Nucleic Acids Research

Nucleic Acids Research Contents

Volume 34 number 21

CHEMISTRY Z.Yang, D.Hutter, P.Sheng, A.M.Sismour and S.A.Benner

6095–6101

M,S Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins

B.Jayaram, K.Bhushan, S.R.Shenoy, P.Narang, S.Bose, P.Agrawal, D.Sahu and V.Pandey

6195–6204

M,S Identification of alternative 50 /30 splice sites based on the mechanism of splice site competition

H.Xia, J.Bi and Y.Li

6305–6313

J.M.Goodenbour and T.Pan

6137–6146

S

Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern COMPUTATIONAL BIOLOGY

GENOMICS

M,S Diversity of tRNA genes in eukaryotes MOLECULAR BIOLOGY

S

ZNF366 is an estrogen receptor corepressor that acts through CtBP and histone deacetylases

J.Lopez-Garcia, M.Periyasamy, R.S.Thomas, M.Christian, M.Leao, P.Jat, K.B.Kindle, D.M.Heery, M.G.Parker, L.Buluwela, T.Kamalati and S.Ali

6126–6136

S

NSPc1 is a cell growth regulator that acts as a transcriptional repressor of p21Waf1/Cip1 via the RARE element

Y.Gong, J.Yue, X.Wu, X.Wang, J.Wen, L.Lu, X.Peng, B.Qiang and J.Yuan

6158–6169

S

PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways

M.Wang, W.Wu, W.Wu, B.Rosidi, L.Zhang, H.Wang and G.Iliakis

6170–6182

The involvement of replication in single stranded oligonucleotide-mediated gene repair

M.S.Y.Huen, X.Li, L.-Y.Lu, R.M.Watt, D.-P.Liu and J.-D.Huang

6183–6194

S

The mechanism of gene targeting in Physcomitrella patens: homologous recombination, concatenation and multiple integration

Y.Kamisugi, K.Schlink, S.A.Rensing, G.Schween, M.von Stackelberg, A.C.Cuming, R.Reski and D.J.Cove

6205–6214

M

Chromosomal integration of LTR-flanked DNA in yeast expressing HIV-1 integrase: down regulation by RAD51

S.Desfarges, J.San Filippo, M.Fournier, C.Calmels, A.Caumont-Sarcos, S.Litvak, P.Sung and V.Parissi

6215–6224

SAGA-associated Sgf73p facilitates formation of the preinitiation complex assembly at the promoters either in a HAT-dependent or independent manner in vivo

A.Shukla, P.Bajwa and S.R.Bhaumik

6225–6232

S

Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing

T.Blevins, R.Rajeswaran, P.V.Shivaprasad, D.Beknazariants, A.Si-Ammour, H.-S.Park, F.Vazquez, D.Robertson, F.Meins,Jr, T.Hohn and M.M.Pooggin

6233–6246

S

Proteolysis restricts localization of CID, the centromere-specific histone H3 variant of Drosophila, to centromeres

O.Moreno-Moreno, M.Torras-Llort and F.Azorı´n

6247–6255

Continued

Contents S

S

S

Volume 34 number 21

(Continued)

Inhibition of CBF/NF-Y mediated transcription activation arrests cells at G2/M phase and suppresses expression of genes activated at G2/M phase of the cell cycle

Q.Hu, J.-F.Lu, R.Luo, S.Sen and S.N.Maity

6272–6285

DAXX interacts with phage FC31 integrase and inhibits recombination

J.Chen, C.Ji, G.Xu, R.Pang, J.Yao, H.Zhu, J.Xue and W.Jia

6298–6304

Potentiation of Smad-mediated transcriptional activation by the RNA-binding protein RBPMS

Y.Sun, L.Ding, H.Zhang, J.Han, X.Yang, J.Yan, Y.Zhu, J.Li, H.Song and Q.Ye

6314–6326

The telomerase-recruitment domain of the telomere binding protein Cdc13 is regulated by Mec1p/Tel1pdependent phosphorylation

