Progress of mutant resource development and tilling on starch biosynthesis in wheat.

2021 ◽  
pp. 280-284
Author(s):  
Hui-jun Guo ◽  
Yong-dun Xie ◽  
Lin-shu Zhao ◽  
Hong-chun Xiong ◽  
Jia-yu Gu ◽  
...  
Keyword(s):  
Target Genes ◽  
Functional Characterization ◽  
Resource Development ◽  
Starch Biosynthesis ◽  
Genomic Research ◽  
Functional Genomic ◽  
Induced Mutations ◽  
The World ◽  
Diversity Enhancement ◽  
Reference Genomes

Abstract Induced mutations have been widely utilized for the development of plant mutant germplasm and varieties since 1927 and have contributed to genetic diversity enhancement and food security in the world. Mutant resources are essential for gene identification and functional characterization by forward and reverse genetic strategies. The publishing of annotated wheat reference genomes is greatly promoting the progress of wheat functional genomic research. Mutant resources of a broad spectrum and diversified wild- types will be the prerequisites in this process, in part due to the polyploid nature of wheat. This review describes the progress of mutant resource development derived from the winter wheat cultivar 'Jing411'. The segregating M2 population has been used for mining functional mutant alleles of key genes involved in starch biosynthesis and could be further used for allele mining of any other target genes. The morphological mutant resources developed from various mutagens have been, and are going to be, used to develop genetic populations for gene mapping and the genetic analysis of biological functions.

scholarly journals Regulatory Network Analysis in Estradiol-Treated Human Endothelial Cells

2021 ◽  
Vol 22 (15) ◽  
pp. 8193
Author(s):  
Daniel Pérez-Cremades ◽  
Ana B. Paes ◽  
Xavier Vidal-Gómez ◽  
Ana Mompeón ◽  
Carlos Hermenegildo ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Regulatory Network ◽  
Mirna Target ◽  
Target Genes ◽  
Functional Characterization ◽  
Human Endothelial Cells ◽  
Mrna Targets ◽  
Canonical Pathways

Background/Aims: Estrogen has been reported to have beneficial effects on vascular biology through direct actions on endothelium. Together with transcription factors, miRNAs are the major drivers of gene expression and signaling networks. The objective of this study was to identify a comprehensive regulatory network (miRNA-transcription factor-downstream genes) that controls the transcriptomic changes observed in endothelial cells exposed to estradiol. Methods: miRNA/mRNA interactions were assembled using our previous microarray data of human umbilical vein endothelial cells (HUVEC) treated with 17β-estradiol (E2) (1 nmol/L, 24 h). miRNA–mRNA pairings and their associated canonical pathways were determined using Ingenuity Pathway Analysis software. Transcription factors were identified among the miRNA-regulated genes. Transcription factor downstream target genes were predicted by consensus transcription factor binding sites in the promoter region of E2-regulated genes by using JASPAR and TRANSFAC tools in Enrichr software. Results: miRNA–target pairings were filtered by using differentially expressed miRNAs and mRNAs characterized by a regulatory relationship according to miRNA target prediction databases. The analysis identified 588 miRNA–target interactions between 102 miRNAs and 588 targets. Specifically, 63 upregulated miRNAs interacted with 295 downregulated targets, while 39 downregulated miRNAs were paired with 293 upregulated mRNA targets. Functional characterization of miRNA/mRNA association analysis highlighted hypoxia signaling, integrin, ephrin receptor signaling and regulation of actin-based motility by Rho among the canonical pathways regulated by E2 in HUVEC. Transcription factors and downstream genes analysis revealed eight networks, including those mediated by JUN and REPIN1, which are associated with cadherin binding and cell adhesion molecule binding pathways. Conclusion: This study identifies regulatory networks obtained by integrative microarray analysis and provides additional insights into the way estradiol could regulate endothelial function in human endothelial cells.

scholarly journals In Silico Identification and Functional Characterization of Conserved miRNAs in the Genome of Cryptosporidium parvum

2021 ◽  
Vol 15 ◽  
pp. 117793222110276
Author(s):  
Md. Irtija Ahsan ◽  
Md. Shahidur Rahman Chowdhury ◽  
Moumita Das ◽  
Sharmin Akter ◽  
Sawrab Roy ◽  
...  
Keyword(s):  
Cryptosporidium Parvum ◽  
Target Genes ◽  
Expressed Sequence Tag ◽  
Functional Characterization ◽  
Childhood Mortality ◽  
Homology Search ◽  
Health Concern ◽  
Nutrient Metabolism ◽  
Screening Process ◽  
Computational Screening

