Advance online publication
The latest research papers, published online ahead of print. These online versions are definitive and may be cited using the digital object identifier (DOI).
About advance online publicationArticles
The splicing factor SC35 has an active role in transcriptional elongation
Shengrong Lin, Gabriela Coutinho-Mansfield, Dong Wang, Shatakshi Pandit & Xiang-Dong Fu
Published online: 20 July 2008; | doi:10.1038/nsmb.1461
It is known that components of the splicing machinery are guided to nascent transcripts through interactions with the Pol II transcriptional complex. Data now indicate that depletion of SC35, a splicing factor, leads to defective elongation as well as reduced Pol II phosphorylation and association with elongation factors. This leads to a model where components of the splicing machinery have a role in promoting elongation of the transcriptional machinery.
Abstract - | Full Text - The splicing factor SC35 has an active role in transcriptional elongation | PDF (450 KB) - The splicing factor SC35 has an active role in transcriptional elongation | Supplementary information
The ClC-0 chloride channel is a 'broken' Cl-/H+ antiporter
Jiří Lísal & Merritt Maduke
Published online: 20 July 2008; | doi:10.1038/nsmb.1466
The CLC protein family consists of chloride-selective ion channels and Cl-/H+ antiporters. Functional studies on the ClC-0 chloride channel, the founding member of the CLC family, reveals that channel gating is coupled to proton-transport events, providing a mechanistic connection between channels and transporters in this family of proteins.
Abstract - | Full Text - The ClC-0 chloride channel is a 'broken' Cl-/H+ antiporter | PDF (355 KB) - The ClC-0 chloride channel is a 'broken' Cl-/H+ antiporter | Supplementary information
Synaptotagmin arrests the SNARE complex before triggering fast, efficient membrane fusion in response to Ca2+
Michael C Chicka, Enfu Hui, Huisheng Liu & Edwin R Chapman
Published online: 11 July 2008; | doi:10.1038/nsmb.1463
Synaptotagmin is generally accepted as being the calcium sensor in SNARE-mediated calcium-triggered synaptic vesicle fusion. New data now indicate that synaptotagmin may negatively regulate the SNARE complex in the absence of calcium, and that interactions with target SNARE proteins may help steer synaptotagmin to the target membrane in a calcium-independent manner.
Abstract - | Full Text - Synaptotagmin arrests the SNARE complex before triggering fast, efficient membrane fusion in response to Ca2+ | PDF (525 KB) - Synaptotagmin arrests the SNARE complex before triggering fast, efficient membrane fusion in response to Ca2+ | Supplementary information
Antisense transcripts are targets for activating small RNAs
Jacob C Schwartz, Scott T Younger, Ngoc-Bich Nguyen, Daniel B Hardy, Brett P Monia, David R Corey & Bethany A Janowski
Published online: 06 July 2008; | doi:10.1038/nsmb.1444
The manner in which antigene RNAs (agRNAs) are complementary to the progesterone receptor promoter is further examined, and the presence of an antisense transcript overlapping the promoter detected. Presence of the transcript correlates with the ability of agRNAs to activate expression and physically interact with it. Argonaute, hnRNP-k and HP1 association with the promoter DNA or antisense RNA are detected to alter upon agRNA application.
Abstract - | Full Text - Antisense transcripts are targets for activating small RNAs | PDF (281 KB) - Antisense transcripts are targets for activating small RNAs | Supplementary information
Eukaryotic translation initiation machinery can operate in a bacterial-like mode without eIF2
Ilya M Terenin, Sergey E Dmitriev, Dmitry E Andreev & Ivan N Shatsky
Published online: 06 July 2008; | doi:10.1038/nsmb.1445
Viruses have found mechanisms to translate their RNAs in the face of antiviral responses. Data now indicate that the hepatitis C virus internal ribosome entry site can use eIF5B to initiate translation in a bacterial-like mode when eIF2 is inactivated under stress.
Abstract - | Full Text - Eukaryotic translation initiation machinery can operate in a bacterial-like mode without eIF2 | PDF (402 KB) - Eukaryotic translation initiation machinery can operate in a bacterial-like mode without eIF2
Structural basis of transcription inhibition by 
-amanitin and implications for RNA polymerase II translocation
Florian Brueckner & Patrick Cramer
Published online: 13 June 2008; | doi:10.1038/nsmb.1458
PDB code
3D view
The crystal structure of the yeast RNA Pol II elongation complex bound to the inhibitor 
-amanitin is solved, revealing that two functional elements, the trigger loop and the bridge helix, are trapped in a position different from their pre- and post-translocation states. This is proposed to be a translocation intermediate, lending support to a Brownian ratchet mechanism for RNA Pol II translocation during elongation.
