Nucleic Acids Research

Nucleic Acids Research Contents

Volume 37 number 10

SURVEY AND SUMMARY S

Theoretical models of DNA topology simplification by type IIA DNA topoisomerases

A.Vologodskii

3125–3133

A.Oulas, A.Boutla, K.Gkirtzou, M.Reczko, K.Kalantidis and P.Poirazi

3276–3287

COMPUTATIONAL BIOLOGY S,M

Prediction of novel microRNA genes in cancerassociated genomic regions—a combined computational and experimental approach

GENE REGULATION, CHROMATIN AND EPIGENETICS S

CK2 phosphorylation of the PRH/Hex homeodomain functions as a reversible switch for DNA binding

A.Soufi, P.Noy, M.Buckle, A.Sawasdichai, K.Gaston and P.-S.Jayaraman

3288–3300

S

Transcription regulation of restriction-modification system Esp1396I

E.Bogdanova, M.Zakharova, S.Streeter, J.Taylor, T.Heyduk, G.Kneale and K.Severinov

3354–3366

S

Linker histone H1 is present in centromeric chromatin of living human cells next to inner kinetochore proteins

S.Orthaus, K.Klement, N.Happel, C.Hoischen and S.Diekmann

3391–3406

GENOME INTEGRITY, REPAIR AND REPLICATION S

XRCC1 interacts with the p58 subunit of DNA Pol a-primase and may coordinate DNA repair and replication during S phase

N.Le´vy, M.Oehlmann, F.Delalande, H.P.Nasheuer, A.Van Dorsselaer, V.Schreiber, G.de Murcia, J.Me´nissier-de Murcia, D.Maiorano and A.Bresson

3177–3188

S

DIDS, a chemical compound that inhibits RAD51mediated homologous pairing and strand exchange

T.Ishida, Y.Takizawa, T.Kainuma, J.Inoue, T.Mikawa, T.Shibata, H.Suzuki, S.Tashiro and H.Kurumizaka

3367–3376

S

Involvement of Exo1b in DNA damage-induced apoptosis

E.Bolderson, D.J.Richard, W.Edelmann and K.K.Khanna

3452–3463

GENOMICS S

Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes

P.A.Ziolkowski, G.Koczyk, L.Galganski and J.Sadowski

3189–3201

S

Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi

D.C.Bartholomeu, G.C.Cerqueira, A.C.A.Lea˜o, W.D.daRocha, F.S.Pais, C.Macedo, A.Djikeng, S.M.R.Teixeira and N.M.El-Sayed

3407–3417

C.Schwarz, R.Debruyne, M.Kuch, E.McNally, H.Schwarcz, A.D.Aubrey, J.Bada and H.Poinar

3215–3229

MOLECULAR BIOLOGY S

New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains

Continued

Contents

(Continued)

Volume 37 number 10

S

Phosphate control over nitrogen metabolism in Streptomyces coelicolor: direct and indirect negative control of glnR, glnA, glnII and amtB expression by the response regulator PhoP

A.Rodrı´ guez-Garcı´ a, A.Sola-Landa, K.Apel, F.Santos-Beneit and J.F.Martı´ n

3230–3242

S

Evolutionary changes in the Leishmania eIF4F complex involve variations in the eIF4E–eIF4G interactions

Y.Yoffe, M.Le´ger, A.Zinoviev, J.Zuberek, E.Darzynkiewicz, G.Wagner and M.Shapira

3243–3253

S

A WW-like module in the RAG1 N-terminal domain contributes to previously unidentified protein–protein interactions

R.Maitra and M.J.Sadofsky

3301–3309

S

Elevated polyamines induce c-MYC overexpression by perturbing quadruplex–WC duplex equilibrium

N.Kumar, R.Basundra and S.Maiti

3321–3331

Cotranscriptional recruitment of the nuclear poly(A)-binding protein Pab2 to nascent transcripts and association with translating mRNPs

