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https://www.readbyqxmd.com/read/29932056/epigenetics-with-special-reference-to-the-human-x-chromosome-inactivation-and-the-enigma-of-drosophila-dna-methylation
#1
Deepti Deobagkar
Epigenetics confers adaptability and survival advantage to an organism. Most epigenetic processes demonstrate memory and heritability. DNA methylation is an epigenetic process that adds imprints which can be inherited during cell division and across generations. DNA methylation adds an additional level of information to the basic DNA sequence and can influence chromatin organization and the function of the DNA sequence. In bacteria, it works as a defence strategy and preserves genome integrity. DNA methylation in eukaryotes has been implicated in a large number of cellular regulatory processes and is implied in development, differentiation, life style diseases and cancer...
June 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29901763/animal-hen1-2-o-methyltransferases-as-tools-for-3-terminal-functionalization-and-labelling-of-single-stranded-rnas
#2
Milda Mickute, Milda Nainyte, Lina Vasiliauskaite, Alexandra Plotnikova, Viktoras Masevicius, Saulius KlimaŇ°auskas, Giedrius Vilkaitis
S-adenosyl-L-methionine-dependent 2'-O-methylati-on of the 3'-terminal nucleotide plays important roles in biogenesis of eukaryotic small non-coding RNAs, such as siRNAs, miRNAs and Piwi-interacting RNAs (piRNAs). Here we demonstrate that, in contrast to Mg2+/Mn2+-dependent plant and bacterial homologues, the Drosophila DmHen1 and human HsHEN1 piRNA methyltransferases require cobalt cations for their enzymatic activity in vitro. We also show for the first time the capacity of the animal Hen1 to catalyse the transfer of a variety of extended chemical groups from synthetic analogues of the AdoMet cofactor onto a wide range (22-80 nt) of single-stranded RNAs permitting their 3'-terminal functionalization and labelling...
June 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29792159/on-the-possibility-of-death-of-new-genes-evidence-from-the-deletion-of-de-novo-micrornas
#3
Guang-An Lu, Yixin Zhao, Zhongqi Liufu, Chung-I Wu
BACKGROUND: New genes are constantly formed, sometimes from non-genic sequences, creating what is referred to as de novo genes. Since the total number of genes remains relatively steady, gene deaths likely balance out new births. In metazoan genomes, microRNAs (miRs) genes, small and non-coding, account for the bulk of functional de novo genes and are particularly suited to the investigation of gene death. RESULTS: In this study, we discover a Drosophila-specific de novo miRNA (mir-977) that may be facing impending death...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29777401/bantam-regulates-the-axonal-geometry-of-drosophila-larval-brain-by-modulating-actin-regulator-enabled
#4
Animesh Banerjee, Jagat Kumar Roy
During development, axonogenesis, an integral part of neurogenesis, is based on well-concerted events comprising generation, rearrangement, migration, elongation, and adhesion of neurons. Actin, specifically the crosstalk between the guardians of actin polymerization, like enabled, chickadee, capping protein plays an essential role in crafting several events of axonogenesis. Recent evidences reflect multifaceted role of microRNA during axonogenesis. Here, we investigated the role of bantam miRNA, a well-established miRNA in Drosophila, in regulating the actin organization during brain development...
May 18, 2018: Invertebrate Neuroscience: IN
https://www.readbyqxmd.com/read/29764374/direct-measurement-of-pervasive-weak-repression-by-micrornas-and-their-role-at-the-network-level
#5
Fuqiang Ma, Pei Lin, Qingjian Chen, Xuemei Lu, Yong E Zhang, Chung-I Wu
BACKGROUND: A gene regulatory network (GRN) comprises many weak links that are often regulated by microRNAs. Since miRNAs rarely repress their target genes by more than 30%, doubts have been expressed about the biological relevance of such weak effects. These doubts raise the possibility of under-estimation as miRNA repression is usually estimated indirectly from equilibrium expression levels. RESULTS: To measure miRNA repression directly, we inhibited transcript synthesis in Drosophila larvae and collected time-course data on mRNA abundance, the decline of which reflects transcript degradation...
