Showing papers by "Roderic Guigó published in 2011"

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Abstract: The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

Abstract: Chronic lymphocytic leukaemia (CLL), the most frequent leukaemia in adults in Western countries, is a heterogeneous disease with variable clinical presentation and evolution. Two major molecular subtypes can be distinguished, characterized respectively by a high or low number of somatic hypermutations in the variable region of immunoglobulin genes. The molecular changes leading to the pathogenesis of the disease are still poorly understood. Here we performed whole-genome sequencing of four cases of CLL and identified 46 somatic mutations that potentially affect gene function. Further analysis of these mutations in 363 patients with CLL identified four genes that are recurrently mutated: notch 1 (NOTCH1), exportin 1 (XPO1), myeloid differentiation primary response gene 88 (MYD88) and kelch-like 6 (KLHL6). Mutations in MYD88 and KLHL6 are predominant in cases of CLL with mutated immunoglobulin genes, whereas NOTCH1 and XPO1 mutations are mainly detected in patients with unmutated immunoglobulins. The patterns of somatic mutation, supported by functional and clinical analyses, strongly indicate that the recurrent NOTCH1, MYD88 and XPO1 mutations are oncogenic changes that contribute to the clinical evolution of the disease. To our knowledge, this is the first comprehensive analysis of CLL combining whole-genome sequencing with clinical characteristics and clinical outcomes. It highlights the usefulness of this approach for the identification of clinically relevant mutations in cancer.

Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer.

Abstract: Differentiated mammary epithelium shows apicobasal polarity, and loss of tissue organization is an early hallmark of breast carcinogenesis. In BRCA1 mutation carriers, accumulation of stem and progenitor cells in normal breast tissue and increased risk of developing tumors of basal-like type suggest that BRCA1 regulates stem/progenitor cell proliferation and differentiation. However, the function of BRCA1 in this process and its link to carcinogenesis remain unknown. Here we depict a molecular mechanism involving BRCA1 and RHAMM that regulates apicobasal polarity and, when perturbed, may increase risk of breast cancer. Starting from complementary genetic analyses across families and populations, we identified common genetic variation at the low-penetrance susceptibility HMMR locus (encoding for RHAMM) that modifies breast cancer risk among BRCA1, but probably not BRCA2, mutation carriers: n = 7,584, weighted hazard ratio ((w)HR) = 1.09 (95% CI 1.02-1.16), p(trend) = 0.017; and n = 3,965, (w)HR = 1.04 (95% CI 0.94-1.16), p(trend) = 0.43; respectively. Subsequently, studies of MCF10A apicobasal polarization revealed a central role for BRCA1 and RHAMM, together with AURKA and TPX2, in essential reorganization of microtubules. Mechanistically, reorganization is facilitated by BRCA1 and impaired by AURKA, which is regulated by negative feedback involving RHAMM and TPX2. Taken together, our data provide fundamental insight into apicobasal polarization through BRCA1 function, which may explain the expanded cell subsets and characteristic tumor type accompanying BRCA1 mutation, while also linking this process to sporadic breast cancer through perturbation of HMMR/RHAMM.

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.

Abstract: Many genomic alterations associated with human diseases localize in noncoding regulatory elements located far from the promoters they regulate, making it challenging to link noncoding mutations or risk-associated variants with target genes. The range of action of a given set of enhancers is thought to be defined by insulator elements bound by the 11 zinc-finger nuclear factor CCCTC-binding protein (CTCF). Here we analyzed the genomic distribution of CTCF in various human, mouse and chicken cell types, demonstrating the existence of evolutionarily conserved CTCF-bound sites beyond mammals. These sites preferentially flank transcription factor-encoding genes, often associated with human diseases, and function as enhancer blockers in vivo, suggesting that they act as evolutionarily invariant gene boundaries. We then applied this concept to predict and functionally demonstrate that the polymorphic variants associated with multiple sclerosis located within the EVI5 gene impinge on the adjacent gene GFI1.

