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https://www.readbyqxmd.com/read/29775580/znfx-1-functions-within-perinuclear-nuage-to-balance-epigenetic-signals
#1
Takao Ishidate, Ahmet R Ozturk, Daniel J Durning, Rita Sharma, En-Zhi Shen, Hao Chen, Meetu Seth, Masaki Shirayama, Craig C Mello
Animal cells have a remarkable capacity to adopt durable and heritable gene expression programs or epigenetic states that define the physical properties and diversity of somatic cell types. The maintenance of epigenetic programs depends on poorly understood pathways that prevent gain or loss of inherited signals. In the germline, epigenetic factors are enriched in liquid-like perinuclear condensates called nuage. Here, we identify the deeply conserved helicase-domain protein, ZNFX-1, as an epigenetic regulator and component of nuage that interacts with Argonaute systems to balance epigenetic inheritance...
May 17, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29769717/swi2-snf2-atpase-chr2-remodels-pri-mirnas-via-serrate-to-impede-mirna-production
#2
Zhiye Wang, Zeyang Ma, Claudia Castillo-González, Di Sun, Yanjun Li, Bin Yu, Baoyu Zhao, Pingwei Li, Xiuren Zhang
Chromatin remodelling factors (CHRs) typically function to alter chromatin structure. CHRs also reside in ribonucleoprotein complexes, but little is known about their RNA-related functions. Here we show that CHR2 (also known as BRM), the ATPase subunit of the large switch/sucrose non-fermentable (SWI/SNF) complex, is a partner of the Microprocessor component Serrate (SE). CHR2 promotes the transcription of primary microRNA precursors (pri-miRNAs) while repressing miRNA accumulation in vivo. Direct interaction with SE is required for post-transcriptional inhibition of miRNA accumulation by CHR2 but not for its transcriptional activity...
May 16, 2018: Nature
https://www.readbyqxmd.com/read/29765512/dhx9-regulates-production-of-hepatitis-b-virus-derived-circular-rna-and-viral-protein-levels
#3
Kazuma Sekiba, Motoyuki Otsuka, Motoko Ohno, Takahiro Kishikawa, Mari Yamagami, Tatsunori Suzuki, Rei Ishibashi, Takahiro Seimiya, Eri Tanaka, Kazuhiko Koike
Hepatitis B virus (HBV) infection, which is a major health concern worldwide, can lead to liver cirrhosis and hepatocellular carcinoma. Although current nucleos(t)ide analogs efficiently inhibit viral reverse transcription and viral DNA load clinically, episomal viral covalently closed circular DNA (cccDNA) minichromosomes and transcripts from cccDNA continue to be expressed over the long term. We hypothesized that, under these conditions, viral transcripts may have biological functions involved in pathogenesis...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29757259/two-novel-hypovirulence-associated-mycoviruses-in-the-phytopathogenic-fungus-botrytis-cinerea-molecular-characterization-and-suppression-of-infection-cushion-formation
#4
Fangmin Hao, Ting Ding, Mingde Wu, Jing Zhang, Long Yang, Weidong Chen, Guoqing Li
Botrytis cinerea is a necrotrophic fungus causing disease on many important agricultural crops. Two novel mycoviruses, namely Botrytis cinerea hypovirus 1 (BcHV1) and Botrytis cinerea fusarivirus 1 (BcFV1), were fully sequenced. The genome of BcHV1 is 10,214 nt long excluding a poly-A tail and possesses one large open reading frame (ORF) encoding a polyprotein possessing several conserved domains including RNA-dependent RNA polymerase (RdRp), showing homology to hypovirus-encoded polyproteins. Phylogenetic analysis indicated that BcHV1 may belong to the proposed genus Betahypovirus in the viral family Hypoviridae ...
May 13, 2018: Viruses
https://www.readbyqxmd.com/read/29746542/depletion-of-mrna-export-regulator-dbp5-ddx19-gle1-or-ippk-that-is-a-key-enzyme-for-the-production-of-ip6-resulting-in-differentially-altered-cytoplasmic-mrna-expression-and-specific-cell-defect
#5
Masumi Okamura, Yasutaka Yamanaka, Maki Shigemoto, Yuya Kitadani, Yuhko Kobayashi, Taiho Kambe, Masaya Nagao, Issei Kobayashi, Katsuzumi Okumura, Seiji Masuda
DBP5, also known as DDX19, GLE1 and inositol hexakisphosphate (IP6) function in messenger RNA (mRNA) export at the cytoplasmic surface of the nuclear pore complex in eukaryotic cells. DBP5 is a DEAD-box RNA helicase, and its activity is stimulated by interactions with GLE1 and IP6. In addition, these three factors also have unique role(s). To investigate how these factors influenced the cytoplasmic mRNA expression and cell phenotype change, we performed RNA microarray analysis to detect the effect and function of DBP5, GLE1 and IP6 on the cytoplasmic mRNA expression...