May 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29698530/differentially-expressed-micrornas-associated-with-changes-of-transcript-levels-in-detoxification-pathways-and-ddt-resistance-in-the-drosophila-melanogaster-strain-91-r
#6
Keon Mook Seong, Brad S Coates, Do-Hyup Kim, Allison K Hansen, Barry R Pittendrigh
Dichloro-diphenyl-trichloroethane (DDT) resistance among arthropod species is a model for understanding the molecular adaptations in response to insecticide exposures. Previous studies reported that DDT resistance may involve one or multiple detoxification genes, such as cytochrome P450 monooxygenases (P450s), glutathione S-transferases (GSTs), esterases, and ATP binding cassette (ABC) transporters, or changes in the voltage-sensitive sodium channel. However, the possible involvement of microRNAs (miRNAs) in the post-transcriptional regulation of genes associated with DDT resistance in the Drosophila melanogaster strain 91-R remains poorly understood...
2018: PloS One
https://www.readbyqxmd.com/read/29695508/ankyrin-repeat-and-single-kh-domain-1-ankhd1-drives-renal-cancer-cell-proliferation-via-binding-to-and-altering-a-subset-of-mirnas
#7
Maria Fragiadaki, Martin P Zeidler
Clear cell Renal Cell Carcinoma (ccRCC) represents the most common kidney cancer worldwide. Increased cell proliferation associated with abnormal microRNA (miRNA) regulation are hallmarks of carcinogenesis. Ankyrin repeat and single KH domain 1 (ANKHD1) is a highly conserved protein found to interact with core cancer pathways in Drosophila, however its involvement in RCC is completely unexplored. Quantitative PCR studies coupled with large-scale genomics data analyses demonstrated that ANKHD1 is significantly upregulated in kidneys of RCC patients when compared to healthy controls...
April 25, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29688430/regulation-of-large-number-of-weak-targets-new-insights-from-twin-micrornas
#8
Yixin Zhao, Pei Lin, Zhongqi Liufu, Hao Yang, Yang Lyu, Xu Shen, Chung-I Wu, Tian Tang
Each animal microRNA (miRNA) targets many genes for repression. Down-regulation of most of these targets is weak and has no detectable individual phenotypic effect. Whether this extensive weak repression is biologically relevant is a central issue in the debate on miRNA functionality. In the "small (target) pool" view, weak repression is nonfunctional and should be gradually removed during evolution. However, since the selective advantage of removing individual targets is small, testing this hypothesis is a challenge...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29676724/wolbachia-mediated-protection-of-drosophila-melanogaster-against-systemic-infection-with-its-natural-viral-pathogen-drosophila-c-virus-does-not-involve-changes-in-levels-of-highly-abundant-mirnas
#9
Verna Monsanto-Hearne, Karyn N Johnson
The presence of Wolbachia confers virus protection to insects. The molecular mechanism underlying Wolbachia-mediated protection in this tripartite host-endosymbiont-virus interaction is not yet fully understood. In the bipartite association between Drosophila melanogaster and Drosophila C virus (DCV), changes in the expression of microRNAs (miRNAs) influence the outcome of viral pathogenesis. Here we examined whether changes in miRNA expression are similarly involved in the Drosophila-Wolbachia-DCV association...
June 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29663653/the-mir-7-and-bag-of-marbles-genes-regulate-hedgehog-pathway-signaling-in-blood-cell-progenitors-in-drosophila-larval-lymph-glands
#10
Tsuyoshi Tokusumi, Yumiko Tokusumi, Robert A Schulz
Hedgehog (Hh) pathway signaling is crucial for the maintenance of blood cell progenitors in the lymph gland hematopoietic organ present in Drosophila third instar larvae. Previous studies from our lab have likewise shown the importance of the mir-7 and bag of marbles (bam) genes in maintaining the progenitor state. Thus, we sought to investigate a possible interaction between the Hh pathway and mir-7/bam in the prohemocyte population within this hematopoietic tissue. Gain of function mir-7 was able to rescue a blood cell progenitor depletion phenotype caused by Patched (Ptc) inhibition of Hh pathway signaling in these cells...
