Structured RNAs in the ENCODE selected regions of the human genome

Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack characteristic signals in primary sequence, comparative approaches evaluating evolutionary conservation of structures are most promising. We have used three recently introduced programs based on either phylogenetic–stochastic context-free grammar (EvoFold) or energy directed folding (RNAz and AlifoldZ), yielding several thousand candidate structures (corresponding to ∼2.7% of the ENCODE regions). EvoFold has its highest sensitivity in highly conserved and relatively AU-rich regions, while RNAz favors slightly GC-rich regions, resulting in a relatively small overlap between methods. Comparison with the GENCODE annotation points to functional RNAs in all genomic contexts, with a slightly increased density in 3′-UTRs. While we estimate a significant false discovery rate of ∼50%–70% many of the predictions can be further substantiated by additional criteria: 248 loci are predicted by both RNAz and EvoFold, and an additional 239 RNAz or EvoFold predictions are supported by the (more stringent) AlifoldZ algorithm. Five hundred seventy RNAz structure predictions fall into regions that show signs of selection pressure also on the sequence level (i.e., conserved elements). More than 700 predictions overlap with noncoding transcripts detected by oligonucleotide tiling arrays. One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%).

Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.

Evidence on the determinants of foreign direct investment: the case of three european regions

This study aims at analyzing the determinants of FDI (foreign direct investment) inflows for a group of European regions. The originality of this approach lies in the use of disaggregated regional data. First, we develop a qualitative description of our database and discuss the importance of the macroeconomic determinants in attracting FDI. Then, we provide an econometric exercise to identify the potential determinants of FDI. In spite of choosing regions presenting economic similarities, we show that regional FDI inflows rely on a combination of factors that differs from one region to another.

Convergence across countries and regions: theory and empirics

This paper surveys the recent literature on convergence across countries and regions. I discuss the main convergence and divergence mechanisms identified in the literature and develop a simple model that illustrates their implications for income dynamics. I then review the existing empirical evidence and discuss its theoretical implications. Early optimism concerning the ability of a human capital-augmented neoclassical model to explain productivity differences across economies has been questioned on the basis of more recent contributions that make use of panel data techniques and obtain theoretically implausible results. Some recent research in this area tries to reconcile these findings with sensible theoretical models by exploring the role of alternative convergence mechanisms and the possible shortcomings of panel data techniques for convergence analysis.

The effect of structural fund spending on the spanish regions: an assessment of the 1994-99 objective 1 CSF

This paper analyzes the growth and employment effects of the 1994-99 Community Support Framework (CSF) for the Objective 1 Spanish regions using a simple supply-side model estimated with a panel of regional data. The results suggest that the impact of the Structural Funds in Spain has been quite sizable, adding around a percentage point to annual output growth in the average Objective 1 region and 0.4 points to employment growth. Over the period 1994-2000, the Framework has resulted in the creation of over 300,000 new jobs and has eliminated 20% of the initial gap in income per capita between the assisted regions and the rest of the country.

Spillover effects of public capital formation: evidence from the spanish regions

Maybe because of the inconclusive nature of the results on the impact of public capital on output at the regional level, the issue of the possible existence of the regional spillovers from public capital formation has received little attention. The objective of this paper is to provide evidence on the possible existence of such spillovers. We consider the case of Spain and its seventeen regions. Our methodological approach consists in estimating an aggregate VAR model for Spain as well as seventeen region-specific VAR models in which both capital installed in the region and capital installed outside the region are allowed to play a role in enhancing regional output. The estimation results can be summarized as follows. The aggregate effects of public capital formation in Spain are important. They cannot, however, be captured in their entirety by the direct effects in each region from public capital installed in the region itself. When for each region both the capital installed in the region and the capital installed outside the region are considered the total disaggregated effect from the seventeen regional models are very much in line with the aggregate results. Furthermore, the aggregate effect seems to be due in almost equal parts to the direct and spillover effects of public capital formation. Ultimately, this paper establishes the relevance of both capital installed in each region and spillover effects in the understanding of the regional decomposition of the aggregate effects of public capital formation. In doing so it opens the door to some tantalizing and potentially highly charged research issues in terms of the determination of the optimal location of public investment projects.

