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 Cas-CLIP: a method for customizing pooled CRISPR libraries

2018 ◽  
Author(s):  
Jiyeon Kweon ◽  
Da-eun Kim ◽  
An-Hee Jang ◽  
Yongsub Kim
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Target Genes ◽  
Biological Processes ◽  
Precise Method ◽  
Library Construction ◽  
Expensive Process ◽  
Screening Technology

ABSCTRACTAlthough pooled CRISPR libraries are widely used in high-throughput screening to study various biological processes, library construction for researcher’s own study is a time-consuming, labor-intensive, and expensive process. In this study, we develop a simple, scalable method, called Cas-CLIP, to customize conventional pooled CRISPR libraries using the CRISPR/Cas9 system. We show that conventional pooled CRISPR libraries can be modified by eliminating gRNAs that target positive genes, enabling the identification of unknown target genes in CRISPR screening. Cas-CLIP is a precise method for customizing conventional pooled CRISPR libraries and will broaden the scope of high-throughput screening technology.

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 EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species

2019 ◽  
Author(s):  
Tianshun Gao ◽  
Jiang Qian
Keyword(s):  
Large Scale ◽  
Target Gene ◽  
Target Genes ◽  
Cell Types ◽  
Regulatory Elements ◽  
Tissue Cell ◽  
Normal Tissues ◽  
Genome Wide ◽  
Wide Range ◽  
User Friendly

Abstract Enhancers are distal cis-regulatory elements that activate the transcription of their target genes. They regulate a wide range of important biological functions and processes, including embryogenesis, development, and homeostasis. As more and more large-scale technologies were developed for enhancer identification, a comprehensive database is highly desirable for enhancer annotation based on various genome-wide profiling datasets across different species. Here, we present an updated database EnhancerAtlas 2.0 (http://www.enhanceratlas.org/indexv2.php), covering 586 tissue/cell types that include a large number of normal tissues, cancer cell lines, and cells at different development stages across nine species. Overall, the database contains 13 494 603 enhancers, which were obtained from 16 055 datasets using 12 high-throughput experiment methods (e.g. H3K4me1/H3K27ac, DNase-seq/ATAC-seq, P300, POLR2A, CAGE, ChIA-PET, GRO-seq, STARR-seq and MPRA). The updated version is a huge expansion of the first version, which only contains the enhancers in human cells. In addition, we predicted enhancer–target gene relationships in human, mouse and fly. Finally, the users can search enhancers and enhancer–target gene relationships through five user-friendly, interactive modules. We believe the new annotation of enhancers in EnhancerAtlas 2.0 will facilitate users to perform useful functional analysis of enhancers in various genomes.

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.

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.

scholarly journals Expression of miRNAs in Serum Exosomes versus Hippocampus in Methamphetamine-Induced Rats and Intervention of Rhynchophylline

2018 ◽  
Vol 2018 ◽  
pp. 1-11
Author(s):  
Han-cheng Li ◽  
Ying-bo Lin ◽  
Chan Li ◽  
Chao-hua Luo ◽  
Yu-ting Zhou ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Target Gene ◽  
Target Genes ◽  
Gene Prediction ◽  
Biological Processes ◽  
Biological Functions ◽  
Chip Sequencing ◽  
Central Nervous Systems ◽  
Serum Exosomes ◽  
Nonpreferred Side

