prediction ◽  
Prediction Tools ◽  
Network Properties

MicroRNAs control the expression of their target genes by translational repression and transcriptional cleavage. They are involved in various biological processes including development and progression of cancer. To uncover the biological role of miRNAs it is important to identify their target genes. The small number of experimentally validated target genes makes computer prediction methods very important. However, state-of-the-art prediction tools result in a great number of putative targets with an unpredictable number of false positives. In this paper, we propose and evaluate two approaches for ranking the biological relevance of putative targets of miRNAs which are associated with breast cancer.

scholarly journals High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Md. Tariqul Islam ◽  
Ahlan Sabah Ferdous ◽  
Rifat Ara Najnin ◽  
Suprovath Kumar Sarker ◽  
Haseena Khan
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Kegg Pathway ◽  
Translational Repression ◽  
Biological Processes ◽  
Rt Pcr ◽  
Stem Loop ◽  
Evolutionarily Conserved ◽  
Pathway Analyses ◽  
Species Specific

MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.

scholarly journals Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense-transcribed sequences

2019 ◽  
Author(s):  
Lydia Gramzow ◽  
Dajana Lobbes ◽  
Sophia Walter ◽  
Nathan Innard ◽  
Günter Theißen
Keyword(s):  
Transcription Factors ◽  
Target Gene ◽  
Target Genes ◽  
Mirna Biogenesis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Developmental Processes ◽  
Inverted Duplication ◽  
The Future ◽  
Transcribed Sequences

AbstractSome microRNAs (miRNAs) are key regulators of developmental processes, mainly by controlling the accumulation of transcripts encoding transcription factors that are important for morphogenesis. MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants. Here we study the convergent evolution of two MIRNA (MIR) gene families, named MIR444 and MIR824, targeting members of the same clade of MIKCC-group MADS-box genes. We show that these two MIR genes most likely originated independently in monocots (MIR444) and in Brassicales (eudicots, MIR824). We provide evidence that in both cases the future target gene was transcribed in antisense prior to the evolution of the MIR genes. Both MIR genes then likely originated by a partial inverted duplication of their target genes, resulting in natural antisense organization of the newly evolved MIR gene and its target gene at birth. We thus propose a new model for the origin of MIR genes, MEPIDAS (MicroRNA Evolution by Partial Inverted Duplication of Antisense-transcribed Sequences). MEPIDAS is a refinement of the inverted duplication hypothesis. According to MEPIDAS, a MIR gene evolves at a genomic locus at which the future target gene is also transcribed in the antisense direction. A partial inverted duplication at this locus causes the antisense transcript to fold into a stem-loop structure that is recognized by the miRNA biogenesis machinery to produce a miRNA that regulates the gene at this locus. Our analyses exemplify how to elucidate the origin of conserved miRNAs by comparative genomics and will guide future studies.

scholarly journals Analysis of Long Noncoding RNA and mRNA Expression Profiles of Testes with High and Low Sperm Motility in Domestic Pigeons (Columba livia)

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 349
Author(s):  
Xiuli Xu ◽  
Yuge Tan ◽  
Haiguang Mao ◽  
Honghua Liu ◽  
Xinyang Dong ◽  
...  
Keyword(s):  
Sperm Motility ◽  
Noncoding Rna ◽  
Target Gene ◽  
Target Genes ◽  
Semen Quality ◽  
Expression Profiles ◽  
Columba Livia ◽  
Ion Binding ◽  
Biological Processes ◽  
Domestic Pigeons

Sperm motility is one of the most important indicators in assessing semen quality, and it is used to evaluate poultry fertility. Many long noncoding RNAs (lncRNAs) and mRNAs are involved in regulating testis development and spermatogenesis. In this study, we employed RNA sequencing to analyse the testis transcriptome (lncRNA and mRNA) of ten pigeons with high and low sperm motility. In total, 46,117 mRNAs and 17,463 lncRNAs were identified, of which 2673 mRNAs and 229 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the high and low sperm motility groups. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis showed that target genes of DE lncRNAs and DE mRNAs were related to calcium ion binding, ATP binding, and spermatogenesis. Moreover, we found that UBB, a target gene of lncRNA MSTRG.7787.5, was involved in germ cell development. Our study provided a catalogue of lncRNAs and mRNAs associated with sperm motility, and they deserve further study to deepen the understanding of biological processes in the pigeon testis.

scholarly journals KETCH1 imports HYL1 to nucleus for miRNA biogenesis in Arabidopsis

2017 ◽  
Vol 114 (15) ◽  
pp. 4011-4016 ◽  
Author(s):  
Zhonghui Zhang ◽  
Xinwei Guo ◽  
Chunxiao Ge ◽  
Zeyang Ma ◽  
Mengqiu Jiang ◽  
...  
Keyword(s):  
Protein A ◽  
Mirna Biogenesis ◽  
Null Mutation ◽  
Core Component ◽  
Mirna Processing ◽  
Embryonic Lethal ◽  
Morphological Defects ◽  
Hairpin Structures ◽  
Mirna Pathway ◽  
Insight Into

MicroRNA (miRNA) is processed from primary transcripts with hairpin structures (pri-miRNAs) by microprocessors in the nucleus. How cytoplasmic-borne microprocessor components are transported into the nucleus to fulfill their functions remains poorly understood. Here, we report KETCH1 (karyopherin enabling the transport of the cytoplasmic HYL1) as a partner of hyponastic leaves 1 (HYL1) protein, a core component of microprocessor in Arabidopsis and functional counterpart of DGCR8/Pasha in animals. Null mutation of ketch1 is embryonic-lethal, whereas knockdown mutation of ketch1 caused morphological defects, reminiscent of mutants in the miRNA pathway. ketch1 knockdown mutation also substantially reduced miRNA accumulation, but did not alter nuclear-cytoplasmic shuttling of miRNAs. Rather, the mutation significantly reduced nuclear portion of HYL1 protein and correspondingly compromised the pri-miRNA processing in the nucleus. We propose that KETCH1 transports HYL1 from the cytoplasm to the nucleus to constitute functional microprocessor in Arabidopsis. This study provides insight into the largely unknown nuclear-cytoplasmic trafficking process of miRNA biogenesis components through eukaryotes.

