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Nucleic Acids Research

Zhifeng Wang, Yamin Gong, Bin Peng, Ruifeng Shi, Dan Fan, Hongchang Zhao, Min Zhu, Haoxing Zhang, Zhenkun Lou, Jianwei Zhou, Wei-Guo Zhu, Yu-Sheng Cong, Xingzhi Xu
A proper DNA damage response (DDR) is essential to maintain genome integrity and prevent tumorigenesis. DNA double-strand breaks (DSBs) are the most toxic DNA lesion and their repair is orchestrated by the ATM kinase. ATM is activated via the MRE11-RAD50-NBS1 (MRN) complex along with its autophosphorylation at S1981 and acetylation at K3106. Activated ATM rapidly phosphorylates a vast number of substrates in local chromatin, providing a scaffold for the assembly of higher-order complexes that can repair damaged DNA...
February 20, 2019: Nucleic Acids Research
Xiankun Cheng, Yanxiang Zhao, Qingshan Jiang, Jun Yang, Wensheng Zhao, Ian A Taylor, You-Liang Peng, Dongli Wang, Junfeng Liu
In rice, the critical regulator of the salicylic acid signalling pathway is OsWRKY45, a transcription factor (TF) of the WRKY TF family that functions by binding to the W-box of gene promoters, but the structural basis of OsWRKY45/W-box DNA recognition is unknown. Here, we show the crystal structure of the DNA binding domain of OsWRKY45 (OsWRKY45-DBD, i.e. the WRKY and zinc finger domain) in complex with a W-box DNA. Surprisingly, two OsWRKY45-DBD molecules exchange β4-β5 strands to form a dimer. The domain swapping occurs at the hinge region between the β3 and β4 strands, and is bridged and stabilized by zinc ion via coordinating residues from different chains...
February 20, 2019: Nucleic Acids Research
Yang Liao, Gordon K Smyth, Wei Shi
We present Rsubread, a Bioconductor software package that provides high-performance alignment and read counting functions for RNA-seq reads. Rsubread is based on the successful Subread suite with the added ease-of-use of the R programming environment, creating a matrix of read counts directly as an R object ready for downstream analysis. It integrates read mapping and quantification in a single package and has no software dependencies other than R itself. We demonstrate Rsubread's ability to detect exon-exon junctions de novo and to quantify expression at the level of either genes, exons or exon junctions...
February 20, 2019: Nucleic Acids Research
Hyeon J Lee, Ramu Gopalappa, Hongjae Sunwoo, Seo-Won Choi, Suresh Ramakrishna, Jeannie T Lee, Hyongbum H Kim, Jin-Wu Nam
The XIST RNA is a non-coding RNA that induces X chromosome inactivation (XCI). Unlike the mouse Xist RNA, how the human XIST RNA controls XCI in female cells is less well characterized, and its functional motifs remain unclear. To systematically decipher the XCI-involving elements of XIST RNA, 11 smaller XIST segments, including repeats A, D and E; human-specific repeat elements; the promoter; and non-repetitive exons, as well as the entire XIST gene, were homozygously deleted in K562 cells using the Cas9 nuclease and paired guide RNAs at high efficiencies, followed by high-throughput RNA sequencing and RNA fluorescence in situ hybridization experiments...
February 20, 2019: Nucleic Acids Research
Pradip K Biswas, Sandipan Chakraborty
Molecular insight into electronic rearrangements and structural trajectories arising from oxidative damages to DNA backbone is of crucial importance in understanding the effect of ionizing radiation, developing DNA biosensors and designing effective DNA cleaving molecules. Employing a Density Functional Theory based multi-scale Quantum-Mechanical-Molecular-Mechanical (QM/MM) simulation and a suitable partitioning of the Hamiltonian on solvated nucleotide, and single-, and double-stranded DNA, we mimic hydrogen transfer reactions from the backbone by OH radicals and report structural trajectories arising from on-the-fly electronic charge- and spin-density redistribution in these three different structural topologies of DNA...
