Identification and Functional Characterization of Somatic Mutations in Human MicroRNAs and their Responsive Elements in Target Genes in Ovarian Tumor Tissues

2009 ◽  
Author(s):  
Hua Zhao
Keyword(s):  
Ovarian Tumor ◽  
Somatic Mutations ◽  
Target Genes ◽  
Functional Characterization ◽  
Tumor Tissues

scholarly journals Functional characterization of somatic mutations in cancer using network-based inference of protein activity

2016 ◽  
Vol 48 (8) ◽  
pp. 838-847 ◽  
Author(s):  
Mariano J Alvarez ◽  
Yao Shen ◽  
Federico M Giorgi ◽  
Alexander Lachmann ◽  
B Belinda Ding ◽  
...  
Keyword(s):  
Somatic Mutations ◽  
Functional Characterization ◽  
Protein Activity

scholarly journals Serotonin and Melatonin Biosynthesis in Plants: Genome-Wide Identification of the Genes and Their Expression Reveal a Conserved Role in Stress and Development

2021 ◽  
Vol 22 (20) ◽  
pp. 11034
Author(s):  
Bidisha Bhowal ◽  
Annapurna Bhattacharjee ◽  
Kavita Goswami ◽  
Neeti Sanan-Mishra ◽  
Sneh L. Singla-Pareek ◽  
...  
Keyword(s):  
Target Genes ◽  
Functional Characterization ◽  
Gene Families ◽  
Pcr Analysis ◽  
Tryptophan Decarboxylase ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Suitable Target

Serotonin (Ser) and melatonin (Mel) serve as master regulators of plant growth and development by influencing diverse cellular processes. The enzymes namely, tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) catalyse the formation of Ser from tryptophan. Subsequently, serotonin N-acetyl transferase (SNAT) and acetyl-serotonin methyltransferase (ASMT) form Mel from Ser. Plant genomes harbour multiple genes for each of these four enzymes, all of which have not been identified. Therefore, to delineate information regarding these four gene families, we carried out a genome-wide analysis of the genes involved in Ser and Mel biosynthesis in Arabidopsis, tomato, rice and sorghum. Phylogenetic analysis unravelled distinct evolutionary relationships among these genes from different plants. Interestingly, no gene family except ASMTs showed monocot- or dicot-specific clustering of respective proteins. Further, we observed tissue-specific, developmental and stress/hormone-mediated variations in the expression of the four gene families. The light/dark cycle also affected their expression in agreement with our quantitative reverse transcriptase-PCR (qRT-PCR) analysis. Importantly, we found that miRNAs (miR6249a and miR-1846e) regulated the expression of Ser and Mel biosynthesis under light and stress by influencing the expression of OsTDC5 and OsASMT18, respectively. Thus, this study may provide opportunities for functional characterization of suitable target genes of the Ser and Mel pathway to decipher their exact roles in plant physiology.

scholarly journals Functional characterization of endogenous siRNA target genes in Caenorhabditis elegans

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 270 ◽  
Author(s):  
Suvi Asikainen ◽  
Liisa Heikkinen ◽  
Garry Wong ◽  
Markus Storvik
Keyword(s):  
Caenorhabditis Elegans ◽  
Target Genes ◽  
Functional Characterization ◽  
Sirna Target

scholarly journals Tools for Characterization of Escherichia coli Genes of Unknown Function

2002 ◽  
Vol 184 (16) ◽  
pp. 4573-4581 ◽  
Author(s):  
Christophe Merlin ◽  
Sean McAteer ◽  
Millicent Masters
Keyword(s):  
Escherichia Coli ◽  
Target Gene ◽  
Target Genes ◽  
Functional Characterization ◽  
Phenotypic Characterization ◽  
Gene Encoding ◽  
Flp Recombinase ◽  
Short Scar

ABSTRACT Despite the power of sequencing and of emerging high-throughput technologies to collect data rapidly, the definitive functional characterization of unknown genes still requires biochemical and genetic analysis in case-by-case studies. This often involves the deletion of target genes and phenotypic characterization of the deletants. We describe here modifications of an existing deletion method which facilitates the deletion process and enables convenient analysis of the expression properties of the target gene by replacing it with an FRT-lacZ-aph-Plac -FRT cassette. The lacZ gene specifically reports the activity of the deleted gene and therefore allows the determination of the conditions under which it is actively expressed. The aph gene, encoding resistance to kanamycin, provides a selectable means of transducing a deleted locus between strains so that the deletion can be combined with other relevant mutations. The lac promoter helps to overcome possible polar effects on downstream genes within an operon. Because the cassette is flanked by two directly repeated FRT sites, the cassette can be excised by the Flp recombinase provided in trans. Removing the cassette leaves an in-frame deletion with a short scar which should not interfere with downstream expression. Replacements of yacF, yacG, yacH, yacK (cueO), yacL, ruvA, ruvB, yabB, and yabC made with the cassette were used to verify its properties.

