Volume 43; Issue 3

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Nucleic Acids Research
Volume 43; Issue 3

Nucleic Acids Research

Volume 43; Issue 3

1

Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines

Ho, T.-T., Zhou, N., Huang, J., Koirala, P., Xu, M., Fung, R., Wu, F., Mo, Y.-Y.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.85 MB

english, 2015

2

Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells

Byrne, S. M., Ortiz, L., Mali, P., Aach, J., Church, G. M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.22 MB

english, 2015

3

Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14

Ning, Y.-Q., Ma, Z.-Y., Huang, H.-W., Mo, H., Zhao, T.-t., Li, L., Cai, T., Chen, S., Ma, L., He, X.-J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.67 MB

english, 2015

4

Multilayered genetic safeguards limit growth of microorganisms to defined environments

Gallagher, R. R., Patel, J. R., Interiano, A. L., Rovner, A. J., Isaacs, F. J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.58 MB

english, 2015

5

Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities

Wang, B., Barahona, M., Buck, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.94 MB

english, 2015

6

DICER-dependent biogenesis of let-7 miRNAs affects human cell response to DNA damage via targeting p21/p27

Liu, B., Liu, M., Wang, J., Zhang, X., Wang, X., Wang, P., Wang, H., Li, W., Wang, Y.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.97 MB

english, 2015

7

53BP1 promotes microhomology-mediated end-joining in G1-phase cells

Xiong, X., Du, Z., Wang, Y., Feng, Z., Fan, P., Yan, C., Willers, H., Zhang, J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.11 MB

english, 2015

8

Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus

Wei, Y., Chesne, M. T., Terns, R. M., Terns, M. P.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.03 MB

english, 2015

9

Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner

Ebina, I., Takemoto-Tsutsumi, M., Watanabe, S., Koyama, H., Endo, Y., Kimata, K., Igarashi, T., Murakami, K., Kudo, R., Ohsumi, A., Noh, A. L., Takahashi, H., Naito, S., Onouchi, H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.46 MB

english, 2015

10

Protein mistranslation protects bacteria against oxidative stress

Fan, Y., Wu, J., Ung, M. H., De Lay, N., Cheng, C., Ling, J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.77 MB

english, 2015

11

The Kruppel-associated box repressor domain induces reversible and irreversible regulation of endogenous mouse genes by mediating different chromatin states

Ying, Y., Yang, X., Zhao, K., Mao, J., Kuang, Y., Wang, Z., Sun, R., Fei, J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 15.04 MB

english, 2015

12

Defining the transcriptomic landscape of Candida glabrata by RNA-Seq

Linde, J., Duggan, S., Weber, M., Horn, F., Sieber, P., Hellwig, D., Riege, K., Marz, M., Martin, R., Guthke, R., Kurzai, O.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.91 MB

english, 2015

13

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer

Sebestyen, E., Zawisza, M., Eyras, E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.30 MB

english, 2015

14

RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information

Suresh, V., Liu, L., Adjeroh, D., Zhou, X.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.30 MB

english, 2015

15

Bacterial global regulators DksA/ppGpp increase fidelity of transcription

Roghanian, M., Zenkin, N., Yuzenkova, Y.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 5.26 MB

english, 2015

16

Sparse expression bases in cancer reveal tumor drivers

Logsdon, B. A., Gentles, A. J., Miller, C. P., Blau, C. A., Becker, P. S., Lee, S.-I.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.88 MB

english, 2015

17

Recombinase and translesion DNA polymerase decrease the speed of replication fork progression during the DNA damage response in Escherichia coli cells

Tan, K. W., Pham, T. M., Furukohri, A., Maki, H., Akiyama, M. T.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 541 KB

english, 2015

18

A minimal ubiquitous chromatin opening element (UCOE) effectively prevents silencing of juxtaposed heterologous promoters by epigenetic remodeling in multipotent and pluripotent stem cells

Muller-Kuller, U., Ackermann, M., Kolodziej, S., Brendel, C., Fritsch, J., Lachmann, N., Kunkel, H., Lausen, J., Schambach, A., Moritz, T., Grez, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.14 MB

english, 2015

19

ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites

Carissimi, C., Laudadio, I., Cipolletta, E., Gioiosa, S., Mihailovich, M., Bonaldi, T., Macino, G., Fulci, V.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.37 MB

english, 2015

20

Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark

Corley, M., Solem, A., Qu, K., Chang, H. Y., Laederach, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.27 MB

english, 2015

21

A basal level of DNA damage and telomere deprotection increases the sensitivity of cancer cells to G-quadruplex interactive compounds