Objective. To compare the expressions of miRNAs (microRNAs) in serum exosomes and in hippocampus and to provide insights into the miRNA-mediated relationship between peripheral and central nervous systems in the presence of methamphetamine. Methods. Published results on conditioned place preference (CPP) in rats conditioned by methamphetamine were replicated. The expressions of miRNAs in serum exosomes and hippocampus were determined by gene-chip sequencing. We then predicted the potential target genes of selected, differentially expressed (DE) miRNAs and then carried out functional analysis of these target genes. We also verified our results by RT-qPCR. Results. Methamphetamine reward could greatly increase the activity time and distance in the intrinsically nonpreferred side of the behavioral apparatus compared with control rats (P<0.01). Rhynchophylline treatment significantly counteracted these changes (P<0.01). Methamphetamine-induced CPP upregulated 23 miRNAs (log2 fold change [FC] > 1, P<0.01) in serum exosomes, whereas rhynchophylline treatment could downregulate these miRNAs (log2 FC < −1, P<0.01). Analysis of hippocampal miRNAs profiles found 22 DE miRNAs (log2 FC > 1 or <−1, P<0.01). When methamphetamine induced CPP, 11 of those miRNAs were upregulated, whereas rhynchophylline treatment could downregulate these miRNAs. The other 11 miRNAs behaved in the opposite way. We selected six DE miRNAs from each of serum exosomes and hippocampus for target gene prediction and functional analysis. We found that, in both, the DE miRNAs and their target genes may be related to neuronal information transmission and synaptic transmission. Conclusions. Rhynchophylline blocked the alteration of behavior and the expression of some DE miRNAs induced by methamphetamine. The biological functions of these DE miRNAs target genes are correlated between serum exosomes and hippocampus. As to these biological processes and pathways which are involved in the development of addiction at multiple stages, we speculate that these DE miRNAs in serum exosomes and hippocampus are closely related to methamphetamine addiction.

scholarly journals Comparative Transcriptome Profiling of mRNA and lncRNA of Ovaries in High and Low Egg Production Performance in Domestic Pigeons (Columba livia)

2021 ◽  
Vol 12 ◽  
Author(s):  
Haiguang Mao ◽  
Xiuli Xu ◽  
Haiyue Cao ◽  
Xinyang Dong ◽  
Xiaoting Zou ◽  
...  
Keyword(s):  
Egg Production ◽  
Target Gene ◽  
Target Genes ◽  
Transcriptome Profiling ◽  
Columba Livia ◽  
Production Performance ◽  
Biological Processes ◽  
Economic Traits ◽  
Non Coding Rnas ◽  
Domestic Pigeons

Egg production performance is one of the most important economic traits in pigeon industry. However, little is known regarding how egg production performance is regulated by long non-coding RNAs (lncRNAs) in pigeons. To evaluate the lncRNAs and mRNAs in ovaries associated with egg production performance in domestic pigeons, high-throughput RNA sequencing of ovaries between high and low egg production performance groups were performed and analyzed in this study. A total of 34,346 mRNAs and 24,601 lncRNAs were identified, including 14,525 known lncRNAs and 10,076 novel lncRNAs, of which 811 mRNAs and 148 lncRNAs (P &lt; 0.05) were significantly differentially expressed (DE) between the groups of high and low egg production performance. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to cell differentiation, ATP binding and methylation. Moreover, we found that FOXK2, a target gene of lncRNA MSTRG.7894.4, was involved in regulating estrogen receptors. Our study provided a catalog of lncRNAs and mRNAs associated with egg production performance, and they deserve further study to deepen the understanding of biological processes in the ovaries of pigeons.

Abiotic Stress Tolerance in Soybean : Regulated by ncRNA

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
YASIN JESHIMA KHAN ◽  
HUSNARA Tyagi ◽  
Anil kumar Singh ◽  
Santosh kumar. Magadum
Keyword(s):  
Abiotic Stresses ◽  
Target Genes ◽  
Abiotic Stress Tolerance ◽  
Crop Improvement ◽  
Vital Role ◽  
Grain Legume ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Cellular Environment ◽  
Non Coding Rnas

Plants respond through a cascade of reactions resulting in varied cellular environment leading to alterations in the patterns of protein expression resulting in phonotypic changes. Single cell genomics and global proteomics came out to be powerful tools and efficient techniques in studying stress tolerant plants. Non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. Small ncRNAs play a vital role in post transcriptional gene regulation by either translational repression or by inducing mRNA cleavage. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs too have a similar structure, function, and biogenesis like miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences.In this review, we focus on the involvement of ncRNAs in comabting abiotic stresses of soybean. This review emphasis on previously known miRNAs as they play important role in several abiotic stresses like drought, salinity, chilling and heat stress by their diverse roles in mediating biological processes like gene expression, chromatin formation, defense of genome against invading viruses. This review attempts to elucidate the various kinds of non-coding RNAs explored, their discovery, biogenesis, functions, and response for different type of abiotic stresses and future aspects for crop improvement in the context of soybean, a representative grain legume.