Cryptosporidium parvum, a predominant causal agent of a fatal zoonotic protozoan diarrhoeal disease called cryptosporidiosis, bears a worldwide public health concern for childhood mortality and poses a key threat to the dairy and water industries. MicroRNAs (miRNAs), small but powerful posttranscriptional gene silencing RNA molecules, regulate a variety of molecular, biological, and cellular processes in animals and plants. As to the present date, there is a paucity of information regarding miRNAs of C. parvum; hence, this study was used to identify miRNAs in the organism using a comprehensible expressed sequence tag–based homology search approach consisting of a series of computational screening process from the identification of putative miRNA candidates to the functional annotation of the important gene targets in C. parvum. The results revealed a conserved miRNA that targeted 487 genes in the model organism ( Drosophila melanogaster) and 85 genes in C. parvum, of which 11 genes had direct involvements in several crucial virulence factors such as environmental oocyst protection, excystation, locomotion, adhesion, invasion, stress protection, intracellular growth, and survival. Besides, 20 genes showed their association with various major pathways dedicated for the ribosomal biosynthesis, DNA repair, transportation, protein production, gene expression, cell cycle, cell proliferation, development, immune response, differentiation, and nutrient metabolism of the organism in the host. Thus, this study provides a strong evidence of great impact of identified miRNA on the biology, virulence, and pathogenesis of C. parvum. Furthermore, the study suggests that the detected miRNA could be a potential epigenomic tool for controlling the protozoon through silencing those virulent and pathway-related target genes.

scholarly journals Two highly representative rice BAC libraries of japonica cv Tainung 67 suitable for rice structural and functional genomic research

Plant Science ◽  
2006 ◽  
Vol 170 (4) ◽  
pp. 889-896
Author(s):  
Yann-Rong Lin ◽  
Teh-Yuan Chow ◽  
Meizhong Luo ◽  
Dave Kudrna ◽  
Chih-Chi Lin ◽  
...  
Keyword(s):  
Genomic Research ◽  
Functional Genomic ◽  
Bac Libraries

Boosting dsRNA delivery in plant and insect cells with peptide- and polymer-based carriers: case-based current status and future perspectives.

2021 ◽  
pp. 102-116
Author(s):  
Kristof de Schutter ◽  
Olivier Christiaens ◽  
Clauvis Nji Tizi Taning ◽  
Guy Smagghe
Keyword(s):  
Plant Cell Wall ◽  
Endosomal Escape ◽  
Genomic Research ◽  
Current Status ◽  
Functional Genomic ◽  
Future Perspectives ◽  
Agricultural Industry ◽  
Efficient Delivery ◽  
Rnai Response ◽  
Carrier Systems

Abstract Since the discovery of this naturally occurring endogenous regulatory and defence mechanism, RNA interference (RNAi) has been exploited as a powerful tool for functional genomic research. In addition, it has evolved as a promising candidate for a sustainable, specific and ecofriendly strategy for pest management and plant improvement. A key element in this technology is the efficient delivery of dsRNAs into the pest or plant tissues. While several examples using transgenic plants expressing the dsRNAs have proved the potential of this technology, nontransgenic approaches are investigated as alternatives, allowing flexibility and circumventing technical limitations of the transgenic approach. However, the efficacy of environmental RNAi is affected by several barriers, such as extracellular degradation of the dsRNA, inefficient internalization of the dsRNA in the cell and low endosomal escape into the cytoplasm, resulting in variable or low RNAi responses. In the medical field, carrier systems are commonly used to enhance RNA delivery and these systems are being rapidly adopted by the agricultural industry. Using four case studies, this chapter demonstrates the potential of carriers to improve the RNAi response in pest control for aquatic-living mosquito larvae and RNAi-resilient Lepidoptera and to cross the plant cell wall, allowing efficient environmental RNAi in plants.

scholarly journals The Role of MicroRNAs in Muscle Tissue Development in Beef Cattle

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 295 ◽  
Author(s):  
Sayed Haidar Abbas Raza ◽  
Nurgulsim Kaster ◽  
Rajwali Khan ◽  
Sameh A. Abdelnour ◽  
Mohamed E. Abd El-Hack ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Target Genes ◽  
Functional Characterization ◽  
Carcass Composition ◽  
Regulatory Function ◽  
Myoblast Differentiation ◽  
Mammalian Skeletal Muscle ◽  
Meat Tenderness ◽  
And Migration ◽  
Bovine Adipocytes