scholarly journals Genome-Wide Identification and Characterization of the AREB/ABF/ABI5 Subfamily Members from Solanum tuberosum

2019 ◽  
Vol 20 (2) ◽  
pp. 311 ◽  
Author(s):  
Tengfei Liu ◽  
Tingting Zhou ◽  
Meiting Lian ◽  
Tiantian Liu ◽  
Juan Hou ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Leucine Zipper ◽  
Target Genes ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Mobility Shift ◽  
Potato Genome

Abscisic acid (ABA) plays crucial roles in plant development and adaption to environmental stresses. The ABA-responsive element binding protein/ABRE-binding factor and ABA INSENSITIVE 5 (AREB/ABF/ABI5) gene subfamily members, which belong to the basic domain/leucine zipper (bZIP) transcription factors family, participate in the ABA-mediated signaling pathway by regulating the expression of their target genes. However, information about potato (Solanum tuberosum) AREB/ABF/ABI5 subfamily members remains scarce. Here, seven putative AREB/ABF/ABI5 members were identified in the potato genome. Sequences alignment revealed that these members shared high protein sequence similarity, especially in the bZIP region, indicating that they might possess overlapping roles in regulating gene expression. Subcellular localization analysis illustrated that all seven AREB/ABF/ABI5 members were localized in the nucleus. Transactivation activity assays in yeast demonstrated that these AREB/ABF/ABI5 members possessed distinct transcriptional activity. Electrophoretic mobility shift assays (EMSA) confirmed that all of these AREB/ABF/ABI5 members could have an affinity to ABRE in vitro. The expression patterns of these AREB/ABF/ABI5 genes showed that they were in response to ABA or osmotic stresses in varying degrees. Moreover, most AREB/ABF/ABI5 genes were induced during stolon swelling. Overall, these results provide the first comprehensive identification of the potato AREB/ABF/ABI5 subfamily and would facilitate further functional characterization of these subfamily members in future work.

MicroRNA-548-3p overexpression inhibits proliferation, migration and invasion in osteoblast-like cells by targeting STAT1 and MAFB

2020 ◽  
Vol 168 (3) ◽  
pp. 203-211 ◽  
Author(s):  
Eric G Ramírez-Salazar ◽  
Erika V Almeraya ◽  
Tania V López-Perez ◽  
Nelly Patiño ◽  
Jorge Salmeron ◽  
...  
Keyword(s):  
Cell Lines ◽  
Target Genes ◽  
Bone Remodelling ◽  
Functional Characterization ◽  
Migration And Invasion ◽  
Public Health Issue ◽  
Bone Remodelling Process ◽  
First Time

Abstract Osteoporosis is the most common bone disease and a public health issue with increasing prevalence in Mexico. This disease is caused by an imbalance in the bone remodelling process mediated by osteoclast and osteoblast. MicroRNAs have emerged as key players during the differentiation of both types of cells specialized involved in bone metabolism. We found high expression levels of miR-548x-3p in circulating monocytes derived from postmenopausal osteoporotic women. This study aimed to analyse the functional characterization of miR-548x-3p roles in the bone remodelling process. We validated by RT-qPCR, the elevated levels of miR-548x-3p in circulating monocytes derived from osteoporosis women. Through bioinformatics analysis, we identify MAFB and STAT1 as potential target genes for miR-548x-3p. Both genes showed low levels of expression in circulating monocytes derived from osteoporotic women. In addition, we demonstrated the binding of miR-548x-3p to the 3′-UTR of both mRNAs. MiR-548x-3p was overexpressed in osteoblasts-like cell lines decreasing the levels of MAFB and STAT1 mRNA and protein. We found that miR-548x-3p overexpression inhibits the proliferation, migration and invasion of the cell lines evaluated. Our results identified, by the first time, the potential role of miR-548x-3p as a modulator of the bone remodelling process by regulating the expression of MAFB and STAT1.

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