2018: PloS One
https://www.readbyqxmd.com/read/29742983/dead-box-helicases-the-yin-and-yang-roles-in-viral-infections
#6
Vanessa Meier-Stephenson, Tyler Mrozowich, Mimi Pham, Trushar R Patel
Viruses hijack the host cell machinery and recruit host proteins to aid their replication. Several host proteins also play vital roles in inhibiting viral replication. Emerging class of host proteins central to both of these processes are the DEAD-box helicases: a highly conserved family of ATP-dependent RNA helicases, bearing a common D-E-A-D (Asp-Glu-Ala-Asp) motif. They play key roles in numerous cellular processes, including transcription, splicing, miRNA biogenesis and translation. Though their sequences are highly conserved, these helicases have quite diverse roles in the cell...
May 9, 2018: Biotechnology & Genetic Engineering Reviews
https://www.readbyqxmd.com/read/29742442/rna-dna-hybrid-interactome-identifies-dxh9-as-a-molecular-player-in-transcriptional-termination-and-r-loop-associated-dna-damage
#7
Agnese Cristini, Matthias Groh, Maiken S Kristiansen, Natalia Gromak
R-loops comprise an RNA/DNA hybrid and displaced single-stranded DNA. They play important biological roles and are implicated in pathology. Even so, proteins recognizing these structures are largely undefined. Using affinity purification with the S9.6 antibody coupled to mass spectrometry, we defined the RNA/DNA hybrid interactome in HeLa cells. This consists of known R-loop-associated factors SRSF1, FACT, and Top1, and yet uncharacterized interactors, including helicases, RNA processing, DNA repair, and chromatin factors...
May 8, 2018: Cell Reports
https://www.readbyqxmd.com/read/29740493/bioinformatic-analysis-and-prediction-of-the-function-and-regulatory-network-of-long-non-coding-rnas-in-hepatocellular-carcinoma
#8
Ming-Rong Cao, Ze-Ping Han, Ji-Ming Liu, Yu-Guang Li, Yu-Bing Lv, Jia-Bin Zhou, Jin-Hua He
Computational analysis and bioinformatics have significantly advanced the ability of researchers to process and analyze biological data. Molecular data from human and model organisms may facilitate drug target validation and identification of biomarkers with increased predictive accuracy. The aim of the present study was to investigate the function of long non-coding RNAs (lncRNAs) in hepatocellular carcinoma (HCC) using online databases, and to predict their regulatory mechanism. HCC-associated lncRNAs, their downstream transcription factors and microRNAs (miRNAs/miRs), as well as the HCC-associated target genes, were identified using online databases...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29731414/rna-helicase-ddx1-converts-rna-g-quadruplex-structures-into-r-loops-to-promote-igh-class-switch-recombination
#9
Claudia Ribeiro de Almeida, Somdutta Dhir, Ashish Dhir, Amin E Moghaddam, Quentin Sattentau, Anton Meinhart, Nicholas J Proudfoot
Class switch recombination (CSR) at the immunoglobulin heavy-chain (IgH) locus is associated with the formation of R-loop structures over switch (S) regions. While these often occur co-transcriptionally between nascent RNA and template DNA, we now show that they also form as part of a post-transcriptional mechanism targeting AID to IgH S-regions. This depends on the RNA helicase DDX1 that is also required for CSR in vivo. DDX1 binds to G-quadruplex (G4) structures present in intronic switch transcripts and converts them into S-region R-loops...
April 30, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29729328/structural-characterization-of-%C3%AE-catenin-and-rx-5902-binding-to-phospho-p68-rna-helicase-by-molecular-dynamics-simulation
#10
Waqar Ali, Shagufta Shafique, Sajid Rashid
Emerging implications of probable ATP-dependent RNA helicase p68 in tumorigenesis and progression makes it a discerning target for cancer therapy. Recently it has been reported that tyrosyl-phosphorylation of p68 promotes β-catenin nuclear translocation and cancer metastasis through elevating the epithelial-mesenchymal transition. Despite recent advances, the structural characterization of this interaction, mode of action and induced conformational changes remain elusive. Here, through comparative structure analysis and molecular dynamics simulation assays, we explored comparative binding pattern of phospho-p68 against β-catenin...
