Volume 47, Issue 17, 26 September 2019

NAR Breakthrough Article

CtIP is essential for telomere replication

Susanna Stroik and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 8927–8940, https://doi.org/10.1093/nar/gkz652

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Chemical Biology and Nucleic Acid Chemistry

DNA polymerase activity on synthetic N3′→P5′ phosphoramidate DNA templates

Victor S Lelyveld and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 8941–8949, https://doi.org/10.1093/nar/gkz707

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Systematic minimization of RNA ligase ribozyme through large-scale design-synthesis-sequence cycles

Yoko Nomura and Yohei Yokobayashi

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 8950–8960, https://doi.org/10.1093/nar/gkz729

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Computational Biology

Reconstructing complex lineage trees from scRNA-seq data using MERLoT

R Gonzalo Parra and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 8961–8974, https://doi.org/10.1093/nar/gkz706

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Gene Regulation, Chromatin and Epigenetics

RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit

Paula Allepuz-Fuster and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 8975–8987, https://doi.org/10.1093/nar/gkz597

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Functional interplay between Mediator and RNA polymerase II in Rad2/XPG loading to the chromatin

Adrien Georges and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 8988–9004, https://doi.org/10.1093/nar/gkz598

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KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity

Anne H Turberfield and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9005–9023, https://doi.org/10.1093/nar/gkz607

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The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation

Jered M Wendte and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9024–9036, https://doi.org/10.1093/nar/gkz615

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The NRPD1 N-terminus contains a Pol IV-specific motif that is critical for genome surveillance in Arabidopsis

Laura Ferrafiat and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9037–9052, https://doi.org/10.1093/nar/gkz618

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SET8 prevents excessive DNA methylation by methylation-mediated degradation of UHRF1 and DNMT1

Huifang Zhang and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9053–9068, https://doi.org/10.1093/nar/gkz626

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Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2

Filippo M Cernilogar and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9069–9086, https://doi.org/10.1093/nar/gkz627

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DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation

Sigrid Uxa and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9087–9103, https://doi.org/10.1093/nar/gkz635

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Post-transcriptional gene silencing triggers dispensable DNA methylation in gene body in Arabidopsis

Christelle Taochy and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9104–9114, https://doi.org/10.1093/nar/gkz636

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SIRT6 transcriptionally regulates global protein synthesis through transcription factor Sp1 independent of its deacetylase activity

Venkatraman Ravi and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9115–9131, https://doi.org/10.1093/nar/gkz648

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Genome Integrity, Repair and Replication

Synthetic lethality between BRCA1 deficiency and poly(ADP-ribose) polymerase inhibition is modulated by processing of endogenous oxidative DNA damage

Sara Giovannini and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9132–9143, https://doi.org/10.1093/nar/gkz624

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Rad5 dysregulation drives hyperactive recombination at replication forks resulting in cisplatin sensitivity and genome instability

Eric E Bryant and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9144–9159, https://doi.org/10.1093/nar/gkz631

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CTCF cooperates with CtIP to drive homologous recombination repair of double-strand breaks

Soon Young Hwang and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9160–9179, https://doi.org/10.1093/nar/gkz639

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Trypanosoma brucei ribonuclease H2A is an essential R-loop processing enzyme whose loss causes DNA damage during transcription initiation and antigenic variation

Emma Briggs and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9180–9197, https://doi.org/10.1093/nar/gkz644

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Bacillus subtilis RecA interacts with and loads RadA/Sms to unwind recombination intermediates during natural chromosomal transformation

Rubén Torres and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9198–9215, https://doi.org/10.1093/nar/gkz647

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Genomics

RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4

Vinay K Nagarajan and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9216–9230, https://doi.org/10.1093/nar/gkz712

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Molecular Biology

Adenovirus major core protein condenses DNA in clusters and bundles, modulating genome release and capsid internal pressure

Natalia Martín-González and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9231–9242, https://doi.org/10.1093/nar/gkz687

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eRF1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons

Qian Yang and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9243–9258, https://doi.org/10.1093/nar/gkz710

