Molecular Systems Biology - New articles published - 1 Feb 2015

January 2015 | Volume 11, Number 1 Submit Table of Contents Articles News and Views Reports Articles Volume 11, Number 1 Articles Deciphering preferential interactions within supramolecular protein complexes: the proteasome case A new approach for analyzing sub‐complex composition by combining affinity purification and protein abundance correlation profiling by mass spectrometry is employed to characterize the dynamic and heterogeneous nature of human proteasome complexes. Bertrand Fabre, Thomas Lambour, Luc Garrigues, François Amalric, Nathalie Vigneron, Thomas Menneteau, Alexandre Stella, Bernard Monsarrat, Benoît Van den Eynde, Odile Burlet‐Schiltz, and Marie‐Pierre Bousquet‐Dubouch Published online 05.01.2015 A high‐throughput ChIP‐Seq for large‐scale chromatin studies A new approach provides a rapid and accurate genome‐wide overview of the chromatin status of multiple yeast chromatin‐associated mutants at once. The simultaneous profiling of epigenetic marks in the mutants is achieved by multiplex immuno‐precipitation of barcoded chromatin samples. Christophe D Chabbert, Sophie H Adjalley, Bernd Klaus, Emilie S Fritsch, Ishaan Gupta, Vicent Pelechano, and Lars M Steinmetz Published online 12.01.2015 Genome‐wide study of mRNA degradation and transcript elongation in Escherichia coli Genome‐wide measurements of mRNA degradation and transcription elongation rates allow the quantitative description of gene expression coordination in bacteria and establish a model for RNA processing involving co‐transcriptional RNA degradation. Huiyi Chen, Katsuyuki Shiroguchi, Hao Ge, and Xiaoliang Sunney Xie Published online 12.01.2015 Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature Crosstalk between the circadian clock and light/temperature signals controls seasonal plant development. Integrated mathematical models of the clock, flowering and elongation pathways identify new behaviours in light and temperature signalling. Daniel D Seaton, Robert W Smith, Young Hun Song, Dana R MacGregor, Kelly Stewart, Gavin Steel, Julia Foreman, Steven Penfield, Takato Imaizumi, Andrew J Millar, and Karen J Halliday Published online 19.01.2015 Essential gene disruptions reveal complex relationships between phenotypic robustness, pleiotropy, and fitness Mutations that alter expression of essential genes are potent regulators of phenotypic heterogeneity. Reducing gene function can result in global changes in morphological variation that are related to pleiotropy but initially have minimal impacts on fitness. Christopher R Bauer, Shuang Li, and Mark L Siegal Published online 21.01.2015 Proteomic analyses reveal distinct chromatin‐associated and soluble transcription factor complexes Chromatin‐associated and soluble complexes for 56 human transcription factors (TFs), identified by tandem affinity purification followed by mass spectrometry, indicate that distinct binding partners dictate the regulation and functions of TFs. Xu Li, Wenqi Wang, Jiadong Wang, Anna Malovannaya, Yuanxin Xi, Wei Li, Rudy Guerra, David H Hawke, Jun Qin, and Junjie Chen Published online 21.01.2015 News and Views Changing partners: transcription factors form different complexes on and off chromatin A proteomic analysis of the interactomes of 56 transcription factors (TFs) by Chen and colleagues (Li et al, 2015) reveals distinct chromatin‐associated and soluble TF complexes and provides a resource for further analyses of TF function and regulation. Zongling Ji and Andrew D Sharrocks Published online 21.01.2015 Reports Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome‐reduced bacterium A genome essentiality analysis in the genome‐reduced bacterium Mycoplasma pneumoniae, reveals that protein essentiality should be considered at the domain level and that small proteins (<0ESCAPE1LESS2THAN3/> 100 aa) and ncRNAs are frequently essential genomic elements. Maria Lluch‐Senar, Javier Delgado, Wei‐Hua Chen, Verónica Lloréns‐Rico, Francis J O'Reilly, Judith AH Wodke, E Besray Unal, Eva Yus, Sira Martínez, Robert J Nichols, Tony Ferrar, Ana Vivancos, Arne Schmeisky, Jörg Stülke, Vera van Noort, Anne‐Claude Gavin, Peer Bork, and Luis Serrano Published online 21.01.2015 Articles From intracellular signaling to population oscillations: bridging size‐ and time‐scales in collective behavior A simple two‐variable model in combination with quantitative in vivo measurements of single‐cell and population signaling dynamics is used to analyze the emergence of collective cAMP oscillations in Dictyostelium discoideum. Allyson E Sgro, David J Schwab, Javad Noorbakhsh, Troy Mestler, Pankaj Mehta, and Thomas Gregor Published online 23.01.2015 Negative feedback buffers effects of regulatory variants Local trans regulation, mainly due to negative feedback, buffers effects of cis‐regulatory variants by about 15%. This buffering is stronger for essential genes and genes with low to middle expression levels, for which tight regulation matters most. Daniel M Bader, Stefan Wilkening, Gen Lin, Manu M Tekkedil, Kim Dietrich, Lars M Steinmetz, and Julien Gagneur Published online 29.01.2015   Unsubscribe from or edit your subscription for this service. Or by mail: Customer Service * 425 Broadway St * Redwood City, CA 94063 * U.S.A. Copyright © 2015 by the European Molecular Biology Organisation.