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https://www.readbyqxmd.com/read/28432871/mir-24-3p-is-overexpressed-in-hodgkin-lymphoma-and-protects-hodgkin-and-reed-sternberg-cells-from-apoptosis
#1
Ye Yuan, Joost Kluiver, Jasper Koerts, Debora de Jong, Bea Rutgers, Fazlyn Reeny Abdul Razak, Martijn Terpstra, Boudewijn Plaat, Ilja M Nolte, Arjan Diepstra, Lydia Visser, Klaas Kok, Anke van den Berg
miRNAs play important roles in biological processes, such as proliferation, metabolism, differentiation, and apoptosis, whereas altered expression levels contribute to diseases, such as cancers. We identified miRNAs with aberrant expression in Hodgkin lymphoma (HL) and investigated their role in pathogenesis. Small RNA sequencing revealed 84 significantly differentially expressed miRNAs in HL cell lines as compared to germinal center B cells. Three up-regulated miRNAs-miR-23a-3p, miR-24-3p, and miR-27a-3p-were derived from one primary miRNA transcript...
April 19, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28432817/factors-involved-in-early-polarization-of-the-anterior-posterior-axis-in-the-milkweed-bug-oncopeltus-fasciatus
#2
Neta Ginzburg, Mira Cohen, Ariel D Chipman
The axes of insect embryos are defined early in the blastoderm stage. Genes involved in this polarization are well known in Drosophila, but less so in other insects, such as the milkweed bug Oncopeltus fasciatus. Using quantitative PCR, we looked at differential expression of several candidate genes for early anterior-posterior patterning and found that none of them are expressed asymmetrically in the early blastoderm. We then used an RNA-Seq approach to identify novel candidate genes that might be involved in early polarization in Oncopeltus...
April 22, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28432618/the-identification-of-key-genes-and-pathways-in-hepatocellular-carcinoma-by-bioinformatics-analysis-of-high-throughput-data
#3
Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma (HCC) initiation and progression. HCC-associated gene expression dataset was downloaded from Gene Expression Omnibus database. Statistical software R was used for significance analysis of differentially expressed genes (DEGs) between liver cancer samples and normal samples. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, based on R software, were applied for the identification of pathways in which DEGs significantly enriched...
June 2017: Medical Oncology
https://www.readbyqxmd.com/read/28432338/crispr-cas9-mediated-inactivation-of-argonaute-2-reveals-its-differential-involvement-in-antiviral-responses
#4
Márta Ludman, József Burgyán, Károly Fátyol
RNA silencing constitutes an important antiviral mechanism in plants. Small RNA guided Argonaute proteins fulfill essential role in this process by acting as executors of viral restriction. Plants encode multiple Argonaute proteins of which several exhibit antiviral activities. A recent addition to this group is AGO2. Its involvement in antiviral responses is established predominantly by studies employing mutants of Arabidopsis thaliana. In the virological model plant, Nicotiana benthamiana, the contribution of AGO2 to antiviral immunity is much less certain due to the lack of appropriate genetic mutants...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432092/a-genome-wide-investigation-on-biofilm-formation-in-bacillus-cereus
#5
Fang Yan, Yiyang Yu, Kevin Gozzi, Yun Chen, Jian-Hua Guo, Yunrong Chai
Bacillus cereus is a soil-dwelling Gram-positive bacterium capable of forming structured multicellular communities, or biofilms. However, the regulatory pathways controlling biofilm formation are less well understood in B. cereus In this work, we developed a method to study B. cereus biofilms formed at the air-liquid interface. We applied two genome-wide approaches, random transposon insertion mutagenesis to identify genes that are potentially important for biofilm formation, and transcriptome analyses by RNA-seq to characterize genes that are differentially expressed in B...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431938/selective-inhibition-of-ezh2-by-a-small-molecule-inhibitor-regulates-microglial-gene-expression-essential-for-inflammation
#6
Sarder Arifuzzaman, Amitabh Das, Sun Hwa Kim, Taeho Yoon, Young Seek Lee, Kyoung Hwa Jung, Young Gyu Chai
Multiple studies have documented that Enhancer of zeste homolog 2 (EZH2) could play a role in inflammation and a wide range of malignancies; however, the underlying mechanisms remain largely unaddressed. Microglial activation is a key process in the production and release of numerous pro-inflammatory mediators that play important roles in inflammation and neurodegeneration in the central nervous system (CNS). Therefore, our aim was to investigate whether inhibition of EZH2 with the selective small molecule inhibitor EPZ-6438 protects against neonatal microglial activation...
