Volume 43; Issue 1

Main
Nucleic Acids Research
Volume 43; Issue 1

Nucleic Acids Research

Volume 43; Issue 1

1

Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression

Luo, M. L., Mullis, A. S., Leenay, R. T., Beisel, C. L.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 434 KB

english, 2015

2

Efficient programmable gene silencing by Cascade

Rath, D., Amlinger, L., Hoekzema, M., Devulapally, P. R., Lundgren, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.17 MB

english, 2015

3

Rho and RNase play a central role in FMN riboswitch regulation in Corynebacterium glutamicum

Takemoto, N., Tanaka, Y., Inui, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 734 KB

english, 2015

4

CRISPR RNA binding and DNA target recognition by purified Cascade complexes from Escherichia coli

Beloglazova, N., Kuznedelov, K., Flick, R., Datsenko, K. A., Brown, G., Popovic, A., Lemak, S., Semenova, E., Severinov, K., Yakunin, A. F.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.89 MB

english, 2015

5

An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments

Heyer, E. E., Ozadam, H., Ricci, E. P., Cenik, C., Moore, M. J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.87 MB

english, 2015

6

Meclofenamic acid selectively inhibits FTO demethylation of m6A over ALKBH5

Huang, Y., Yan, J., Li, Q., Li, J., Gong, S., Zhou, H., Gan, J., Jiang, H., Jia, G.-F., Luo, C., Yang, C.-G.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.44 MB

english, 2015

7

A new heavy lanthanide-dependent DNAzyme displaying strong metal cooperativity and unrescuable phosphorothioate effect

Huang, P.-J. J., Vazin, M., Matuszek, Z., Liu, J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.44 MB

english, 2015

8

Structural basis for the interaction of protein S1 with the Escherichia coli ribosome

Byrgazov, K., Grishkovskaya, I., Arenz, S., Coudevylle, N., Temmel, H., Wilson, D. N., Djinovic-Carugo, K., Moll, I.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.78 MB

english, 2015

9

A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy

Garcia-Sacristan, A., Moreno, M., Ariza-Mateos, A., Lopez-Camacho, E., Jaudenes, R. M., Vazquez, L., Gomez, J., Martin-Gago, J. A., Briones, C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.50 MB

english, 2015

10

The association of late-acting snoRNPs with human pre-ribosomal complexes requires the RNA helicase DDX21

Sloan, K. E., Leisegang, M. S., Doebele, C., Ramirez, A. S., Simm, S., Safferthal, C., Kretschmer, J., Schorge, T., Markoutsa, S., Haag, S., Karas, M., Ebersberger, I., Schleiff, E., Watkins, N. J., B

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.58 MB

english, 2015

11

Small antisense oligonucleotides against G-quadruplexes: specific mRNA translational switches

Rouleau, S. G., Beaudoin, J.-D., Bisaillon, M., Perreault, J.-P.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.45 MB

english, 2015

12

Conformation transitions of eukaryotic polyribosomes during multi-round translation

Afonina, Z. A., Myasnikov, A. G., Shirokov, V. A., Klaholz, B. P., Spirin, A. S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.14 MB

english, 2015

13

An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference

Peng, W., Feng, M., Feng, X., Liang, Y. X., She, Q.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.98 MB

english, 2015

14

High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4

Yamaichi, Y., Chao, M. C., Sasabe, J., Clark, L., Davis, B. M., Yamamoto, N., Mori, H., Kurokawa, K., Waldor, M. K.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.48 MB

english, 2015

15

Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD

Davis, E., Chen, J., Leon, K., Darst, S. A., Campbell, E. A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.04 MB

english, 2015

16

Nucleic Acids Research: VOLUME 43 ISSUE 1 2015

Journal:

Nucleic Acids Research

Year:

2015

File:

PDF, 4.09 MB

2015

17

Topological constraints strongly affect chromatin reconstitution in silico

Brackley, C. A., Allan, J., Keszenman-Pereyra, D., Marenduzzo, D.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.54 MB

english, 2015

18

Multiple roles of the coding sequence 5' end in gene expression regulation

Tuller, T., Zur, H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.54 MB

english, 2015

19

The high mobility group A2 protein epigenetically silences the Cdh1 gene during epithelial-to-mesenchymal transition