Salvati, E., Rizzo, A., Iachettini, S., Zizza, P., Cingolani, C., D'Angelo, C., Porru, M., Mondello, C., Aiello, A., Farsetti, A., Gilson, E., Leonetti, C., Biroccio, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 11.60 MB

english, 2015

22

Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein

Matsumoto, S., Fischer, E. S., Yasuda, T., Dohmae, N., Iwai, S., Mori, T., Nishi, R., Yoshino, K.-i., Sakai, W., Hanaoka, F., Thoma, N. H., Sugasawa, K.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.12 MB

english, 2015

23

A systematic survey of the Cys2His2 zinc finger DNA-binding landscape

Persikov, A. V., Wetzel, J. L., Rowland, E. F., Oakes, B. L., Xu, D. J., Singh, M., Noyes, M. B.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 11.96 MB

english, 2015

24

Arrangements of human telomere DNA quadruplex in physiologically relevant K+ solutions

Ren iuk, D., Kejnovska, I., kolakova, P., Bedna ova, K., Motlova, J., Vorli kova, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 27 KB

english, 2015

25

Alternative splicing regulates the expression of G9A and SUV39H2 methyltransferases, and dramatically changes SUV39H2 functions

Mauger, O., Klinck, R., Chabot, B., Muchardt, C., Allemand, E., Batsche, E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 5.79 MB

english, 2015

26

Repressor activity of the RpoS/ S-dependent RNA polymerase requires DNA binding

Levi-Meyrueis, C., Monteil, V., Sismeiro, O., Dillies, M.-A., Kolb, A., Monot, M., Dupuy, B., Duarte, S. S., Jagla, B., Coppee, J.-Y., Beraud, M., Norel, F.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.67 MB

english, 2015

27

Evaluating the potential for undesired genomic effects of the piggyBac transposon system in human cells

Saha, S., Woodard, L. E., Charron, E. M., Welch, R. C., Rooney, C. M., Wilson, M. H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.69 MB

english, 2015

28

GRASP: Guided Reference-based Assembly of Short Peptides

Zhong, C., Yang, Y., Yooseph, S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 860 KB

english, 2015

29

Function of the N-terminal segment of the RecA-dependent nuclease Ref

Gruber, A. J., Olsen, T. M., Dvorak, R. H., Cox, M. M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.97 MB

english, 2015

30

A KALA-modified lipid nanoparticle containing CpG-free plasmid DNA as a potential DNA vaccine carrier for antigen presentation and as an immune-stimulative adjuvant

Miura, N., Shaheen, S. M., Akita, H., Nakamura, T., Harashima, H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.55 MB

english, 2015

31

Opposing roles of H3- and H4-acetylation in the regulation of nucleosome structure--a FRET study

Gansen, A., Toth, K., Schwarz, N., Langowski, J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 529 KB

english, 2015

32

ModuleBlast: identifying activated sub-networks within and across species

Zinman, G. E., Naiman, S., O'Dee, D. M., Kumar, N., Nau, G. J., Cohen, H. Y., Bar-Joseph, Z.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.07 MB

english, 2015

33

The ATP binding site of the chromatin remodeling homolog Lsh is required for nucleosome density and de novo DNA methylation at repeat sequences

Ren, J., Briones, V., Barbour, S., Yu, W., Han, Y., Terashima, M., Muegge, K.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.27 MB

english, 2015

34

Nucleic Acids Research: Editorial Board

Journal:

Nucleic Acids Research

Year:

2015

File:

PDF, 1.04 MB

2015

35

The POLD3 subunit of DNA polymerase can promote translesion synthesis independently of DNA polymerase

Hirota, K., Yoshikiyo, K., Guilbaud, G., Tsurimoto, T., Murai, J., Tsuda, M., Phillips, L. G., Narita, T., Nishihara, K., Kobayashi, K., Yamada, K., Nakamura, J., Pommier, Y., Lehmann, A., Sale, J. E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.34 MB

english, 2015

36

Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork

Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., Bakail, M., Moal-Raisin, G., Guerois, R., Compper, C., Besle, A., Guichard, B., Almouzni, G., Ochsenbein, F.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.21 MB

english, 2015

37

A defense-offense multi-layered regulatory switch in a pathogenic bacterium

Nitzan, M., Fechter, P., Peer, A., Altuvia, Y., Bronesky, D., Vandenesch, F., Romby, P., Biham, O., Margalit, H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.73 MB

english, 2015

38

Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia

Carradec, Q., Gotz, U., Arnaiz, O., Pouch, J., Simon, M., Meyer, E., Marker, S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.19 MB

english, 2015

39

DNA lesion identity drives choice of damage tolerance pathway in murine cell chromosomes