April 18, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28431281/dengue-virus-replicates-and-accumulates-in-aedes-aegypti-salivary-glands
#7
Vincent Raquin, Louis Lambrechts
Dengue virus (DENV) is an RNA virus transmitted among humans by mosquito vectors, mainly Aedes aegypti. DENV transmission requires viral dissemination from the mosquito midgut to the salivary glands. During this process the virus undergoes several population bottlenecks, which are stochastic reductions in population size that restrict intra-host viral genetic diversity and limit the efficiency of natural selection. Despite the implications for virus transmission and evolution, DENV replication in salivary glands has not been directly demonstrated...
April 18, 2017: Virology
https://www.readbyqxmd.com/read/28431250/nuclear-proximity-of-mtr4-to-rna-exosome-restricts-dna-mutational-asymmetry
#8
Junghyun Lim, Pankaj Kumar Giri, David Kazadi, Brice Laffleur, Wanwei Zhang, Veronika Grinstein, Evangelos Pefanis, Lewis M Brown, Erik Ladewig, Ophélie Martin, Yuling Chen, Raul Rabadan, François Boyer, Gerson Rothschild, Michel Cogné, Eric Pinaud, Haiteng Deng, Uttiya Basu
The distribution of sense and antisense strand DNA mutations on transcribed duplex DNA contributes to the development of immune and neural systems along with the progression of cancer. Because developmentally matured B cells undergo biologically programmed strand-specific DNA mutagenesis at focal DNA/RNA hybrid structures, they make a convenient system to investigate strand-specific mutagenesis mechanisms. We demonstrate that the sense and antisense strand DNA mutagenesis at the immunoglobulin heavy chain locus and some other regions of the B cell genome depends upon localized RNA processing protein complex formation in the nucleus...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431233/a-compendium-of-rna-binding-proteins-that-regulate-microrna-biogenesis
#9
Thomas Treiber, Nora Treiber, Uwe Plessmann, Simone Harlander, Julia-Lisa Daiß, Norbert Eichner, Gerhard Lehmann, Kevin Schall, Henning Urlaub, Gunter Meister
During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28431232/genome-wide-mapping-of-drosha-cleavage-sites-on-primary-micrornas-and-noncanonical-substrates
#10
Baekgyu Kim, Kyowon Jeong, V Narry Kim
MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective gatekeeper for the canonical miRNA pathway. However, the sites of DROSHA-mediated processing have not been annotated, and it remains unclear to what extent DROSHA functions outside the miRNA pathway. Here, we establish a protocol termed "formaldehyde crosslinking, immunoprecipitation, and sequencing (fCLIP-seq)," which allows identification of DROSHA cleavage sites at single-nucleotide resolution...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28431230/structural-basis-for-guide-rna-processing-and-seed-dependent-dna-targeting-by-crispr-cas12a
#11
Daan C Swarts, John van der Oost, Martin Jinek
The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28431179/mirna-regulation-in-gliomas-usual-suspects-in-glial-tumorigenesis-and-evolving-clinical-applications
#12
Heather Ames, Marc K Halushka, Fausto J Rodriguez
In recent years, an increasing role for noncoding small RNAs (miRNA) has been uncovered in carcinogenesis. These oligonucleotides can promote degradation and/or inhibit translation of key mRNAs. Recent studies have also highlighted a possible role for miRNAs in adult and pediatric brain tumors, including high- and low-grade gliomas, medulloblastoma, ependymoma, and neoplasms associated with neurofibromatosis type 1. Gliomas represent the most common category of primary intraparenchymal brain tumors, and, for example, manipulation of signaling pathways, through inhibition of PTEN transcription appears to be an important function of miRNA dysregulation through miR-21, miR-106b, and miR-26a...
April 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28430982/evidence-of-nuclei-encoded-spliceosome-mediating-splicing-of-mitochondrial-rna
#13
Roberto H Herai, Priscilla D Negraes, Alysson R Muotri
Mitochondria are thought to have originated as free-living prokaryotes. Mitochondria organelles have small circular genomes with substantial structural (absence of histones and introns) and genetic similarity to bacteria. Contrary to the prevailing concept of intronless mitochondria, here we present evidences that mitochondrial RNA transcripts (mtRNA) are not limited to policystronic molecules, but also processed as nuclei-like transcripts that are differentially spliced and expressed in a cell-type specific manner...
April 19, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28430964/metalims-a-simple-open-source-laboratory-information-management-system-for-small-metagenomic-labs
#14
Cassie Elizabeth Heinle, Nicolas Paul Eugène Gaultier, Dana Miller, Rikky Wenang Purbojati, Federico M Lauro
BACKGROUND: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated IT position, so LIMS must also be easy to setup and maintain with minimal technical proficiency...
