PU.1 and C/EBP{alpha} synergistically program distinct response to NF-{kappa}B activation through establishing monocyte specific enhancers [Cell Biology]

PU.1 and C/EBP{alpha} synergistically program distinct response to NF-{kappa}B activation through establishing monocyte specific enhancers [Cell Biology]: "Unraveling the complexity of transcriptional programs coded by different cell types has been one of the central goals of cell biology. By using genome-wide location analysis, we examined how two different cell types generate different responses to the NF-κB signaling pathway. We showed that, after TNF-α treatment, the NF-κB p65 subunit binds to distinct genome locations and subsequently induces different subsets of genes in human monocytic THP-1 cells versus HeLa cells. Interestingly, the differential p65 binding in two cell types correlates with preexisting cell type-specific enhancers before TNF-α stimulation, marked by histone modifications. We also found that two transcription factors, PU.1 and C/EBPα, appear to synergistically mediate enhancer creation and affect NF-κB target selection in THP-1 cells. In HeLa cells, coexpression of PU.1 and C/EBPα conferred TNF-α responsiveness to a subset of THP-1–specific NF-κB target genes. These results suggest that the diversity of transcriptional programs in mammalian cells arises, at least in part, from preexisting enhancers that are established by cell-specific transcription factors."

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor: "

Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor

Nature Genetics 43, 379 (2011).
doi:10.1038/ng.790

Authors: Sandra Ruf, Orsolya Symmons, Veli Vural Uslu, Dirk Dolle, Chloé Hot, Laurence Ettwiller & François Spitz

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The dawn of beer remains elusive in archaeological record

The dawn of beer remains elusive in archaeological record: "

NEW YORK CITY--Who brewed--and then enjoyed--the first beer? The civilization responsible for the widely beloved beverage must have been a very old one, but we don't yet know who first brewed up a batch of beer, Christine Hastorf explained in a March 10 lecture at New York University on the archaeology of beer. [More]

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Interactions among Polycomb Domains Are Guided by Chromosome Architecture

Interactions among Polycomb Domains Are Guided by Chromosome Architecture: "Author Summary

The folding of chromosomes inside the cell nucleus is a fascinating yet poorly understood topological problem. It is thought that certain genomic loci that are distant in the linear genome may come together in nuclear space by folding of the chromosome fiber. Previously, such a long-range interaction was found in Drosophila for two genomic loci that are known to be bound by the Polycomb Repressive Complex. Because hundreds of genes are known to be bound by Polycomb proteins, we asked whether such long-range contacts are more common. To address this, we optimized the Chromosome Conformation Capture on Chip (4C) technology for use in small tissue samples. Using this technique in dissected larval brains, we found that indeed Polycomb target genes interact frequently with each other, even when they are separated by megabases of sequence. However, these long-range interactions occur almost exclusively on the same chromosome arm. By using a rearranged chromosome in which segments are swapped between two arms, we demonstrate that not DNA sequence but chromosome architecture imposes this restriction. Taken together, our data demonstrate that Polycomb target genes extensively interact in nuclear space, but only when they are located on the same chromosome arm.

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An Early Cambrian Hemichordate Zooid

An Early Cambrian Hemichordate Zooid: "Xian-guang Hou, Richard J. Aldridge, David J. Siveter, Derek J. Siveter, Mark Williams, Jan Zalasiewicz, Xiao-ya Ma. Hemichordates are known as fossils from at least the earliest mid-Cambrian Period (ca. 510 Ma) and are well represented in the fossil record by the graptolithinid pterobranchs (“graptolites”), whi...."

A cis-regulatory map of the Drosophila genome

A cis-regulatory map of the Drosophila genome: "

A cis-regulatory map of the Drosophila genome

Nature 471, 7339 (2011). doi:10.1038/nature09990

Authors: Nicolas Nègre, Christopher D. Brown, Lijia Ma, Christopher Aaron Bristow, Steven W. Miller, Ulrich Wagner, Pouya Kheradpour, Matthew L. Eaton, Paul Loriaux, Rachel Sealfon, Zirong Li, Haruhiko Ishii, Rebecca F. Spokony, Jia Chen, Lindsay Hwang, Chao Cheng, Richard P. Auburn, Melissa B. Davis, Marc Domanus, Parantu K. Shah, Carolyn A. Morrison, Jennifer Zieba, Sarah Suchy, Lionel Senderowicz, Alec Victorsen, Nicholas A. Bild, A. Jason Grundstad, David Hanley, David M. MacAlpine, Mattias Mannervik, Koen Venken, Hugo Bellen, Robert White, Mark Gerstein, Steven Russell, Robert L. Grossman, Bing Ren, James W. Posakony, Manolis Kellis & Kevin P. White

Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II regulation and insulator elements; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships.

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The developmental transcriptome of Drosophila melanogaster

The developmental transcriptome of Drosophila melanogaster: "

The developmental transcriptome of Drosophila melanogaster

Nature 471, 7339 (2011). doi:10.1038/nature09715

Authors: Brenton R. Graveley, Angela N. Brooks, Joseph W. Carlson, Michael O. Duff, Jane M. Landolin, Li Yang, Carlo G. Artieri, Marijke J. van Baren, Nathan Boley, Benjamin W. Booth, James B. Brown, Lucy Cherbas, Carrie A. Davis, Alex Dobin, Renhua Li, Wei Lin, John H. Malone, Nicolas R. Mattiuzzo, David Miller, David Sturgill, Brian B. Tuch, Chris Zaleski, Dayu Zhang, Marco Blanchette, Sandrine Dudoit, Brian Eads, Richard E. Green, Ann Hammonds, Lichun Jiang, Phil Kapranov, Laura Langton, Norbert Perrimon, Jeremy E. Sandler, Kenneth H. Wan, Aarron Willingham, Yu Zhang, Yi Zou, Justen Andrews, Peter J. Bickel, Steven E. Brenner, Michael R. Brent, Peter Cherbas, Thomas R. Gingeras, Roger A. Hoskins, Thomas C. Kaufman, Brian Oliver & Susan E. Celniker

Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA

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