May 2, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/29725819/senataxin-mutations-elicit-motor-neuron-degeneration-phenotypes-and-yield-tdp-43-mislocalization-in-als4-mice-and-human-patients
#11
Craig L Bennett, Somasish G Dastidar, Shuo-Chien Ling, Bilal Malik, Travis Ashe, Mandheer Wadhwa, Derek B Miller, Changwoo Lee, Matthew B Mitchell, Michael A van Es, Christopher Grunseich, Yingzhang Chen, Bryce L Sopher, Linda Greensmith, Don W Cleveland, Albert R La Spada
Amyotrophic lateral sclerosis type 4 (ALS4) is a rare, early-onset, autosomal dominant form of ALS, characterized by slow disease progression and sparing of respiratory musculature. Dominant, gain-of-function mutations in the senataxin gene (SETX) cause ALS4, but the mechanistic basis for motor neuron toxicity is unknown. SETX is a RNA-binding protein with a highly conserved helicase domain, but does not possess a low-complexity domain, making it unique among ALS-linked disease proteins. We derived ALS4 mouse models by expressing two different senataxin gene mutations (R2136H and L389S) via transgenesis and knock-in gene targeting...
May 3, 2018: Acta Neuropathologica
https://www.readbyqxmd.com/read/29718972/structure-of-frequency-interacting-rna-helicase-from-neurospora-crassa-reveals-high-flexibility-in-a-domain-critical-for-circadian-rhythm-and-rna-surveillance
#12
Yalemi Morales, Keith J Olsen, Jacqueline M Bulcher, Sean J Johnson
The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact...
2018: PloS One
https://www.readbyqxmd.com/read/29706542/cryo-em-structure-of-human-dicer-and-its-complexes-with-a-pre-mirna-substrate
#13
Zhongmin Liu, Jia Wang, Hang Cheng, Xin Ke, Lei Sun, Qiangfeng Cliff Zhang, Hong-Wei Wang
Human Dicer (hDicer) is a multi-domain protein belonging to the RNase III family. It plays pivotal roles in small RNA biogenesis during the RNA interference (RNAi) pathway by processing a diverse range of double-stranded RNA (dsRNA) precursors to generate ∼22 nt microRNA (miRNA) or small interfering RNA (siRNA) products for sequence-directed gene silencing. In this work, we solved the cryoelectron microscopy (cryo-EM) structure of hDicer in complex with its cofactor protein TRBP and revealed the precise spatial arrangement of hDicer's multiple domains...
April 20, 2018: Cell
https://www.readbyqxmd.com/read/29706536/repetitive-dna-reeling-by-the-cascade-cas3-complex-in-nucleotide-unwinding-steps
#14
Luuk Loeff, Stan J J Brouns, Chirlmin Joo
CRISPR-Cas provides RNA-guided adaptive immunity against invading genetic elements. Interference in type I systems relies on the RNA-guided Cascade complex for target DNA recognition and the Cas3 helicase/nuclease protein for target degradation. Even though the biochemistry of CRISPR interference has been largely covered, the biophysics of DNA unwinding and coupling of the helicase and nuclease domains of Cas3 remains elusive. Here, we employed single-molecule Förster resonance energy transfer (FRET) to probe the helicase activity with high spatiotemporal resolution...
April 17, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29696407/a-novel-endornavirus-isolated-from-cluster-bean-cyamopsis-tetragonoloba
#15
Ricardo Iván Alcalá-Briseño, Ryo Okada, Favio Herrera, Rodrigo A Valverde
Cluster bean (Cyamopsis tetragonoloba), also called guar, is a drought-tolerant annual legume. We conducted investigations to characterize a large dsRNA (~13-14 kbp) detected in a symptomless cluster bean genotype. The dsRNA was gel-purified and used for Illumina MiSeq sequencing. Reads were assembled, and BLASTx search results showed sequence similarity with viruses classified within the family Endornaviridae. The complete sequence of the putative endornavirus consisted of 12,895 nt and contained an open reading frame which coded for a polyprotein of 4,207 aa with conserved domains for methyltransferase, helicase, and RNA-dependent RNA polymerase...