scholarly journals Stress-mediated Sin3B activation leads to negative regulation of subset of p53 target genes

2015 ◽  
Vol 35 (4) ◽  
Author(s):  
Rama Kadamb ◽  
Shilpi Mittal ◽  
Nidhi Bansal ◽  
Daman Saluja
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Epigenetic Modifications ◽  
Negative Regulation ◽  
Stress Conditions ◽  
Gene Repression ◽  
Gene Promoters ◽  
P53 Target Genes

Sin3B expression and its interaction with phosphorylated p53 increases under stress conditions. Recruitment of Sin3B by p53 at its target gene promoters is essential for the maintenance of inhibitory chromatin environment by inducing epigenetic modifications that brings about their target gene repression.

scholarly journals MeCP2 knockdown reveals DNA methylation-independent gene repression of target genes in living cells and a bias in the cellular location of target gene products

2008 ◽  
Vol 83 (2) ◽  
pp. 199-208 ◽  
Author(s):  
Shinya Yakabe ◽  
Hidenobu Soejima ◽  
Hitomi Yatsuki ◽  
Hirotaka Tominaga ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Target Gene ◽  
Target Genes ◽  
Living Cells ◽  
Gene Repression ◽  
Gene Products ◽  
Cellular Location ◽  
Independent Gene

The Crosstalk between MicroRNAs and Gibberellin Signaling in Plants

2020 ◽  
Vol 61 (11) ◽  
pp. 1880-1890 ◽  
Author(s):  
Sha Yu ◽  
Jia-Wei Wang
Keyword(s):  
Target Genes ◽  
Floral Induction ◽  
Stem Elongation ◽  
Mirna Biogenesis ◽  
Biological Processes ◽  
Master Regulators ◽  
The Past ◽  
Della Proteins ◽  
Wide Range ◽  
Ga Response

Abstract Gibberellin (GA) is an integral phytohormone that plays prominent roles in controlling seed germination, stem elongation, leaf development and floral induction. It has been shown that GA regulates these diverse biological processes mainly through overcoming the suppressive effects of the DELLA proteins, a family of nuclear repressors of GA response. MicroRNAs (miRNAs), which have been identified as master regulators of gene expression in eukaryotes, are also involved in a wide range of plant developmental events through the repression of their target genes. The pathways of GA biosynthesis and signaling, as well as the pathways of miRNA biogenesis and regulation, have been profoundly delineated in the past several decades. Growing evidence has shown that miRNAs and GAs are coordinated in regulating plant development, as several components in GA pathways are targeted by miRNAs, and GAs also regulate the expression of miRNAs or their target genes vice versa. Here, we review the recent advances in our understanding of the molecular connections between miRNAs and GA, with an emphasis on the two miRNAs, miR156 and miR159.

scholarly journals Tr-milRNA1 Contributes to Lignocellulase Secretion under Heat Stress by Regulating the Lectin-Type Cargo Receptor Gene Trvip36 in Trichoderma guizhouence NJAU 4742

2021 ◽  
Vol 7 (12) ◽  
pp. 997
Author(s):  
Tuo Li ◽  
Jinding Liu ◽  
Qin Wang ◽  
Yang Liu ◽  
Ting Li ◽  
...  
Keyword(s):  
Heat Stress ◽  
Target Gene ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Receptor Gene ◽  
Biological Processes ◽  
Overexpression Strain ◽  
Cargo Receptor ◽  
Lignocellulose Utilization ◽  
Lignocellulase Secretion

Background: MicroRNA plays an important role in multifarious biological processes by regulating their corresponding target genes. However, the biological function and regulatory mechanism of fungal microRNA-like RNAs (milRNAs) remain poorly understood. Methods: In this study, combined with deep sequencing and bioinformatics analysis, milRNAs and their targets from Trichoderma guizhouence NJAU 4742 were isolated and identified under solid-state fermentation (SSF) by using rice straw as the sole carbon source at 28 °C and 37 °C, respectively. Results: A critical milRNA, TGA1_S04_31828 (Tr-milRNA1), was highly expressed under heat stress (37 °C) and adaptively regulated lignocellulase secretion. Overexpression of Tr-milRNA1 (OE-Tr-milRNA1) did not affect vegetative growth, but significantly increased lignocellulose utilization under heat stress. Based on the bioinformatics analysis and qPCR validation, a target of Tr-milRNA1 was identified as Trvip36, a lectin-type cargo receptor. The expression of Tr-milRNA1 and Trvip36 showed a divergent trend under SSF when the temperature was increased from 28 °C to 37 °C. In addition, the expression of Trvip36 was suppressed significantly in Tr-milRNA1 overexpression strain (OE-Tr-milRNA1). Compared with the wild type, deletion of Trvip36 (ΔTrvip36) significantly improved the secretion of lignocellulases by reducing the retention of lignocellulases in the ER under heat stress. Conclusions: Tr-milRNA1 from NJAU 4742 improved lignocellulose utilization under heat stress by regulating the expression of the corresponding target gene Trvip36. These findings might open avenues for exploring the mechanism of lignocellulase secretion in filamentous fungi.

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