February 18, 2019: Nucleic Acids Research
Tanmoy Roychowdhury, Alexej Abyzov
Structural variations (SVs) in the human genome originate from different mechanisms related to DNA repair, replication errors, and retrotransposition. Our analyses of 26 927 SVs from the 1000 Genomes Project revealed differential distributions and consequences of SVs of different origin, e.g. deletions from non-allelic homologous recombination (NAHR) are more prone to disrupt chromatin organization while processed pseudogenes can create accessible chromatin. Spontaneous double stranded breaks (DSBs) are the best predictor of enrichment of NAHR deletions in open chromatin...
February 18, 2019: Nucleic Acids Research
Zhiqun Shang, Jianpeng Yu, Libin Sun, Jing Tian, Shimiao Zhu, Boya Zhang, Qian Dong, Ning Jiang, Amilcar Flores-Morales, Chawnshang Chang, Yuanjie Niu
In PTEN-deficient prostate cancers, AKT signaling may be activated upon suppression of androgen receptor signaling. Activation of AKT as well as NF-κB signaling involves a key regulatory protein complex containing PHLPP, FKBP51 and IKKα. Here, we report a critical role of lncRNA PCAT1 in regulating the PHLPP/FKBP51/IKKα complex and progression of castration-resistant prostate cancer (CRPC). Using database queries, bioinformatic analyses, as well as RIP and RNA pull-down assays, we discovered and validated that the lncRNA-PCAT1 perturbs the PHLPP/FKBP51/IKKα complex and activates AKT and NF-κB signaling...
February 18, 2019: Nucleic Acids Research
Yi Han, Juze Yang, Xinyi Qian, Wei-Chung Cheng, Shu-Hsuan Liu, Xing Hua, Liyuan Zhou, Yaning Yang, Qingbiao Wu, Pengyuan Liu, Yan Lu
Although rapid progress has been made in computational approaches for prioritizing cancer driver genes, research is far from achieving the ultimate goal of discovering a complete catalog of genes truly associated with cancer. Driver gene lists predicted from these computational tools lack consistency and are prone to false positives. Here, we developed an approach (DriverML) integrating Rao's score test and supervised machine learning to identify cancer driver genes. The weight parameters in the score statistics quantified the functional impacts of mutations on the protein...
February 18, 2019: Nucleic Acids Research
Shuyi Zhao, Yayue Chen, Feng Chen, Delai Huang, Hui Shi, Li Jan Lo, Jun Chen, Jinrong Peng
Mpp10 forms a complex with Imp3 and Imp4 that serves as a core component of the ribosomal small subunit (SSU) processome. Mpp10 also interacts with the nucleolar protein Sas10/Utp3. However, it remains unknown how the Mpp10-Imp3-Imp4 complex is delivered to the nucleolus and what biological function the Mpp10-Sas10 complex plays. Here, we report that the zebrafish Mpp10 and Sas10 are conserved nucleolar proteins essential for the development of the digestive organs. Mpp10, but not Sas10/Utp3, is a target of the nucleolus-localized Def-Capn3 protein degradation pathway...
February 18, 2019: Nucleic Acids Research
Suryasree Subramania, Laurence M Gagné, Sébastien Campagne, Victoire Fort, Julia O'Sullivan, Karel Mocaer, Miki Feldmüller, Jean-Yves Masson, Frédéric H T Allain, Samer M Hussein, Marc-Étienne Huot
Src associated in mitosis (SAM68) plays major roles in regulating RNA processing events, such as alternative splicing and mRNA translation, implicated in several developmental processes. It was previously shown that SAM68 regulates the alternative splicing of the mechanistic target of rapamycin (mTor), but the mechanism regulating this process remains elusive. Here, we report that SAM68 interacts with U1 small nuclear ribonucleoprotein (U1 snRNP) to promote splicing at the 5' splice site in intron 5 of mTor...
