Volume 42; Issue 9

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Nucleic Acids Research
Volume 42; Issue 9

Nucleic Acids Research

Volume 42; Issue 9

1

The DNA damage checkpoint pathway promotes extensive resection and nucleotide synthesis to facilitate homologous recombination repair and genome stability in fission yeast

Blaikley, E. J., Tinline-Purvis, H., Kasparek, T. R., Marguerat, S., Sarkar, S., Hulme, L., Hussey, S., Wee, B.-Y., Deegan, R. S., Walker, C. A., Pai, C.-C., Bahler, J., Nakagawa, T., Humphrey, T. C.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.02 MB

english, 2014

2

Molecular dissection of the domain architecture and catalytic activities of human PrimPol

Keen, B. A., Jozwiakowski, S. K., Bailey, L. J., Bianchi, J., Doherty, A. J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.67 MB

english, 2014

3

Pervasive generation of oppositely oriented spacers during CRISPR adaptation

Shmakov, S., Savitskaya, E., Semenova, E., Logacheva, M. D., Datsenko, K. A., Severinov, K.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.52 MB

english, 2014

4

Large-scale analysis of tandem repeat variability in the human genome

Duitama, J., Zablotskaya, A., Gemayel, R., Jansen, A., Belet, S., Vermeesch, J. R., Verstrepen, K. J., Froyen, G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.51 MB

english, 2014

5

Boronic acid-mediated polymerase chain reaction for gene- and fragment-specific detection of 5-hydroxymethylcytosine

Zhao, C., Wang, H., Zhao, B., Li, C., Yin, R., Song, M., Liu, B., Liu, Z., Jiang, G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.02 MB

english, 2014

6

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

Guglielmini, J., Neron, B., Abby, S. S., Garcillan-Barcia, M. P., la Cruz, F. d., Rocha, E. P. C.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.32 MB

english, 2014

7

Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ)

Kim, D., Hur, J., Park, K., Bae, S., Shin, D., Ha, S. C., Hwang, H.-Y., Hohng, S., Lee, J.-H., Lee, S., Kim, Y.-G., Kim, K. K.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 7.51 MB

english, 2014

8

RepARK--de novo creation of repeat libraries from whole-genome NGS reads

Koch, P., Platzer, M., Downie, B. R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

9

Mechanistic insight into ligand binding to G-quadruplex DNA

Di Leva, F. S., Novellino, E., Cavalli, A., Parrinello, M., Limongelli, V.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.50 MB

english, 2014

10

miR-Synth: a computational resource for the design of multi-site multi-target synthetic miRNAs

Lagana, A., Acunzo, M., Romano, G., Pulvirenti, A., Veneziano, D., Cascione, L., Giugno, R., Gasparini, P., Shasha, D., Ferro, A., Croce, C. M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.13 MB

english, 2014

11

Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering

Sun, P., Speicher, N. K., Rottger, R., Guo, J., Baumbach, J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.79 MB

english, 2014

12

HSCARG, a novel regulator of H2A ubiquitination by downregulating PRC1 ubiquitin E3 ligase activity, is essential for cell proliferation

Hu, B., Li, S., Zhang, X., Zheng, X.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.26 MB

english, 2014

13

A concomitant loss of dormant origins and FANCC exacerbates genome instability by impairing DNA replication fork progression

Luebben, S. W., Kawabata, T., Johnson, C. S., O'Sullivan, M. G., Shima, N.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.61 MB

english, 2014

14

Modulating TRAP-mediated transcription termination by AT during transcription of the leader region of the Bacillus subtilis trp operon

Sharma, S., Gollnick, P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.50 MB

english, 2014

15

Myc-induced anchorage of the rDNA IGS region to nucleolar matrix modulates growth-stimulated changes in higher-order rDNA architecture

Shiue, C.-N., Nematollahi-Mahani, A., Wright, A. P. H.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 5.84 MB

english, 2014

16

Identification of novel non-canonical RNA-binding sites in Gemin5 involved in internal initiation of translation

Fernandez-Chamorro, J., Pineiro, D., Gordon, J. M. B., Ramajo, J., Francisco-Velilla, R., Macias, M. J., Martinez-Salas, E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 5.82 MB

english, 2014

17

Structural and functional studies of Stf76 from the Sulfolobus islandicus plasmid-virus pSSVx: a novel peculiar member of the winged helix-turn-helix transcription factor family

Contursi, P., Farina, B., Pirone, L., Fusco, S., Russo, L., Bartolucci, S., Fattorusso, R., Pedone, E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.33 MB

english, 2014

18

The E3 ubiquitin ligase UBE3A is an integral component of the molecular circadian clock through regulating the BMAL1 transcription factor