May 2018: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/29550490/loquacious-pd-removes-phosphate-inhibition-of-dicer-2-processing-of-hairpin-rnas-into-sirnas
#11
Ryuya Fukunaga
Drosophila Dicer-2 processes RNA substrates into short interfering RNAs (siRNAs). Loquacious-PD (Loqs-PD), a dsRNA-binding protein that associates with Dicer-2, is required for processing of a subset of RNA substrates including hairpin RNAs into siRNAs. Inorganic phosphate-a small molecule present in all cell types-inhibits Dicer-2 from processing precursor of microRNAs (pre-miRNAs), which are processed by Dicer-1. Whether or how Loqs-PD modulates the inhibitory effect of inorganic phosphate on Dicer-2 processing of RNA substrates is unknown...
April 15, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29543534/ecdysone-responsive-microrna-252-5p-controls-the-cell-cycle-by-targeting-abi-in-drosophila
#12
Do-Hwan Lim, Seungjae Lee, Jee Yun Han, Min-Seok Choi, Jae-Sang Hong, Youngmo Seong, Young-Soo Kwon, Young Sik Lee
The steroid hormone ecdysone has a central role in the developmental transitions of insects through its control of responsive protein-coding and microRNA (miRNA) gene expression. However, the complete regulatory network controlling the expression of these genes remains to be elucidated. In this study, we performed cross-linking immunoprecipitation coupled with deep sequencing of endogenous Argonaute 1 (Ago1) protein, the core effector of the miRNA pathway, in Drosophila S2 cells. We found that regulatory interactions between miRNAs and their cognate targets were substantially altered by Ago1 in response to ecdysone signaling...
March 15, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29540498/the-mir-279-996-cluster-represses-receptor-tyrosine-kinase-signaling-to-determine-cell-fates-in-the-drosophila-eye
#13
Hong Duan, Luis F de Navas, Fuqu Hu, Kailiang Sun, Yannis E Mavromatakis, Kayla Viets, Cyrus Zhou, Joshua Kavaler, Robert J Johnston, Andrew Tomlinson, Eric C Lai
Photoreceptors in the crystalline Drosophila eye are recruited by receptor tyrosine kinase (RTK)/Ras signaling mediated by Epidermal growth factor receptor (EGFR) and the Sevenless (Sev) receptor. Analyses of an allelic deletion series of the mir-279/996 locus, along with a panel of modified genomic rescue transgenes, show that Drosophila eye patterning depends on both miRNAs. Transcriptional reporter and activity sensor transgenes reveal expression and function of miR-279/996 in non-neural cells of the developing eye...
April 9, 2018: Development
https://www.readbyqxmd.com/read/29519294/hippo-signaling-special-issue-of-bmb-reports-in-2018
#14
Eek-Hoon Jho
Since the first component of Hippo signaling, Wts in Drosophila, was identified in 1995, the progress of Hippo signaling studies has been very slow initially. However, after the findings suggesting that the core kinase pathway established in Drosophila was evolutionarily conserved in metazoans for the determination of organ size around 2008, the number of publications related to Hippo signaling has grown exponentially. Identification of molecular mechanisms underlying Hippo signaling response to intrinsic cues, such as cell-cell contact and mechanotransduction, as well as extrinsic cues, such as nutrients and soluble factors, has been one of the key topics of Hippo signaling...