February 15, 2019: Nucleic Acids Research
Zhenghui Lu, Shihui Yang, Xin Yuan, Yunyun Shi, Li Ouyang, Sijing Jiang, Li Yi, Guimin Zhang
Fine-tuning of gene expression is crucial for protein expression and pathway construction, but it still faces formidable challenges due to the hierarchical gene regulation at multiple levels in a context-dependent manner. In this study, we defined the optimal targeting windows for CRISPRa and CRISPRi of the dCas9-α/ω system, and demonstrated that this system could act as a single master regulator to simultaneously activate and repress the expression of different genes by designing position-specific gRNAs...
February 15, 2019: Nucleic Acids Research
Mauro Eric, Lesbats Paul, Lapaillerie Delphine, Chaignepain Stephane, Maillot Benoit, Oladosu Oyindamola, Robert Xavier, Fiorini Francesca, Kieffer Bruno, Bouaziz Serge, Gouet Patrice, Ruff Marc, Parissi Vincent
The integration of the retroviral genome into the chromatin of the infected cell is catalysed by the integrase (IN)•viral DNA complex (intasome). This process requires functional association between the integration complex and the nucleosomes. Direct intasome/histone contacts have been reported to modulate the interaction between the integration complex and the target DNA (tDNA). Both prototype foamy virus (PFV) and HIV-1 integrases can directly bind histone amino-terminal tails. We have further investigated this final association by studying the effect of isolated histone tails on HIV-1 integration...
February 15, 2019: Nucleic Acids Research
Ryan C Heller, Suhman Chung, Katarzyna Crissy, Kyle Dumas, David Schuster, Thomas W Schoenfeld
Reverse transcription is an essential initial step in the analysis of RNA for most PCR-based amplification and detection methods. Despite advancements in these technologies, efficient conversion of RNAs that form stable secondary structures and double-stranded RNA targets remains challenging as retroviral-derived reverse transcriptases are often not sufficiently thermostable to catalyze synthesis at temperatures high enough to completely relax these structures. Here we describe the engineering and improvement of a thermostable viral family A polymerase with inherent reverse transcriptase activity for use in RT-PCR...
February 15, 2019: Nucleic Acids Research
Lisanne M Spenkelink, Jacob S Lewis, Slobodan Jergic, Zhi-Qiang Xu, Andrew Robinson, Nicholas E Dixon, Antoine M van Oijen
Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the replisome that is much more complex in how it retains or recycles protein components. Here, we visualize how an in vitro reconstituted Escherichia coli replisome recruits SSB by relying on two different molecular mechanisms...
February 15, 2019: Nucleic Acids Research
Qianqian Zhai, Chao Gao, Jieqin Ding, Yashu Zhang, Barira Islam, Wenxian Lan, Haitao Hou, Hua Deng, Jun Li, Zhe Hu, Hany I Mohamed, Shengzhen Xu, Chunyang Cao, Shozeb M Haider, Dengguo Wei
Nucleic acid mimics of fluorescent proteins can be valuable tools to locate and image functional biomolecules in cells. Stacking between the internal G-quartet, formed in the mimics, and the exogenous fluorophore probes constitutes the basis for fluorescence emission. The precision of recognition depends upon probes selectively targeting the specific G-quadruplex in the mimics. However, the design of probes recognizing a G-quadruplex with high selectivity in vitro and in vivo remains a challenge. Through structure-based screening and optimization, we identified a light-up fluorescent probe, 9CI that selectively recognizes c-MYC Pu22 G-quadruplex both in vitro and ex vivo...