Gossan, N. C., Zhang, F., Guo, B., Jin, D., Yoshitane, H., Yao, A., Glossop, N., Zhang, Y. Q., Fukada, Y., Meng, Q.-J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.39 MB

english, 2014

19

A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress

Elfving, N., Chereji, R. V., Bharatula, V., Bjorklund, S., Morozov, A. V., Broach, J. R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 7.68 MB

english, 2014

20

Estimating telomere length from whole genome sequence data

Ding, Z., Mangino, M., Aviv, A., Spector, T., Durbin, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.25 MB

english, 2014

21

The histone chaperones Vps75 and Nap1 form ring-like, tetrameric structures in solution

Bowman, A., Hammond, C. M., Stirling, A., Ward, R., Shang, W., El-Mkami, H., Robinson, D. A., Svergun, D. I., Norman, D. G., Owen-Hughes, T.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.54 MB

english, 2014

22

A novel mechanism for regulating the activity of proliferating cell nuclear antigen by a small protein

Li, Z., Huang, R. Y.- C., Yopp, D. C., Hileman, T. H., Santangelo, T. J., Hurwitz, J., Hudgens, J. W., Kelman, Z.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 6.31 MB

english, 2014

23

Bacterial promoter repression by DNA looping without protein-protein binding competition

Becker, N. A., Greiner, A. M., Peters, J. P., Maher, L. J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.57 MB

english, 2014

24

Molecular population dynamics of DNA structures in a bcl-2 promoter sequence is regulated by small molecules and the transcription factor hnRNP LL

Cui, Y., Koirala, D., Kang, H., Dhakal, S., Yangyuoru, P., Hurley, L. H., Mao, H.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.71 MB

english, 2014

25

A high-throughput chemical screen with FDA approved drugs reveals that the antihypertensive drug Spironolactone impairs cancer cell survival by inhibiting homology directed repair

Shahar, O. D., Kalousi, A., Eini, L., Fisher, B., Weiss, A., Darr, J., Mazina, O., Bramson, S., Kupiec, M., Eden, A., Meshorer, E., Mazin, A. V., Brino, L., Goldberg, M., Soutoglou, E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.49 MB

english, 2014

26

Internally labeled Cy3/Cy5 DNA constructs show greatly enhanced photo-stability in single-molecule FRET experiments

Lee, W., von Hippel, P. H., Marcus, A. H.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.18 MB

english, 2014

27

Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1

Wang, I., Hennig, J., Jagtap, P. K. A., Sonntag, M., Valcarcel, J., Sattler, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 16.01 MB

english, 2014

28

Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments

Lu, Z., Matera, A. G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.42 MB

english, 2014

29

Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases

Araiso, Y., Huot, J. L., Sekiguchi, T., Frechin, M., Fischer, F., Enkler, L., Senger, B., Ishitani, R., Becker, H. D., Nureki, O.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.79 MB

english, 2014

30

Human RECQL1 participates in telomere maintenance

Popuri, V., Hsu, J., Khadka, P., Horvath, K., Liu, Y., Croteau, D. L., Bohr, V. A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 6.85 MB

english, 2014

31

Single nucleotide polymorphism-specific regulation of matrix metalloproteinase-9 by multiple miRNAs targeting the coding exon

Duellman, T., Warren, C., Yang, J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.29 MB

english, 2014

32

Fail-safe mechanism of GCN4 translational control--uORF2 promotes reinitiation by analogous mechanism to uORF1 and thus secures its key role in GCN4 expression

Guni ova, S., Vala ek, L. S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 7.76 MB

english, 2014

33

Nucleic Acids Research: Editorial Board

Journal:

Nucleic Acids Research

Year:

2014

File:

PDF, 421 KB

2014

34

Scm3 deposits a (Cse4-H4)2 tetramer onto DNA through a Cse4-H4 dimer intermediate

Dechassa, M. L., Wyns, K., Luger, K.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.67 MB

english, 2014

35

A bifunctional protein regulates mitochondrial protein synthesis

Richman, T. R., Davies, S. M. K., Shearwood, A.-M. J., Ermer, J. A., Scott, L. H., Hibbs, M. E., Rackham, O., Filipovska, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 6.54 MB

english, 2014

36

Nonsense-mediated decay as a terminating mechanism for antisense oligonucleotides

Ward, A. J., Norrbom, M., Chun, S., Bennett, C. F., Rigo, F.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.43 MB

english, 2014

37

A eukaryotic-like 3' untranslated region in Salmonella enterica hilD mRNA

Lopez-Garrido, J., Puerta-Fernandez, E., Casadesus, J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.67 MB

english, 2014

38

Different gene-specific mechanisms determine the 'revised-response' memory transcription patterns of a subset of A. thaliana dehydration stress responding genes

Liu, N., Ding, Y., Fromm, M., Avramova, Z.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.88 MB

english, 2014

39

Nucleic Acids Research: VOLUME 42 ISSUE 9 2014

Journal:

Nucleic Acids Research

Year:

2014

File:

PDF, 125 KB

2014

40

Bacteriophage N protein inhibits transcription slippage by Escherichia coli RNA polymerase

Parks, A. R., Court, C., Lubkowska, L., Jin, D. J., Kashlev, M., Court, D. L.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 582 KB

english, 2014

41

Exonic splicing signals impose constraints upon the evolution of enzymatic activity

Falanga, A., Stojanovi , O., Kiffer-Moreira, T., Pinto, S., Millan, J. L., Vlahovi ek, K., Baralle, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.59 MB

english, 2014

42

Systematic design and functional analysis of artificial microRNAs

Arroyo, J. D., Gallichotte, E. N., Tewari, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 8.77 MB

english, 2014

43

Impact of sequencing depth in ChIP-seq experiments

Jung, Y. L., Luquette, L. J., Ho, J. W. K., Ferrari, F., Tolstorukov, M., Minoda, A., Issner, R., Epstein, C. B., Karpen, G. H., Kuroda, M. I., Park, P. J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 8.62 MB

english, 2014

44

Crosstalk between transposase subunits during cleavage of the mariner transposon

Claeys Bouuaert, C., Walker, N., Liu, D., Chalmers, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 6.71 MB

english, 2014

45

Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNA

Gutjahr, A., Xu, S.-y.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 6.23 MB

english, 2014

46

Regulation of FANCD2 and FANCI monoubiquitination by their interaction and by DNA

Longerich, S., Kwon, Y., Tsai, M.-S., Hlaing, A. S., Kupfer, G. M., Sung, P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 7.05 MB

english, 2014

47

Synthetic circuit for exact adaptation and fold-change detection

Kim, J., Khetarpal, I., Sen, S., Murray, R. M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 563 KB

english, 2014

48

SAXS analysis of the tRNA-modifying enzyme complex MnmE/MnmG reveals a novel interaction mode and GTP-induced oligomerization

Fislage, M., Brosens, E., Deyaert, E., Spilotros, A., Pardon, E., Loris, R., Steyaert, J., Garcia-Pino, A., Versees, W.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 5.78 MB

english, 2014

49

Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction

Aiyer, S., Swapna, G. V. T., Malani, N., Aramini, J. M., Schneider, W. M., Plumb, M. R., Ghanem, M., Larue, R. C., Sharma, A., Studamire, B., Kvaratskhelia, M., Bushman, F. D., Montelione, G. T., Roth

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 7.97 MB

english, 2014

50

Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues

Xu, L., Butler, K. V., Chong, J., Wengel, J., Kool, E. T., Wang, D.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 630 KB

english, 2014

51

Similarity in targets with REST points to neural and glioblastoma related miRNAs

Gebhardt, M. L., Reuter, S., Mrowka, R., Andrade-Navarro, M. A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.77 MB

english, 2014

52

A role for WDR5 in TRA-1/Gli mediated transcriptional control of the sperm/oocyte switch in C. elegans

Li, T., Kelly, W. G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.74 MB

english, 2014

53

Subscriptions

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 417 KB

english, 2014

54

TstI, a Type II restriction-modification protein with DNA recognition, cleavage and methylation functions in a single polypeptide

Smith, R. M., Pernstich, C., Halford, S. E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.26 MB

english, 2014

55

Structural insights into RNA encapsidation and helical assembly of the Toscana virus nucleoprotein

Olal, D., Dick, A., Woods, V. L., Liu, T., Li, S., Devignot, S., Weber, F., Saphire, E. O., Daumke, O.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.83 MB

english, 2014

56

Solution structure of a 2:1 complex of anticancer drug XR5944 with TFF1 estrogen response element: insights into DNA recognition by a bis-intercalator

Lin, C., Mathad, R. I., Zhang, Z., Sidell, N., Yang, D.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.21 MB

english, 2014

57

Inferring probabilistic miRNA-mRNA interaction signatures in cancers: a role-switch approach

Li, Y., Liang, C., Wong, K.-C., Jin, K., Zhang, Z.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 19.09 MB

english, 2014

58

Genome-wide analysis of regulation of gene expression and H3K9me2 distribution by JIL-1 kinase mediated histone H3S10 phosphorylation in Drosophila

Cai, W., Wang, C., Li, Y., Yao, C., Shen, L., Liu, S., Bao, X., Schnable, P. S., Girton, J., Johansen, J., Johansen, K. M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.43 MB

english, 2014

59

Cellular location and activity of Escherichia coli RecG proteins shed light on the function of its structurally unresolved C-terminus

Upton, A. L., Grove, J. I., Mahdi, A. A., Briggs, G. S., Milner, D. S., Rudolph, C. J., Lloyd, R. G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.51 MB

english, 2014

60

The use of interatomic contact areas to quantify discrepancies between RNA 3D models and reference structures

Olechnovi , K., Venclovas, eslovas

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 4.72 MB

english, 2014

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