Abstract - | Full Text - Structural basis of transcription inhibition by -amanitin and implications for RNA polymerase II translocation | PDF (1,523 KB) - Structural basis of transcription inhibition by -amanitin and implications for RNA polymerase II translocation
Brief Communications
Mutation in TERT separates processivity from anchor-site function
Arthur J Zaug, Elaine R Podell & Thomas R Cech
Published online: 20 July 2008; | doi:10.1038/nsmb.1462
Repeat-addition processivity (RAP), that is, generating multiple DNA repeats from a single template without primer dissociation, is a key property of telomerase. In the Tetrahymena reverse-transcriptase component of telomerase, a single amino acid mutation causes a profound and specific defect in RAP without altering enzymatic activity.
Abstract - | Full Text - Mutation in TERT separates processivity from anchor-site function | PDF (225 KB) - Mutation in TERT separates processivity from anchor-site function | Supplementary information
NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B
Zheng Zhou, Hanqiao Feng, D Flemming Hansen, Hidenori Kato, Ed Luk, Daron I Freedberg, Lewis E Kay, Carl Wu & Yawen Bai
Published online: 20 July 2008; | doi:10.1038/nsmb.1465
PDB code
3D view
The NMR structure of the H2A.Z-H2B histone chaperone, Chz1, reveals electrostatic interactions between Chz1 and the histone pair via a long, irregular chain with two capping helices, and, based on a model, the possibility that Chz1 has a more active role in histone replacement is suggested.
Abstract - | Full Text - NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B | PDF (334 KB) - NMR structure of chaperone Chz1 complexed with histones H2A.Z-H2B | Supplementary information
Molecular recognition of nitrated fatty acids by PPAR
Yong Li, Jifeng Zhang, Francisco J Schopfer, Dariusz Martynowski, Minerva T Garcia-Barrio, Amanda Kovach, Kelly Suino-Powell, Paul R S Baker, Bruce A Freeman, Y Eugene Chen & H Eric Xu
Published online: 06 July 2008; | doi:10.1038/nsmb.1447
PDB code
3D view
PPAR
is a nuclear receptor that regulates metabolic homeostasis. It is activated by nitrated and oxidized fatty acids. The crystal structure of the ligand binding domain of PPAR in complex with a physiological ligand, nitrated linoleic acid, is now described, showing differences with synthetic agonists that may have physiological relevance.
Abstract - | Full Text - Molecular recognition of nitrated fatty acids by PPAR | PDF (390 KB) - Molecular recognition of nitrated fatty acids by PPAR | Supplementary information
Resources
Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast
Brendon J Monahan, Judit Villén, Samuel Marguerat, Jürg Bähler, Steven P Gygi & Fred Winston
Published online: 11 July 2008; | doi:10.1038/nsmb.1452
The Schizosaccharomyces pombe SWI/SNF family of ATP-dependent chromatin-remodeling complexes is now comprehensively analyzed, through composition, phenotypic and microarray analyses, thus broadly setting the stage for S. pombe as a new model organism for examining the SWI/SNF family remodelers. The S. pombe complexes are more akin to the metazoan SWI/SNF remodelers and have specific roles in repression of iron-transport genes.
Abstract - | Full Text - Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast | PDF (426 KB) - Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast | Supplementary information
A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation
Shima Nakanishi, Brian W Sanderson, Kym M Delventhal, William D Bradford, Karen Staehling-Hampton & Ali Shilatifard
Published online: 11 July 2008; | doi:10.1038/nsmb.1454
A comprehensive library encompassing alanine scanning mutations across yeast histones is presented as a Resource that will facilitate screening of chromatin processes. The utility of the library is indicated by screening in cis and in trans for residues that affect histone H3K4 trimethylation, a modification that is associated with actively transcribed genes and known to be mediated by the Set1-COMPASS complex.
Abstract - | Full Text - A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation | PDF (634 KB) - A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation
Until print versions of AOP papers are published, they should be cited in the style "Author(s) Nature Structural & Molecular Biology advance online publication, day month year (doi:10.1038/nsmbXXXXX)". Once the print version (identical to the AOP) is published, it should be cited as follows: "Author(s) Nature Structural & Molecular Biology volume, page (year); advance online publication, (doi:10.1038/nsmbXXXXX)".
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