Tan, E.-J., Kahata, K., Idas, O., Thuault, S., Heldin, C.-H., Moustakas, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.48 MB

english, 2015

20

Subgenomic promoter recognition by the norovirus RNA-dependent RNA polymerases

Lin, X., Thorne, L., Jin, Z., Hammad, L. A., Li, S., Deval, J., Goodfellow, I. G., Kao, C. C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.66 MB

english, 2015

21

A common set of distinct features that characterize noncoding RNAs across multiple species

Hu, L., Di, C., Kai, M., Yang, Y.-C. T., Li, Y., Qiu, Y., Hu, X., Yip, K. Y., Zhang, M. Q., Lu, Z. J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.13 MB

english, 2015

22

LKB1 preserves genome integrity by stimulating BRCA1 expression

Gupta, R., Liu, A. Y., Glazer, P. M., Wajapeyee, N.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1013 KB

english, 2015

23

Novel RNA chaperone domain of RNA-binding protein La is regulated by AKT phosphorylation

Kuehnert, J., Sommer, G., Zierk, A. W., Fedarovich, A., Brock, A., Fedarovich, D., Heise, T.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.39 MB

english, 2015

24

Extendable blocking probe in reverse transcription for analysis of RNA variants with superior selectivity

Ho, T. H., Dang, K. X., Lintula, S., Hotakainen, K., Feng, L., Olkkonen, V. M., Verschuren, E. W., Tenkanen, T., Haglund, C., Kolho, K.-L., Stenman, U.-H., Stenman, J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 781 KB

english, 2015

25

A novel RNA molecular signature for activation of 2'-5' oligoadenylate synthetase-1

Vachon, V. K., Calderon, B. M., Conn, G. L.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.56 MB

english, 2015

26

Specific recognition of guanines in non-duplex regions of nucleic acids with potassium tungstate and hydrogen peroxide

Mao, W., Xu, X., He, H., Huang, R., Chen, X., Xiao, H., Yu, Z., Liu, Y., Zhou, X.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.46 MB

english, 2015

27

Identifying causal regulatory SNPs in ChIP-seq enhancers

Huang, D., Ovcharenko, I.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.94 MB

english, 2015

28

ARTD1-induced poly-ADP-ribose formation enhances PPAR ligand binding and co-factor exchange

Lehmann, M., Pirinen, E., Mirsaidi, A., Kunze, F. A., Richards, P. J., Auwerx, J., Hottiger, M. O.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.95 MB

english, 2015

29

Multilayer regulatory mechanisms control cleavage factor I proteins in filamentous fungi

Rodriguez-Romero, J., Franceschetti, M., Bueno, E., Sesma, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.17 MB

english, 2015

30

Adhesin competence repressor (AdcR) from Streptococcus pyogenes controls adaptive responses to zinc limitation and contributes to virulence

Sanson, M., Makthal, N., Flores, A. R., Olsen, R. J., Musser, J. M., Kumaraswami, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.96 MB

english, 2015

31

Nucleic Acids Research: Editorial Board

Journal:

Nucleic Acids Research

Year:

2015

File:

PDF, 1.04 MB

2015

32

Depletion of REF/Aly alters gene expression and reduces RNA polymerase II occupancy

Stubbs, S. H., Conrad, N. K.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.00 MB

english, 2015

33

Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA

Buyst, D., Gheerardijn, V., Feher, K., Van Gasse, B., Van Den Begin, J., Martins, J. C., Madder, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.16 MB

english, 2015

34

DEEP: a general computational framework for predicting enhancers

Kleftogiannis, D., Kalnis, P., Bajic, V. B.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.38 MB

english, 2015

35

Bi-specific splice-switching PMO oligonucleotides conjugated via a single peptide active in a mouse model of Duchenne muscular dystrophy

Shabanpoor, F., McClorey, G., Saleh, A. F., Jarver, P., Wood, M. J. A., Gait, M. J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.59 MB

english, 2015

36

Mg2+-dependent conformational changes and product release during DNA-catalyzed RNA ligation monitored by Bimane fluorescence

Turriani, E., Hobartner, C., Jovin, T. M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.11 MB

english, 2015

37

The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli

Srinivasan, R., Scolari, V. F., Lagomarsino, M. C., Seshasayee, A. S. N.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.86 MB

english, 2015

38

Operator recognition by the ROK transcription factor family members, NagC and Mlc