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Nucleic Acid Enzymes

Cyclic oligoadenylate signalling mediates Mycobacterium tuberculosis CRISPR defence

Sabine Grüschow and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9259–9270, https://doi.org/10.1093/nar/gkz676

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TrmB, a tRNA m⁷G46 methyltransferase, plays a role in hydrogen peroxide resistance and positively modulates the translation of katA and katB mRNAs in Pseudomonas aeruginosa

Narumon Thongdee and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9271–9281, https://doi.org/10.1093/nar/gkz702

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RNA and RNA-protein complexes

A low-complexity region in human XRN1 directly recruits deadenylation and decapping factors in 5′–3′ messenger RNA decay

Chung-Te Chang and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9282–9295, https://doi.org/10.1093/nar/gkz633

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Structural and phenotypic analysis of Chikungunya virus RNA replication elements

Catherine Kendall and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9296–9312, https://doi.org/10.1093/nar/gkz640

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Staufen1 and UPF1 exert opposite actions on the replacement of the nuclear cap-binding complex by eIF4E at the 5′ end of mRNAs

Kwon Jeong and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9313–9328, https://doi.org/10.1093/nar/gkz643

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A 212-nt long RNA structure in the Tobacco necrosis virus-D RNA genome is resistant to Xrn degradation

Chaminda D Gunawardene and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9329–9342, https://doi.org/10.1093/nar/gkz668

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Highly efficacious antiviral protection of plants by small interfering RNAs identified in vitro

Selma Gago-Zachert and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9343–9357, https://doi.org/10.1093/nar/gkz678

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Impacts of uORF codon identity and position on translation regulation

Yizhu Lin and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9358–9367, https://doi.org/10.1093/nar/gkz681

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KSHV RNA-binding protein ORF57 inhibits P-body formation to promote viral multiplication by interaction with Ago2 and GW182

Nishi R Sharma and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9368–9385, https://doi.org/10.1093/nar/gkz683

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C6orf203 is an RNA-binding protein involved in mitochondrial protein synthesis

Shreekara Gopalakrishna and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9386–9399, https://doi.org/10.1093/nar/gkz684

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Structural Biology

Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome

Sagar Chittori and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9400–9409, https://doi.org/10.1093/nar/gkz670

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Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2′-guanosine

Andrea M Kaminski and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9410–9422, https://doi.org/10.1093/nar/gkz680

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Structural basis of σ appropriation

Jing Shi and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9423–9432, https://doi.org/10.1093/nar/gkz682

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The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions

Lilia Kaustov and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9433–9447, https://doi.org/10.1093/nar/gkz697

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Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage

Carl J Schiltz and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9448–9463, https://doi.org/10.1093/nar/gkz703

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Corrigendum

The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t⁶A tRNA-modification

Sophia Missoury and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Pages 9464–9465, https://doi.org/10.1093/nar/gkz719

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Methods Online

Achieving tight control of a photoactivatable Cre recombinase gene switch: new design strategies and functional characterization in mammalian cells and rodent

Kyle Meador and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Page e97, https://doi.org/10.1093/nar/gkz585

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coMethDMR: accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies with continuous phenotypes

Lissette Gomez and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Page e98, https://doi.org/10.1093/nar/gkz590

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Delivering Cas9/sgRNA ribonucleoprotein (RNP) by lentiviral capsid-based bionanoparticles for efficient ‘hit-and-run’ genome editing

Pin Lyu and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Page e99, https://doi.org/10.1093/nar/gkz605

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Ultra-soft X-ray system for imaging the early cellular responses to X-ray induced DNA damage

Jakub A Kochan and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Page e100, https://doi.org/10.1093/nar/gkz609

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Single-molecule detection of deoxyribonucleoside triphosphates in microdroplets

Boris Breiner and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Page e101, https://doi.org/10.1093/nar/gkz611

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Novel enzymatic single-nucleotide modification of DNA oligomer: prevention of incessant incorporation of nucleotidyl transferase by ribonucleotide-borate complex

Eui Kyoung Jang and others

Nucleic Acids Research, Volume 47, Issue 17, 26 September 2019, Page e102, https://doi.org/10.1093/nar/gkz612

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