Artificial microRNA (amiRNA) induced gene silencing in alfalfa (Medicago sativa)

Botany ◽  
2013 ◽  
Vol 91 (2) ◽  
pp. 117-122 ◽  
Author(s):  
Julian C. Verdonk ◽  
Michael L. Sullivan
Keyword(s):  
Gene Silencing ◽  
Medicago Sativa ◽  
Target Gene ◽  
Target Genes ◽  
Mirna Precursor ◽  
Crop Species ◽  
Forage Crop ◽  
Ribonucleic Acids ◽  
Endogenous Gene ◽  
Medicago Sativa L

Gene silencing is a powerful technique that allows the study of the function of specific genes by selectively reducing their transcription. Several different approaches can be used, however they all have in common the artificial generation of single stranded small ribonucleic acids (RNAs) that are utilized by the endogenous gene silencing machinery of the organism. Artificial microRNAs (amiRNA) can be used to very specifically target genes for silencing because only a short sequence of 21 nucleotides of the gene of interest is used. Gene silencing via amiRNA has been developed for Arabidopsis thaliana (L.) Heynh. and rice using endogenous microRNA (miRNA) precursors and has been shown to also work effectively in other dicot species using the arabidopsis miRNA precursor. Here, we demonstrate that the arabidopsis miR319 precursor can be used to silence genes in the important forage crop species alfalfa (Medicago sativa L.) by silencing the expression of a transgenic beta-glucuronidase (GUSPlus) target gene.

scholarly journals CHOP-Dependent Stress-Inducible Expression of a Novel Form of Carbonic Anhydrase VI

1999 ◽  
Vol 19 (1) ◽  
pp. 495-504 ◽  
Author(s):  
John Sok ◽  
Xiao-Zhong Wang ◽  
Nikoleta Batchvarova ◽  
Masahiko Kuroda ◽  
Heather Harding ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Target Gene ◽  
Target Genes ◽  
Direct Evidence ◽  
Nuclear Protein ◽  
Intracellular Form ◽  
Carbonic Anhydrase Vi ◽  
Responsive Element

ABSTRACT CHOP (also called GADD153) is a stress-inducible nuclear protein that dimerizes with members of the C/EBP family of transcription factors and was initially identified as an inhibitor of C/EBP binding to classic C/EBP target genes. Subsequent experiments suggested a role for CHOP-C/EBP heterodimers in positively regulating gene expression; however, direct evidence that this is the case has so far not been uncovered. Here we describe the identification of a positively regulated direct CHOP-C/EBP target gene, that encoding murine carbonic anhydrase VI (CA-VI). The stress-inducible form of the gene is expressed from an internal promoter and encodes a novel intracellular form of what is normally a secreted protein. Stress-induced expression of CA-VI is both CHOP and C/EBPβ dependent in that it does not occur in cells deficient in either gene. A CHOP-responsive element was mapped to the inducibleCA-VI promoter, and in vitro footprinting revealed binding of CHOP-C/EBP heterodimers to that site. Rescue of CA-VIexpression in c/ebpβ−/− cells by exogenous C/EBPβ and a shorter, normally inhibitory isoform of the protein known as LIP suggests that the role of the C/EBP partner is limited to targeting the CHOP-containing heterodimer to the response element and points to a preeminent role for CHOP in CA-VI induction during stress.

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