Cohen, I. S., Bar, C., Paz-Elizur, T., Ainbinder, E., Leopold, K., de Wind, N., Geacintov, N., Livneh, Z.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.93 MB

english, 2015

40

DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors

Narasimhan, K., Pillay, S., Huang, Y.-H., Jayabal, S., Udayasuryan, B., Veerapandian, V., Kolatkar, P., Cojocaru, V., Pervushin, K., Jauch, R.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 9.64 MB

english, 2015

41

Transient DNMT1 suppression reveals hidden heritable marks in the genome

McGraw, S., Zhang, J. X., Farag, M., Chan, D., Caron, M., Konermann, C., Oakes, C. C., Mohan, K. N., Plass, C., Pastinen, T., Bourque, G., Chaillet, J. R., Trasler, J. M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 7.07 MB

english, 2015

42

BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers

Abo, R. P., Ducar, M., Garcia, E. P., Thorner, A. R., Rojas-Rudilla, V., Lin, L., Sholl, L. M., Hahn, W. C., Meyerson, M., Lindeman, N. I., Van Hummelen, P., MacConaill, L. E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 814 KB

english, 2015

43

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Croucher, N. J., Page, A. J., Connor, T. R., Delaney, A. J., Keane, J. A., Bentley, S. D., Parkhill, J., Harris, S. R.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 740 KB

english, 2015

44

Subscriptions

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 412 KB

english, 2015

45

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis

Diaz, A. A., Qin, H., Ramalho-Santos, M., Song, J. S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.67 MB

english, 2015

46

Nucleic Acids Research: VOLUME 43 ISSUE 3 2015

Journal:

Nucleic Acids Research

Year:

2015

File:

PDF, 5.11 MB

2015

47

Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies

Mukherjee, D., Pal, A., Chakravarty, D., Chakrabarti, P.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.12 MB

english, 2015

48

Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila

Busser, B. W., Haimovich, J., Huang, D., Ovcharenko, I., Michelson, A. M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 12.76 MB

english, 2015

49

Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G

Gumienny, R., Zavolan, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.77 MB

english, 2015

50

The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA

Gully, B. S., Cowieson, N., Stanley, W. A., Shearston, K., Small, I. D., Barkan, A., Bond, C. S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 6.19 MB

english, 2015

51

Human regulator of telomere elongation helicase 1 (RTEL1) is required for the nuclear and cytoplasmic trafficking of pre-U2 RNA

Schertzer, M., Jouravleva, K., Perderiset, M., Dingli, F., Loew, D., Le Guen, T., Bardoni, B., de Villartay, J.-P., Revy, P., Londono-Vallejo, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 8.68 MB

english, 2015

52

The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli

Zhang, W., Collinet, B., Perrochia, L., Durand, D., van Tilbeurgh, H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.12 MB

english, 2015

53

Interaction between the RNA-dependent ATPase and poly(A) polymerase subunits of the TRAMP complex is mediated by short peptides and important for snoRNA processing

Losh, J. S., King, A. K., Bakelar, J., Taylor, L., Loomis, J., Rosenzweig, J. A., Johnson, S. J., van Hoof, A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.00 MB

english, 2015

54

Development of a unique epigenetic signature during in vivo Th17 differentiation

Yang, B.-H., Floess, S., Hagemann, S., Deyneko, I. V., Groebe, L., Pezoldt, J., Sparwasser, T., Lochner, M., Huehn, J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 861 KB

english, 2015

55

An intercalation-locked parallel-stranded DNA tetraplex

Tripathi, S., Zhang, D., Paukstelis, P. J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.58 MB

english, 2015

56

The principal mRNA nuclear export factor NXF1:NXT1 forms a symmetric binding platform that facilitates export of retroviral CTE-RNA

Aibara, S., Katahira, J., Valkov, E., Stewart, M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.85 MB

english, 2015

57

NTF2-like domain of Tap plays a critical role in cargo mRNA recognition and export

Katahira, J., Dimitrova, L., Imai, Y., Hurt, E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.74 MB

english, 2015