The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates

Abstract: Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the contribution of AS to the generation of phenotypic complexity and to study the evolution of splicing patterns. We have compared the AS of 309 protein-coding genes in the human ENCODE pilot regions against their mouse orthologs in unprecedented detail, utilizing traditional transcriptomic and RNAseq data. The conservation status of every transcript has been investigated, and each functionally categorized as coding (separated into coding sequence [CDS] or nonsense-mediated decay [NMD] linked) or noncoding. In total, 36.7% of human and 19.3% of mouse coding transcripts are species specific, and we observe a 3.6 times excess of human NMD transcripts compared with mouse; in contrast to previous studies, the majority of species-specific AS is unlinked to transposable elements. We observe one conserved CDS variant and one conserved NMD variant per 2.3 and 11.4 genes, respectively. Subsequently, we identify and characterize equivalent AS patterns for 22.9% of these CDS or NMD-linked events in nonmammalian vertebrate genomes, and our data indicate that functional NMD-linked AS is more widespread and ancient than previously thought. Furthermore, although we observe an association between conserved AS and elevated sequence conservation, as previously reported, we emphasize that 30% of conserved AS exons display sequence conservation below the average score for constitutive exons. In conclusion, we demonstrate the value of detailed comparative annotation in generating a comprehensive set of AS transcripts, increasing our understanding of AS evolution in vertebrates. Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution.

De longs ARN non codants activateurs de la transcription des gènes

Abstract: m/s n° 4, vol. 27, avril 2011 DOI : 10.1051/medsci/2011274009 6. Turner N, Pearson A, Sharpe R, et al. FGFR1 amplification drives endocrine therapy resistance and is a therapeutic target in breast cancer. Cancer Res 2010 ; 70 : 2085-94. 7. Zhang J, Liu X, Datta A, et al. RCP is a human breast cancer-promoting gene with Ras-activating function. J Clin Invest 2009 ; 119 : 2171-83. 8. Bernard-Pierrot I, Gruel N, Stransky N, et al. Characterization of the recurrent 8p11-12 amplicon identifies PPAPDC1B, a phosphatase protein, as a new therapeutic target in breast cancer. Cancer Res 2008 ; 68 : 7165-75. 9. Kwek SS, Roy R, Zhou H, et al. Co-amplified genes at 8p12 and 11q13 in breast tumors cooperate with two major pathways in oncogenesis. Oncogene 2009 ; 28 : 1892-1903. 10. Nakamura M, Runko AP, Sagerstrom CG. A novel subfamily of zinc finger genes involved in embryonic development. J Cell Biochem 2004 ; 93 : 887-95. REFERENCES

Review of 'Cap‐analysis gene expression'

Abstract: Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain E-mail: roderic.guigo@crg.cat Methods to characterise transcriptomes (i.e. to identify and quantify all transcript species in a given population of cells) have, until very recently, focused either on the qualitative discovery and cataloguing of transcript species in a given cell type or condition through multiplex cDNA cloning and sequencing of normalised cDNA libraries [1] or, alternatively, on the quantification of known transcript species through DNA microarrays [2]. Recent technical developments in massively parallel sequencing seem to have provided, for the first time, the throughput required to offer both transcript discovery and quantification simultaneously. Before the advent of the new sequencing technologies, however, capped analysis of gene expression (CAGE) offered genome wide transcript discovery and quantification. CAGE is a tagging technology in which short (20 or 27 base pair) sequences (tags) are extracted from the 50ends of the capped RNA molecules, concatenated and the concatenamers sequenced. Because many tags (10 to 20) can be collated in a single sequence, even with classic Sanger sequencing, it is possible to perform high throughput genome wide transcriptome surveys; and while CAGE does not provide information on the complete transcript structure, and, therefore, it cannot discern between alternative transcript isoforms, it does provide quantitative information on usage of all transcription start sites (TSS), known and novel, in the cellular condition assayed. It is thus particularly appropriate to measure the genome wide transcriptional activity of promoters. Combined with the throughput of the massively parallel sequencing instruments, which, incidentally, eliminate the need for tag concatenation, it is theoretically possible to identify and measure RNA molecules at a molecular level for each 1 to 10 cells. Capped analysis of gene expression has been an essential tool in transcriptome studies within several large-scale international projects, such as FANTOM3 [3] and ENCODE [4]. CAGE data has enabled valuable insights into promoter architecture and evolution, the discovery of novel TSSs, biological variability in the use of alternative TSSs and description of antisense-transcription. CAGE is, indeed, one of the technologies underlying the paradigmatic shift that we are witnessing on our understanding of eukaryotic transcriptomes. From a view of the genome composed of well defined genes isolated among large intergenic regions and mostly coding for proteins, we are transitioning to a view of the genome as a continuum of transcripts of many different classes with poorly defined boundaries, often overlapping in sense and antisense direction [4, 5]. The book edited by Piero Carninci provides an excellent guide to the CAGE method. Describing experimental procedures and bioinformatic analyses, it appeals to bench scientists and bioinformaticians alike, and even more so to the interested newcomer, as it gives examples of such applications and biological insights drawn from them. Starting with an introduction to CAGE and other technologies used for expression analyses, the book follows up with a well commented (and established) protocol for constructing CAGE libraries and a description of paired end DOI 10.1002/bies.201000144