S.-F.Tseng, J.-J.Lin and S.-C.Teng

6327–6336

NHEJ-deficient DT40 cells have increased levels of immunoglobulin gene conversion: evidence for a double strand break intermediate

E.S.Tang and A.Martin

6345–6351

Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats

P.M.Rindler, R.M.Clark, L.M.Pollard, I.De Biase and S.I.Bidichandani

6352–6361

The oligomeric Rep protein of Mungbean yellow mosaic India virus (MYMIV) is a likely replicative helicase

N.R.Choudhury, P.S.Malik, D.K.Singh, M.N.Islam, K.Kaliappan and S.K.Mukherjee

6362–6377

Role of metal ions in catalysis by HIV integrase analyzed using a quantitative PCR disintegration assay

T.L.Diamond and F.D.Bushman

6116–6125

‘LeishMan’ topoisomerase I: an ideal chimera for unraveling the role of the small subunit of unusual bi-subunit topoisomerase I from Leishmania donovani

A.Ganguly, B.B.Das, N.Sen, A.Roy, S.B.Dasgupta and H.K.Majumder

6286–6297

Stimulation of MCM helicase activity by a Cdc6 protein in the archaeon Thermoplasma acidophilum

G.T.Haugland, J.-H.Shin, N.K.Birkeland and Z.Kelman

6337–6344

Sequence-specific recognition of colicin E5, a tRNAtargeting ribonuclease

T.Ogawa, S.Inoue, S.Yajima, M.Hidaka and H.Masaki

6065–6073

A single tRNA base pair mediates bacterial tRNAdependent biosynthesis of asparagine

M.Bailly, S.Giannouli, M.Blaise, C.Stathopoulos, D.Kern and H.D.Becker

6083–6094

Keeping signals straight in transcription regulation: specificity determinants for the interaction of a family of conserved bacterial RNA–protein couples

O.Schilling, C.Herzberg, T.Hertrich, H.Vo¨rsmann, D.Jessen, S.H€ ubner, F.Titgemeyer and J.St€ ulke

6102–6115

Both introns and long 30 -UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants

S.Kerte´sz, Z.Kere´nyi, Z.Me´rai, I.Bartos, T.Pa´lfy, E.Barta and D.Silhavy

6147–6157

Concentration dependent selection of targets by an SR splicing regulator results in tissue-specific RNA processing

J.Qi, S.Su, M.E.McGuffin and W.Mattox

6256–6263

Knock-down of 25 kDa subunit of cleavage factor Im in Hela cells alters alternative polyadenylation within 30 -UTRs

T.Kubo, T.Wada, Y.Yamaguchi, A.Shimizu and H.Handa

6264–6271

NUCLEIC ACID ENZYMES

S

RNA

s

Continued

Contents

Volume 34 number 21

(Continued)

STRUCTURAL BIOLOGY

S

Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA–tRNA interaction

S.Yajima, S.Inoue, T.Ogawa, T.Nonaka, K.Ohsawa and H.Masaki

6074–6082

METHODS

S

Gene expression profiling of single cells on largescale oligonucleotide arrays

C.H.Hartmann and C.A.Klein

S

A microfluidic-FCS platform for investigation on the dissociation of Sp1-DNA complex by doxorubicin

H.-C.Yeh, C.M.Puleo, T.C.Lim, Y.-P.Ho, P.E.Giza, R.C.C.Huang and T.-H.Wang

e144 (9 pp.)

Eliminating helper phage from phage display

L.Chasteen, J.Ayriss, P.Pavlik and A.R.M.Bradbury

e145 (11 pp.)

A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors

H.Ji, S.A.Vokes and W.H.Wong

e146 (11 pp.)

Generation of a mouse mutant by oligonucleotidemediated gene modification in ES cells

M.Aarts, M.Dekker, S.de Vries, A.van der Wal and H.te Riele

S

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

e143 (11 pp.)

e147 (9 pp.)