C.Lemieux and F.Bachand

3418–3430

NUCLEIC ACID ENZYMES S

Elucidating the mechanism of DNA-dependent ATP hydrolysis mediated by DNA-dependent ATPase A, a member of the SWI2/SNF2 protein family

M.Nongkhlaw, P.Dutta, J.W.Hockensmith, S.S.Komath and R.Muthuswami

3332–3341

S

Type I restriction endonucleases are true catalytic enzymes

P.R.Bianco, C.Xu and M.Chi

3377–3390

Human DNA polymerase b polymorphism, Arg137Gln, impairs its polymerase activity and interaction with PCNA and the cellular base excision repair capacity

Z.Guo, L.Zheng, H.Dai, M.Zhou, H.Xu and B.Shen

3431–3441

RNA S

A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center

C.Hsiao and L.D.Williams

3134–3142

S

A conserved 30 extension in unusual group II introns is important for efficient second-step splicing

F.B.Stabell, N.J.Tourasse and A.-B.Kolstø

3202–3214

S

Peculiarities of piRNA-mediated post-transcriptional silencing of Stellate repeats in testes of Drosophila melanogaster

R.N.Kotelnikov, M.S.Klenov, Y.M.Rozovsky, L.V.Olenina, M.V.Kibanov and V.A.Gvozdev

3254–3263

C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts

M.-L.Bortolin-Cavaille´, M.Dance, M.Weber and J.Cavaille´

3464–3473

Structural insights into the cooperative binding of SeqA to a tandem GATC repeat

Y.S.Chung, T.Brendler, S.Austin and A.Guarne´

3143–3152

S

Structural analysis and DNA binding of the HMG domains of the human mitochondrial transcription factor A

T.A.Gangelhoff, P.S.Mungalachetty, J.C.Nix and M.E.A.Churchill

3153–3164

S

Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling

G.Sicoli, G.Mathis, S.Aci-Se`che, C.Saint-Pierre, Y.Boulard, D.Gasparutto and S.Gambarelli

3165–3176

S

Self-association of short DNA loops through minor groove C:G:G:C tetrads

J.Viladoms, N.Escaja, M.Frieden, I.Go´mez-Pinto, E.Pedroso and C.Gonza´lez

3264–3275

STRUCTURAL BIOLOGY

Continued

Contents

(Continued)

Volume 37 number 10

S

Direct experimental evidence for quadruplex– quadruplex interaction within the human ILPR

J.D.Schonhoft, R.Bajracharya, S.Dhakal, Z.Yu, H.Mao and S.Basu

3310–3320

S

The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs

Y.Bilbille, F.A.P.Vendeix, R.Guenther, A.Malkiewicz, X.Ariza, J.Vilarrasa and P.F.Agris

3342–3353

S

Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition

Y.J.An, B.-E.Ahn, A-R.Han, H.-M.Kim, K.M.Chung, J.-H.Shin, Y.-B.Cho, J.-H.Roe and S.-S.Cha

3442–3451

METHODS ONLINE S,M

Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes

S.Zhang, M.Xu, S.Li and Z.Su

S,M

Assessment of the optimization of affinity and specificity at protein–DNA interfaces

J.Ashworth and D.Baker

e73 (6 pp.)

M

Identification of HCV protease inhibitor resistance mutations by selection pressure-based method

P.Qiu, V.Sanfiorenzo, S.Curry, Z.Guo, S.Liu, A.Skelton, E.Xia, C.Cullen, R.Ralston, J.Greene and X.Tong

e74 (7 pp.)

S,M

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level

S.Zheng and L.Chen

S,M

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

Y.Sun, Y.Cai, L.Liu, F.Yu, M.L.Farrell, W.McKendree and W.Farmerie

S,M

Labeled microRNA pull-down assay system: an experimental approach for high-throughput identification of microRNA-target mRNAs

R.-J.Hsu, H.-J.Yang and H.-J.Tsai

RETRACTION M, contains a novel method S, Supplementary Material available at NAR Online

e72 (21 pp.)

e75 (16 pp.)

e76 (8 pp.) e77 (10 pp.)

3474