April 25, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29684792/global-effects-of-ddx3-inhibition-on-cell-cycle-regulation-identified-by-a-combined-phosphoproteomics-and-single-cell-tracking-approach
#16
Marise R Heerma van Voss, Kai Kammers, Farhad Vesuna, Justin Brilliant, Yehudit Bergman, Saritha Tantravedi, Xinyan Wu, Robert N Cole, Andrew Holland, Paul J van Diest, Venu Raman
DDX3 is an RNA helicase with oncogenic properties. The small molecule inhibitor RK-33 is designed to fit into the ATP binding cleft of DDX3 and hereby block its activity. RK-33 has shown potent activity in preclinical cancer models. However, the mechanism behind the antineoplastic activity of RK-33 remains largely unknown. In this study we used a dual phosphoproteomic and single cell tracking approach to evaluate the effect of RK-33 on cancer cells. MDA-MB-435 cells were treated for 24 hours with RK-33 or vehicle control...
April 20, 2018: Translational Oncology
https://www.readbyqxmd.com/read/29682831/characterization-of-dcl4-missense-alleles-provides-insights-into-its-ability-to-process-distinct-classes-of-dsrna-substrates
#17
Thomas Montavon, Yerim Kwon, Aude Zimmermann, Philippe Hammann, Timothée Vincent, Valérie Cognat, Marc Bergdoll, Fabrice Michel, Patrice Dunoyer
In the model plant Arabidopsis thaliana, four Dicer-like proteins (DCL1-4) mediate the production of various classes of small RNAs (sRNAs). Among these four proteins, DCL4 is by far the most versatile RNaseIII-like enzyme and previously identified dcl4 missense alleles were shown to uncouple the production of the various classes of DCL4-dependent sRNAs. Yet, little is known about the molecular mechanism pertaining this uncoupled production. Here, by studying the subcellular localization, interactome and binding to the sRNA precursors of three distinct dcl4 missense alleles, we simultaneously highlight the absolute requirement of a specific residue in its helicase domain for efficient production of all DCL4-dependent sRNAs, and identify, within its PAZ domain, an important determinant of DCL4 versatility that is mandatory for efficient processing of intramolecular foldback dsRNA precursors but dispensable for the production of siRNAs from RDR-dependent dsRNA susbtrates...
April 22, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29679569/ddx1-regulates-alternative-splicing-and-insulin-secretion-in-pancreatic-%C3%AE-cells
#18
Wen Zhong, Zonghong Li, Maoge Zhou, Tao Xu, You Wang
DEAD-box helicase 1 (DDX1) is a multifunction protein involved in diverse cellular processes including transcription, viral replication, mRNA/miRNA processing, and tRNA splicing. Here, we report a novel function of DDX1 in mRNA alternative splicing in pancreatic β cells. By performing integrated data analysis of high-throughput RNA sequencing (RNA-Seq), and cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq), we identify hundreds of alternative splicing genes that are targeted by DDX1...
June 7, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29677479/rig-i-and-other-rna-sensors-in-antiviral-immunity
#19
Kwan T Chow, Michael Gale, Yueh-Ming Loo
Pattern recognition receptors (PRRs) survey intra- and extracellular spaces for pathogen-associated molecular patterns (PAMPs) within microbial products of infection. Recognition and binding to cognate PAMP ligand by specific PRRs initiates signaling cascades that culminate in a coordinated intracellular innate immune response designed to control infection. In particular, our immune system has evolved specialized PRRs to discriminate viral nucleic acid from host. These are critical sensors of viral RNA to trigger innate immunity in the vertebrate host...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29676248/rnase-e-and-the-high-fidelity-orchestration-of-rna-metabolism
#20
Katarzyna J Bandyra, Ben F Luisi
The bacterial endoribonuclease RNase E occupies a pivotal position in the control of gene expression, as its actions either commit transcripts to an irreversible fate of rapid destruction or unveil their hidden functions through specific processing. Moreover, the enzyme contributes to quality control of rRNAs. The activity of RNase E can be directed and modulated by signals provided through regulatory RNAs that guide the enzyme to specific transcripts that are to be silenced. Early in its evolutionary history, RNase E acquired a natively unfolded appendage that recruits accessory proteins and RNA...
April 2018: Microbiology Spectrum
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