Brechemier-Baey, D., Dominguez-Ramirez, L., Oberto, J., Plumbridge, J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.16 MB

english, 2015

39

Regulation of anti-sense transcription by Mot1p and NC2 via removal of TATA-binding protein (TBP) from the 3'-end of genes

Koster, M. J. E., Timmers, H. T. M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.90 MB

english, 2015

40

Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs

Zheng, Y., Li, X., Hu, H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.58 MB

english, 2015

41

Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition

Kuznetsov, N. A., Bergonzo, C., Campbell, A. J., Li, H., Mechetin, G. V., de los Santos, C., Grollman, A. P., Fedorova, O. S., Zharkov, D. O., Simmerling, C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.41 MB

english, 2015

42

Assessing the gene regulatory properties of Argonaute-bound small RNAs of diverse genomic origin

Thomson, D. W., Pillman, K. A., Anderson, M. L., Lawrence, D. M., Toubia, J., Goodall, G. J., Bracken, C. P.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.87 MB

english, 2015

43

NERF encodes a RING E3 ligase important for drought resistance and enhances the expression of its antisense gene NFYA5 in Arabidopsis

Gao, W., Liu, W., Zhao, M., Li, W.-X.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.65 MB

english, 2015

44

Roles of PCNA ubiquitination and TLS polymerases and in the bypass of methyl methanesulfonate-induced DNA damage

Wit, N., Buoninfante, O. A., van den Berk, P. C. M., Jansen, J. G., Hogenbirk, M. A., de Wind, N., Jacobs, H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.06 MB

english, 2015

45

Microarrays for identifying binding sites and probing structure of RNAs

Kierzek, R., Turner, D. H., Kierzek, E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.16 MB

english, 2015

46

Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes

Tu, S., Wu, M. Z., Wang, J., Cutter, A. D., Weng, Z., Claycomb, J. M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.38 MB

english, 2015

47

The histone demethylase enzyme KDM3A is a key estrogen receptor regulator in breast cancer

Wade, M. A., Jones, D., Wilson, L., Stockley, J., Coffey, K., Robson, C. N., Gaughan, L.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.00 MB

english, 2015

48

Elimination of cap structures generated by mRNA decay involves the new scavenger mRNA decapping enzyme Aph1/FHIT together with DcpS

Taverniti, V., Seraphin, B.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.00 MB

english, 2015

49

Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module

Martino, L., Pennell, S., Kelly, G., Busi, B., Brown, P., Atkinson, R. A., Salisbury, N. J. H., Ooi, Z.-H., See, K.-W., Smerdon, S. J., Alfano, C., Bui, T. T. T., Conte, M. R.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.34 MB

english, 2015

50

Rescue of splicing-mediated intron loss maximizes expression in lentiviral vectors containing the human ubiquitin C promoter

Cooper, A. R., Lill, G. R., Gschweng, E. H., Kohn, D. B.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 946 KB

english, 2015

51

Bacterial initiators form dynamic filaments on single-stranded DNA monomer by monomer

Cheng, H.-M., Groger, P., Hartmann, A., Schlierf, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.99 MB

english, 2015

52

Flexibility and structural conservation in a c-KIT G-quadruplex

Wei, D., Husby, J., Neidle, S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 6.26 MB

english, 2015

53

CSB interacts with SNM1A and promotes DNA interstrand crosslink processing

Iyama, T., Lee, S. Y., Berquist, B. R., Gileadi, O., Bohr, V. A., Seidman, M. M., McHugh, P. J., Wilson, D. M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 5.64 MB

english, 2015

54

HIV-1 nucleocapsid and ESCRT-component Tsg101 interplay prevents HIV from turning into a DNA-containing virus

Chamontin, C., Rassam, P., Ferrer, M., Racine, P.-J., Neyret, A., Laine, S., Milhiet, P.-E., Mougel, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.47 MB

english, 2015

55

Leveraging cross-link modification events in CLIP-seq for motif discovery

Bahrami-Samani, E., Penalva, L. O. F., Smith, A. D., Uren, P. J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 628 KB

english, 2015

56

An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

Sterling, C. H., Veksler-Lublinsky, I., Ambros, V.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.02 MB

english, 2015