February 13, 2019: Nucleic Acids Research
Jennifer Beauvarlet, Paul Bensadoun, Elodie Darbo, Gaelle Labrunie, Benoît Rousseau, Elodie Richard, Irena Draskovic, Arturo Londono-Vallejo, Jean-William Dupuy, Rabindra Nath Das, Aurore Guédin, Guillaume Robert, Francois Orange, Sabrina Croce, Valerie Valesco, Pierre Soubeyran, Kevin M Ryan, Jean-Louis Mergny, Mojgan Djavaheri-Mergny
G-quadruplex ligands exert their antiproliferative effects through telomere-dependent and telomere-independent mechanisms, but the inter-relationships among autophagy, cell growth arrest and cell death induced by these ligands remain largely unexplored. Here, we demonstrate that the G-quadruplex ligand 20A causes growth arrest of cancer cells in culture and in a HeLa cell xenografted mouse model. This response is associated with the induction of senescence and apoptosis. Transcriptomic analysis of 20A treated cells reveals a significant functional enrichment of biological pathways related to growth arrest, DNA damage response and the lysosomal pathway...
February 13, 2019: Nucleic Acids Research
Balveer Singh, Kamlesh K Bisht, Udita Upadhyay, Avinash Chandra Kushwaha, Jagpreet Singh Nanda, Suchita Srivastava, Jai Kumar Saini, Amar J S Klar, Jagmohan Singh
The developmental asymmetry of fission yeast daughter cells derives from inheriting 'older Watson' versus 'older Crick' DNA strand from the parental cell, strands that are complementary but not identical with each other. A novel DNA strand-specific 'imprint', installed during DNA replication at the mating-type locus (mat1), imparts competence for cell type inter-conversion to one of the two chromosome replicas. The catalytic subunit of DNA Polymerase α (Polα) has been implicated in the imprinting process...
February 13, 2019: Nucleic Acids Research
Bryan W Dorsey, Lei Huang, Alfonso Mondragón
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas proteins provide an immune-like response in many prokaryotes against extraneous nucleic acids. CRISPR-Cas systems are classified into different classes and types. Class 1 CRISPR-Cas systems form multi-protein effector complexes that includes a guide RNA (crRNA) used to identify the target for destruction. Here we present crystal structures of Staphylococcus epidermidis Type III-A CRISPR subunits Csm2 and Csm3 and a 5...
February 13, 2019: Nucleic Acids Research
Keiichi Izumikawa, Yuko Nobe, Hideaki Ishikawa, Yoshio Yamauchi, Masato Taoka, Ko Sato, Hiroshi Nakayama, Richard J Simpson, Toshiaki Isobe, Nobuhiro Takahashi
TDP-43 regulates cellular levels of Cajal bodies (CBs) that provide platforms for the assembly and RNA modifications of small nuclear ribonucleoproteins (snRNPs) involved in pre-mRNA splicing. Alterations in these snRNPs may be linked to pathogenesis of amyotrophic lateral sclerosis. However, specific roles for TDP-43 in CBs remain unknown. Here, we demonstrate that TDP-43 regulates the CB localization of four UG-rich motif-bearing C/D-box-containing small Cajal body-specific RNAs (C/D scaRNAs; i.e. scaRNA2, 7, 9 and 28) through the direct binding to these scaRNAs...
February 13, 2019: Nucleic Acids Research
Alexander R Gawronski, Yen-Yi Lin, Brian McConeghy, Stephane LeBihan, Hossein Asghari, Can Koçkan, Baraa Orabi, Nabil Adra, Roberto Pili, Colin C Collins, S Cenk Sahinalp, Faraz Hach
Motivation: Cancer is a complex disease that involves rapidly evolving cells, often forming multiple distinct clones. In order to effectively understand progression of a patient-specific tumor, one needs to comprehensively sample tumor DNA at multiple time points, ideally obtained through inexpensive and minimally invasive techniques. Current sequencing technologies make the 'liquid biopsy' possible, which involves sampling a patient's blood or urine and sequencing the circulating cell free DNA (cfDNA)...
February 13, 2019: Nucleic Acids Research
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