RNAs en todos lados.

A series of reports over the last few years have indicated that a much larger portion of the mammalian genome is transcribed than can be accounted for by currently annotated genes, but the quantity and nature of these additional transcripts remains unclear. Here, we have used data from single- and paired-end RNA-Seq and tiling arrays to assess the quantity and composition of transcripts in PolyA+ RNA from human and mouse tissues. Relative to tiling arrays, RNA-Seq identifies many fewer transcribed regions (“seqfrags”) outside known exons and ncRNAs. Most nonexonic seqfrags are in introns, raising the possibility that they are fragments of pre-mRNAs. The chromosomal locations of the majority of intergenic seqfrags in RNA-Seq data are near known genes, consistent with alternative cleavage and polyadenylation site usage, promoter- and terminator-associated transcripts, or new alternative exons; indeed, reads that bridge splice sites identified 4,544 new exons, affecting 3,554 genes. Most of the remaining seqfrags correspond to either single reads that display characteristics of random sampling from a low-level background or several thousand small transcripts (median length = 111 bp) present at higher levels, which also tend to display sequence conservation and originate from regions with open chromatin. We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known exons, and the genome is not as pervasively transcribed as previously reported.

Citation: van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2010) Most “Dark Matter” Transcripts Are Associated With Known Genes. PLoS Biol 8(5): e1000371. doi:10.1371/journal.pbio.1000371

The DNA-binding landscape

GENE REGULATION

The DNA-binding landscape

Proteins or small molecules designed to bind certain DNA sequences and to regulate target genes have much promise in both basic and applied research. Aseem Ansari and colleagues at the University of Wisconsin, Madison, therefore tested the specificity of factor binding to DNA. They used custom DNA arrays displaying every possible 10-mer sequence—almost a half a million of them—to examine the binding profiles of engineered hairpin polyamides and protein transcription factors, as well as of several natural DNA-binding proteins, across sequence space. They quickly ran into a problem. The data were just too complex to understand intuitively. “We had this comprehensive binding dataset,” says Ansari, “and the first question was, how do you look at these data? If you use colors or tables or graphs to represent it, things begin to get very complicated very quickly.” They saw that protein transcription factors, in particular, bind fairly broadly across sequence space and that, although it is possible to extract a consensus binding motif, this often did not tell the whole story. What is more, the consequences of changing particular residues in a binding motif were not always simple or additive. So they had to find a new way of visualizing the data.

Nature Methods 7, 254 - 255 (2010)
doi:10.1038/nmeth0410-254a

Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible Promoter
Constitutive promoters are used routinely to drive ectopic gene expression. Here, we carried out a systematic comparison of eight commonly used constitutive promoters (SV40, CMV, UBC, EF1A, PGK and CAGG for mammalian systems, and COPIA and ACT5C for Drosophila systems). We also included in the comparison the TRE promoter, which can be activated by the rtTA transcriptional activator in a doxycycline-inducible manner. To make our findings representative, we conducted the comparison in a variety of cell types derived from several species. We found that these promoters vary considerably from one another in their strength. Most promoters have fairly consistent strengths across different cell types, but the CMV promoter can vary considerably from cell type to cell type. At maximal induction, the TRE promoter is comparable to a strong constitutive promoter. These results should facilitate more rational choices of promoters in ectopic gene expression studies.
link

Deciphering the splicing code

Artículo

International network of cancer genome projects

Nature 464, 993-998 (15 April 2010) doi:10.1038/nature08987

International Cancer Genome Consortium
Top of page
The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Cancer remodeling in a basal-like breast cancer metastasis and xenograft.

Nature. April 15, 2010.

Genome remodelling in a basal-like breast cancer metastasis and xenograft

Massively parallel DNA sequencing allows entire genomes to be screened for genetic changes associated with tumour progression. Here, the genomes of four DNA samples from a 44-year-old African-American patient with basal-like breast cancer were analysed. The samples came from peripheral blood, the primary tumour, a brain metastasis and a xenograft derived from the primary tumour. The findings indicate that cells with a distinct subset of the primary tumour mutation might be selected during metastasis and xenografting.

http://www.nature.com/nature/journal/v464/n7291/abs/nature08987.html

doi:10.1038/nature08989

Transcriptome analyses of mouse and human mammary cell subpopulations reveals multiple conserved genes and pathways

Breast Cancer Research 2010, 12:R21doi:10.1186/bcr2560

Published:	26 March 2010

Introduction

Molecular characterization of the normal epithelial cell types that reside in the mammary gland is an important step towards understanding pathways that regulate self-renewal, lineage commitment and differentiation along the hierarchy. Here we determined the gene expression signatures of four distinct subpopulations isolated from the mouse mammary gland. The epithelial cell signatures were used to interrogate mouse models of mammary tumorigenesis, and compared with their normal human counterpart subsets in order to identify conserved genes and networks.

Methods

RNA was prepared from freshly sorted mouse mammary cell subpopulations (mammary stem cell (MaSC)-enriched, committed luminal progenitor, mature luminal and stromal cell) and used for gene expression profiling analysis on the Illumina platform. Gene signatures were derived, and compared with those previously reported for the analogous normal human mammary cell subpopulations. The mouse and human epithelial subset signatures were then subjected to Ingenuity Pathway Analysis (IPA) to identify conserved pathways.