In this review, we highlight information on microRNA (miRNA) identification and functional characterization in the beef for muscle and carcass composition traits, with an emphasis on Qinchuan beef cattle, and discuss the current challenges and future directions for the use of miRNA as a biomarker in cattle for breeding programs to improve meat quality and carcass traits. MicroRNAs are endogenous and non-coding RNA that have the function of making post-transcriptional modifications during the process of preadipocyte differentiation in mammals. Many studies claim that diverse miRNAs have an impact on adipogenesis. Furthermore, their target genes are associated with every phase of adipocyte differentiation. It has been confirmed that, during adipogenesis, several miRNAs are differentially expressed, including miR-204, miR-224, and miR-33. The development of mammalian skeletal muscle is sequentially controlled by somite commitment into progenitor cells, followed by their fusion and migration, the proliferation of myoblasts, and final modification into fast- and slow-twitch muscle fibers. It has been reported that miRNA in the bovine MEG3-DIO3 locus has a regulatory function for myoblast differentiation. Likewise, miR-224 has been associated with controlling the differentiation of bovine adipocytes by targeting lipoprotein lipase. Through the posttranscriptional downregulation of KLF6, miR-148a-3p disrupts the proliferation of bovine myoblasts and stimulates apoptosis while the miR-23a~27a~24-2 cluster represses adipogenesis. Additional to influences on muscle and fat, bta-mir-182, bta-mir-183, and bta-mir-338 represent regulators of proteolysis in muscle, which influences meat tenderness.

scholarly journals Functional characterization of human Polycomb-like 3 isoforms identifies them as components of distinct EZH2 protein complexes

2011 ◽  
Vol 434 (2) ◽  
pp. 333-342 ◽  
Author(s):  
Gaylor Boulay ◽  
Claire Rosnoblet ◽  
Cateline Guérardel ◽  
Pierre-Olivier Angrand ◽  
Dominique Leprince
Keyword(s):  
Cell Fate ◽  
Target Genes ◽  
Protein Complexes ◽  
Functional Characterization ◽  
Polycomb Group ◽  
Phd Finger ◽  
Reverse Transcription Pcr ◽  
Tudor Domain ◽  
Self Association ◽  
Polycomb Repressive Complex 1

PcG (Polycomb group) proteins are conserved transcriptional repressors essential to regulate cell fate and to maintain epigenetic cellular memory. They work in concert through two main families of chromatin-modifying complexes, PRC1 (Polycomb repressive complex 1) and PRC2–4. In Drosophila, PRC2 contains the H3K27 histone methyltransferase E(Z) whose trimethylation activity towards PcG target genes is stimulated by PCL (Polycomb-like). In the present study, we have examined hPCL3, one of its three human paralogues. Through alternative splicing, hPCL3 encodes a long isoform, hPCL3L, containing an N-terminal TUDOR domain and two PHDs (plant homeodomains) and a smaller isoform, hPCL3S, lacking the second PHD finger (PHD2). By quantitative reverse transcription–PCR analyses, we showed that both isoforms are widely co-expressed at high levels in medulloblastoma. By co-immunoprecipitation analyses, we demonstrated that both isoforms interact with EZH2 through their common TUDOR domain. However, the hPCL3L-specific PHD2 domain, which is better conserved than PHD1 in the PCL family, is also involved in this interaction and implicated in the self-association of hPCL3L. Finally, we have demonstrated that both hPCL3 isoforms are physically associated with EZH2, but in different complexes. Our results provide the first evidence that the two hPCL3 isoforms belong to different complexes and raise important questions about their relative functions, particularly in tumorigenesis.

Revealing a natural marine product as a novel agonist for retinoic acid receptors with a unique binding mode and inhibitory effects on cancer cells

2012 ◽  
Vol 446 (1) ◽  
pp. 79-87 ◽  
Author(s):  
Shanshan Wang ◽  
Zhao Wang ◽  
Shengchen Lin ◽  
Weili Zheng ◽  
Rui Wang ◽  
...  
Keyword(s):  
Retinoic Acid ◽  
Cancer Cells ◽  
Target Genes ◽  
Functional Characterization ◽  
Acid Resistance ◽  
Binding Mode ◽  
Therapeutic Agents ◽  
Covalent Modification ◽  
Marine Product

Retinoids display anti-tumour activity on various cancer cells and therefore have been used as important therapeutic agents. However, adverse side effects and RA (retinoic acid) resistance limit further development and clinical application of retinoid-based therapeutic agents. We report in the present paper the identification of a natural marine product that activates RARs (RA receptors) with a chemical structure distinct from retinoids by high-throughput compound library screening. Luffariellolide was uncovered as a novel RAR agonist by inducing co-activator binding to these receptors in vitro, further inhibiting cell growth and regulating RAR target genes in various cancer cells. Structural and molecular studies unravelled a unique binding mode of this natural ligand to RARs with an unexpected covalent modification on the RAR. Functional characterization further revealed that luffariellolide displays chemotherapeutic potentials for overcoming RA resistance in colon cancer cells, suggesting that luffariellolide may represent a unique template for designing novel non-retinoid compounds with advantages over current RA drugs.

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