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Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles

15.09.2013 | Prabhat K. Mandal; Adam D. Ewing; Dustin C. Hancks; Haig H. Kazazian, Jr, Human Molecular Genetics, 2013

Long INterspersed Elements (LINE-1s, L1s) are responsible for over one million retrotransposon insertions and 8000 processed pseudogenes (PPs) in the human genome. An active L1 encodes two proteins (ORF1p and ORF2p) that bind with L1 RNA and form L1-ribonucleoprotein particles (RNPs). Although it ...

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Small RNA sX13: A Multifaceted Regulator of Virulence in the Plant Pathogen Xanthomonas

12.09.2013 | Cornelius Schmidtke et al., PLoS Pathogens, 2013

by Cornelius Schmidtke, Ulrike Abendroth, Juliane Brock, Javier Serrania, Anke Becker, Ulla Bonas Small noncoding RNAs (sRNAs) are ubiquitous posttranscriptional regulators of gene expression. Using the model plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv), we ...

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TLR7 signaling exacerbates CNS autoimmunity through downregulation of Foxp3+ Treg cells

10.09.2013 | Patrice H. Lalive, Mahdia Benkhoucha, Ngoc Lan Tran, Mario Kreutzfeldt, Doron Merkler, Marie‐Laure Santiago‐Raber, European Journal of Immunology, 2013

Abstract The innate Toll‐like receptor 7 (TLR7) detects infections by recognizing viral and bacterial single‐stranded RNA. In addition to pathogen‐derived RNA, immune cells expressing high levels of TLR7, such as B cells and dendritic cells (DCs), can be activated by self‐RNA. During ...

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Type I-E CRISPR-Cas Systems Discriminate Target from Non-Target DNA through Base Pairing-Independent PAM Recognition

05.09.2013 | Edze R. Westra et al., PLoS Genetics, 2013

by Edze R. Westra, Ekaterina Semenova, Kirill A. Datsenko, Ryan N. Jackson, Blake Wiedenheft, Konstantin Severinov, Stan J. J. Brouns Discriminating self and non-self is a universal requirement of immune systems. Adaptive immune systems in prokaryotes are centered around repetitive loci called ...

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Progressive impairment of muscle regeneration in muscleblind-like 3 isoform knockout mice

01.09.2013 | Michael G. Poulos; Ranjan Batra; Moyi Li; Yuan Yuan; Chaolin Zhang; Robert B. Darnell; Maurice S. Swanson, Human Molecular Genetics, 2013

The muscleblind-like (MBNL) genes encode alternative splicing factors that are essential for the postnatal development of multiple tissues, and the inhibition of MBNL activity by toxic C(C)UG repeat RNAs is a major pathogenic feature of the neuromuscular disease myotonic dystrophy. While MBNL1 ...

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Predicted group II intron lineages E and F comprise catalytically active ribozymes [ARTICLES]

01.09.2013 | Vivien Nagy; Nathan Pirakitikulr; Katherine Ismei Zhou; Isabel Chillón; Jerome Luo; Anna Marie Pyle, RNA, 2013

Group II introns are self-splicing, retrotransposable ribozymes that contribute to gene expression and evolution in most organisms. The ongoing identification of new group II introns and recent bioinformatic analyses have suggested that there are novel lineages, which include the group IIE and ...

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Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA [ARTICLES]

01.09.2013 | Hui Zhang; James A. Endrizzi; Yi Shu; Farzin Haque; Claude Sauter; Lyudmila S. Shlyakhtenko; Yuri Lyubchenko; Peixua ..., RNA, 2013

The bacteriophage phi29 DNA packaging motor, one of the strongest biological motors characterized to date, is geared by a packaging RNA (pRNA) ring. When assembled from three RNA fragments, its three-way junction (3WJ) motif is highly thermostable, is resistant to 8 M urea, and remains associated ...

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A Phylogenetic Model for the Detection of Epistatic Interactions

01.09.2013 | Chris A. Nasrallah; John P. Huelsenbeck, Molecular Biology and Evolution, 2013

Paired epistatic interactions, such as those in the stem regions of RNA, play an important role in many biological processes. However, unlike protein-coding regions, paired epistatic interactions have lacked the appropriate statistical tools for the detection of departures from selective ...

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Genome-Wide Analysis Reveals Origin of Transfer RNA Genes from tRNA Halves

01.09.2013 | Zhixiang Zuo; Duo Peng; Xiujuan Yin; Xiang Zhou; Hanhua Cheng; Rongjia Zhou, Molecular Biology and Evolution, 2013

Transfer RNAs (tRNAs) play an important role linking mitochondrial RNA and amino acids during protein biogenesis. Four types of tRNA genes have been identified in living organisms. However, the evolutionary origin of tRNAs remains largely unknown. In this article, we conduct a deep sequence ...

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Stabilization of duplex DNA and RNA by dangling ends studied by free energy simulations

27.08.2013 | Mahmut Kara, Martin Zacharias, Biopolymers, 2013

Abstract Single unpaired nucleotides at the end of double‐stranded nucleic acids, termed dangling ends, can contribute to duplex stability. Umbrella sampling free energy simulations of dangling cytosine and guanine nucleotides at the end of duplex and single stranded RNA and DNA molecules have ...

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