Results

The four mouse mammary cell subpopulations exhibited distinct gene signatures. Comparison of these signatures with the molecular profiles of different mouse models of mammary tumorigenesis revealed that tumors arising in MMTV-Wnt-1 and p53-/- mice were enriched for MaSC-subset genes, while the gene profiles of MMTV-Neu and MMTV-PyMT tumors were most concordant with the luminal progenitor cell signature. Comparison of the mouse mammary epithelial cell signatures with their human counterparts revealed substantial conservation of genes, while IPA highlighted a number of conserved pathways in the three epithelial subsets.

Conclusions

The conservation of genes and pathways across species further validates the use of the mouse as a model to study mammary gland development and highlights pathways that are likely to govern cell-fate decisions and differentiation. It is noteworthy that many of the conserved genes in the MaSC population have been considered as epithelial-mesenchymal transition (EMT) signature genes. Therefore, the expression of these genes in tumor cells may reflect basal epithelial cell characteristics and not necessarily cells that have undergone an EMT. Comparative analyses of normal mouse epithelial subsets with murine tumor models have implicated distinct cell types in contributing to tumorigenesis in different models.

B-cell-derived lymphotoxin promotes castration-resistant prostate cancer.

Searched Keywords: Stat3, IKK, Microenvironment, Inflammation, Cancer

Nature. 2010 Mar 11;464(7286):302-5.

Ammirante M, Luo JL, Grivennikov S, Nedospasov S, Karin M.

Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology and Cancer Center, School of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0723, USA.

Prostate cancer (CaP) progresses from prostatic intraepithelial neoplasia through locally invasive adenocarcinoma to castration-resistant metastatic carcinoma. Although radical prostatectomy, radiation and androgen ablation are effective therapies for androgen-dependent CaP, metastatic castration-resistant CaP is a major complication with high mortality. Androgens stimulate growth and survival of prostate epithelium and early CaP. Although most patients initially respond to androgen ablation, many develop castration-resistant CaP within 12-18 months. Despite extensive studies, the mechanisms underlying the emergence of castration-resistant CaP remain poorly understood and their elucidation is critical for developing improved therapies. Curiously, castration-resistant CaP remains androgen-receptor dependent, and potent androgen-receptor antagonists induce tumour regression in castrated mice. The role of inflammation in castration-resistant CaP has not been addressed, although it was reported that intrinsic NF-kappaB activation supports its growth. Inflammation is a localized protective reaction to injury or infection, but it also has a pathogenic role in many diseases, including cancer. Whereas acute inflammation is critical for host defence, chronic inflammation contributes to tumorigenesis and metastatic progression. The inflammation-responsive IkappaB kinase (IKK)-beta and its target NF-kappaB have important tumour-promoting functions within malignant cells and inflammatory cells. The latter, including macrophages and lymphocytes, are important elements of the tumour microenvironment, but the mechanisms underlying their recruitment remain obscure, although they are thought to depend on chemokine and cytokine production. We found that CaP progression is associated with inflammatory infiltration and activation of IKK-alpha, which stimulates metastasis by an NF-kappaB-independent, cell autonomous mechanism. Here we show that androgen ablation causes infiltration of regressing androgen-dependent tumours with leukocytes, including B cells, in which IKK-beta activation results in production of cytokines that activate IKK-alpha and STAT3 in CaP cells to enhance hormone-free survival.

Do scientists really need a PhD?

Young scientists at a Chinese genomics institute are foregoing conventional postgraduate training for the chance to be part of major scientific initiatives. Is this the way of the future?

nature Vol 464 | Issue no. 7285 | 4 March 2010

www.nature.com/nature/journal/v464/n7285/pdf/464007a.pdf

Method of the Year 2009, pluripotency

Nature Methods' Method of the Year 2009 goes to induced pluripotency for its potential for biological discovery. This series of articles—and the related video—showcase how induced pluripotency is coming into its own in 2009 as a tool for discovery in both basic and disease biology and explore the incredible impact this area promises to have in biological research.

January 2010, Volume 7 No 1 pp1-85

IAP Regulation of Metastasis

Cancer Cell, Volume 17, Issue 1, 53-64, 19 January 2010 | Copyright © 2010 Elsevier Inc. All rights reserved. | 10.1016/j.ccr.2009.11.021

Swarna Mehrotra, Lucia R. Languino, Christopher M. Raskett, Arthur M. Mercurio, Takehiko Dohi, Dario C. Altieri

* Highlights
* Inhibitor-of-Apoptosis (IAP) proteins mediate tumor cell invasion and metastasis
* This pathway requires NF-κB activation and is independent of IAP cytoprotection
* IAP tumor cell invasion involves signaling by fibronectin-β1 integrin and FAK, Src.

* Summary
* Inhibitor-of-Apoptosis (IAP) proteins contribute to tumor progression, but the requirements of this pathway are not understood. Here, we show that intermolecular cooperation between XIAP and survivin stimulates tumor cell invasion and promotes metastasis. This pathway is independent of IAP inhibition of cell death. Instead, a survivin-XIAP complex activates NF-κB, which in turn leads to increased fibronectin gene expression, signaling by β1 integrins, and activation of cell motility kinases FAK and Src. Therefore, IAPs are direct metastasis genes, and their antagonists could provide antimetastatic therapies in patients with cancer.

Journal stem cell work 'blocked'

By Pallab Ghosh Science correspondent, BBC News

Billions of pounds of public money is spent on stem cell research

Stem cell experts say they believe a small group of scientists is effectively vetoing high quality science from publication in journals.

In some cases they say it might be done to deliberately stifle research that is in competition with their own.

It has also emerged that 14 leading stem cell researchers have written an open letter to journal editors in order to highlight their dissatisfaction.

http://news.bbc.co.uk/2/hi/science/nature/8490291.stm