March 2018: BMB Reports
https://www.readbyqxmd.com/read/29487148/regulation-of-circadian-behavior-by-astroglial-micrornas-in-drosophila
#15
Samantha You, Tudor A Fulga, David Van Vactor, F Rob Jackson
We describe a genome-wide microRNA (miRNA)-based screen to identify brain glial cell functions required for circadian behavior. To identify glial miRNAs that regulate circadian rhythmicity, we employed a collection of "miR-sponges" to inhibit miRNA function in a glia-specific manner. Our initial screen identified 20 glial miRNAs that regulate circadian behavior. We studied two miRNAs, miR-263b and miR-274, in detail and found that both function in adult astrocytes to regulate behavior. Astrocyte-specific inhibition of miR-263b or miR-274 in adults acutely impairs circadian locomotor activity rhythms with no effect on glial or clock neuronal cell viability...
March 2018: Genetics
https://www.readbyqxmd.com/read/29481550/cell-type-specific-sequencing-of-micrornas-from-complex-animal-tissues
#16
Chiara Alberti, Raphael A Manzenreither, Ivica Sowemimo, Thomas R Burkard, Jingkui Wang, Katharina Mahofsky, Stefan L Ameres, Luisa Cochella
MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular resolution. We report microRNome by methylation-dependent sequencing (mime-seq), an in vivo enzymatic small-RNA-tagging approach that enables high-throughput sequencing of tissue- and cell-type-specific miRNAs in animals...
April 2018: Nature Methods
https://www.readbyqxmd.com/read/29474379/small-rna-populations-revealed-by-blocking-rrna-fragments-in-drosophila-melanogaster-reproductive-tissues
#17
Emily K Fowler, Irina Mohorianu, Damian T Smith, Tamas Dalmay, Tracey Chapman
RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions...
2018: PloS One
https://www.readbyqxmd.com/read/29435938/transgene-like-animal-models-using-intronic-micrornas
#18
Shi-Lung Lin, Shin-Ju E Chang, Shao-Yao Ying
Transgenic animal models are valuable tools for testing gene functions and drug mechanisms in vivo. They are also the best similitude for a human body for etiological and pathological research of diseases. All pharmaceutically developed medicines must be proven to be safe and effective in animals before approval by the Food and Drug Administration (FDA) to be used in clinical trials. To this end, the transgenic animal models of diseases serve as the front line of drug evaluation. However, there is currently no transgenic animal model for microRNA (miRNA)-related research...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29428901/fragile-x-mental-retardation-protein-participates-in-non-coding-rna-pathways
#19
En-Hui Li, Xin Zhao, Ce Zhang, Wei Liu
Fragile X syndrome is one of the most common forms of inherited intellectual disability. It is caused by mutations of the Fragile X mental retardation 1(FMR1) gene, resulting in either the loss or abnormal expression of the Fragile X mental retardation protein (FMRP). Recent research showed that FMRP participates in non-coding RNA pathways and plays various important roles in physiology, thereby extending our knowledge of the pathogenesis of the Fragile X syndrome. Initial studies showed that the Drosophila FMRP participates in siRNA and miRNA pathways by interacting with Dicer, Ago1 and Ago2, involved in neural activity and the fate determination of the germline stem cells...
February 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29386086/up-regulation-of-mir-324-5p-inhibits-proliferation-and-invasion-of-colorectal-cancer-cells-by-targeting-elavl1
#20
Chijiang Gu, Mingyuan Zhang, Weiliang Sun, Changzheng Dong
Colorectal cancer (CRC) is a common clinical cancer, which remains incurable in most cases. MiRNAs are reported to playa part in development of various tumors. In the present study, we found that miR-324-5p was down-regulated in colorectal cancer cells while ELAV (Embryonic Lethal, Abnormal Vision, Drosophila)-Like Protein 1 (ELAVL1) showed a higher expression. MiR-324-5p transfection significantly inhibited the proliferation as well as invasion in both SW620 and SW480 cells. MiR-324-5p mimics transfection markedly decreased the expression of ELAVL1...
January 31, 2018: Oncology Research
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