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).

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Articles

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.


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.


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.


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.


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.


Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation

Florian Brueckner & Patrick Cramer

Published online: 13 June 2008; | doi:10.1038/nsmb.1458

The crystal structure of the yeast RNA Pol II elongation complex bound to the inhibitor alpha-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.


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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.


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

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.


Molecular recognition of nitrated fatty acids by PPARbold gamma

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

PPARgamma 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 PPARgamma in complex with a physiological ligand, nitrated linoleic acid, is now described, showing differences with synthetic agonists that may have physiological relevance.


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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.


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.


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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