April 18, 2017: GigaScience
https://www.readbyqxmd.com/read/28430877/the-accessible-chromatin-landscape-during-conversion-of-human-embryonic-stem-cells-to-trophoblast-by-bmp4
#15
Yajun Liu, Dewu Ding, Hongde Liu, Xiao Sun
Human embryonic stem cells (hESC) exposed to the growth factor bone morphogenic protein 4 (BMP4) in the absence of FGF2 have been used as a model to study the development of placental development. However, little is known about the cis-regulatory mechanisms underlying this important process. In this study, we used the public available chromatin accessibility data of hESC H1 cells and BMP4-induced trophoblast (TB)cell lines to identify DNase I hypersensitive sites (DHSs) in the two cell lines, as well as the transcription factor binding sites within the DHSs...
April 18, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28430582/lncrna-chrf-induced-mir-489-loss-promotes-metastasis-of-colorectal-cancer-via-twist1-emt-signaling-pathway
#16
Youmao Tao, Tao Han, Tao Zhang, Chong Ma, Caixia Sun
microRNA-489 (miR-489) is a novel cancer-related miRNAs and functions as a tumor suppressor in human cancers. While, the clinical significance of miR-489 and its role in colorectal cancer (CRC) remain rarely known. Here, we found that the levels of miR-489 in CRC tissues were significantly lower than those in matched tumor-adjacent tissues. Furthermore, decreased levels of miR-489 also observed in CRC cell lines compared to HIEC cells. Clinicopathological analysis revealed that miR-489 underexpression was positively correlated with advanced pT stage, pN stage and AJCC stage...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430077/host-pathogen-interactions-modulated-by-small-rnas
#17
Waqar Islam, Zujian Wu, Saif Ul Islam
Biological processes such as defense mechanisms and microbial offence strategies are regulated through RNA induced interference in eukaryotes. Genetic mutations are modulated through biogenesis of small RNAs which directly impacts upon host development. Plant defense mechanisms are regulated and supported by a diversified group of small RNAs which are involved in streamlining several RNA interference pathways leading towards the initiation of pathogen gene silencing mechanisms. In the similar context, pathogens also utilize the support of small RNAs to launch their offensive attacks...
April 21, 2017: RNA Biology
https://www.readbyqxmd.com/read/28429489/transcriptional-analysis-of-the-adaptation-of-ustilago-maydis-during-growth-under-nitrogen-fixation-conditions
#18
José Alejandro Sánchez-Arreguin, Miguel Angel Hernandez-Oñate, Claudia Geraldine León-Ramirez, José Ruiz-Herrera
Regulation of genes involved in nitrogen metabolism likely plays a role in the ability of fungi to exploit and survive under different environmental situations. To learn about the mechanism of adaptation of the biotrophic fungus Ustilago maydis from a medium containing a source of fixed nitrogen, to a medium depending on the ability to fix N2 by its bacterial endosymbiont, we explored gene expression profiles using RNA-Seq analyses under these two conditions. The differentially expressed (DE) fungal genes were analyzed, identifying 90 genes that were regulated 24 h after shifting the fungus to media lacking ammonium nitrate as a nitrogen source...
April 21, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28429354/the-role-of-the-hippocampus-and-the-function-of-calcitonin-gene-related-peptide-in-the-mechanism-of-traumatic-brain-injury-accelerating-fracture-healing
#19
Y Song, G-X Han, L Chen, Y-Z Zhai, J Dong, W Chen, T-S Li, H-Y Zhu
OBJECTIVE: This research attempts to identify the part the hippocampus plays in accelerated fracture-healing after traumatic brain injury as well as to test functions of calcitonin gene-related peptide (CGRP) during this process. MATERIALS AND METHODS: Experiments were carried out on Male Sprague-Dawley rats that were split into four groups at random: TBI-fracture group, fracture-only group, TBI-only group, and control group. In the first week, blood specimen would be drawn from rats among the groups except those of the control group at three-time points (24, 72 and 168 hours) post-damage...
April 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28429321/euglena-transcript-processing
#20
David C McWatters, Anthony G Russell
RNA transcript processing is an important stage in the gene expression pathway of all organisms and is subject to various mechanisms of control that influence the final levels of gene products. RNA processing involves events such as nuclease-mediated cleavage, removal of intervening sequences referred to as introns and modifications to RNA structure (nucleoside modification and editing). In Euglena, RNA transcript processing was initially examined in chloroplasts because of historical interest in the secondary endosymbiotic origin of this organelle in this organism...
2017: Advances in Experimental Medicine and Biology
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