Labor productivity in Europe: evidence from a sample of regions

The present paper aims at analyzing the sources of productivity in Europe to account for its recent underperformance and identify potential geographic idiosyncracies. We study the productivity performance and its sources in a sample of ten European regions belonging to four countries (France, Germany, Italy and Spain). Exploiting the increasing availability of disaggregated data at regional level in Europe, we propose both a descriptive statistics and an econometric analysis of productivity sources since 1995. Our main finding is that the sources of labor productivity are rather heterogeneous across our sample but may be associated with regional or national idiosyncracies.

GenRegion: aplicatiu de generació de màscares per a la codificació d'imatges amb regions d'interès

En aquest projecte, titulat "GenRegion: aplicatiu de generació de màscares per a la codificació d'imatges amb regions d'interès", presentem una aplicació multiplataforma que visualitza imatges PGM i PPM amb un mínim cost de memòria i sobre les quals podrem dibuixar regions d'interès. L'aplicació carregarà només la part de la imatge que podem visualitzar a la pantalla de treball permetent treballar amb imatges de gran tamany. Les regions definides seran accessibles en tot moment, podent modificar-les i esborrar-les. Finalment podrem generar ja sigui una màscara de la imatge actual amb les regions definides o bé una imatge idèntica a l'original però on es visualitzaran les regions definides.

Testing, not modelling, the impact of cohesion support: a theoretical framework and some preliminary results for the Spanish regions

This paper develops a simple model that can be used to estimate the effectiveness of Cohesion expenditure relative to similar but unsubsidized projects, thereby making it possible to explicitly test an important assumption that is often implicit in estimates of the impact of Cohesion policies. Some preliminary results are reported for the case of infrastructure investment in the Spanish regions.

Tax Coordination Between Regions in Spain. The Role of the Courts

Overview of the Tax Coordination of the Regions in Spain from the point of view of the role of the Courts in developing the present system

Tax Coordination Between Regions in Spain - Role of the Courts

Análisis de la jurisprudencia constitucional española sobre la distribución de competencias tributarias entre los distintos niveles de gobierno.

Gender gap index in Spain by regions

Every year, the World Economic Forum publishes the World Gender Gap Report mainly based on the results of the Global Gender Gap Index (GGGI) computed by country. This index is made out of four subindexes to capture the magnitude of the gender gap in 4 areas: educational attainment, economic participation and opportunity, political empowerment, and health and survival; its methodology was reformed in 2006. In this paper we adapt the GGGI to construct a Regional Gender Gap Index (RGGI) and we compute it by regions (Comunidades Autónomas) in Spain with 2006 data. The RGGI could be applied to other regions. Results of the RGGI show that not only are there gender gap differences between Spanish regions in Spain, but that there are at the political empowerment and economic participation and opportunity categories that those differences are strongest. Geographic distribution of the gender gap shows that the deepest gaps are, in general, located in the northern regions (Euskadi, with a high score, and Murcia and Extremadura, with low scores, being exceptions); this is mainly due to the poor participation in politics of women in those regions.

I. Identification and characterisation of epigenetically altered tumor supressor genes by proteomic and genomic approches / II. Studies of genes regualted by MeCP2 union to its promoter regions by proteomic and genmomic approches

DNA methylation has an important impact on normal cell physiology, thus any defects in this mechanism may be related to the development of various diseases In this project we are interested in identifying epigeneticaliy modified genes, in general controlled by processes related to the DNA methylation, by means of a new strategy combining protomic and genomic analyses. First, the two Dimensional-Difference Gel Electrophoresis (2-DIGE) protein analyses of extracts obtained from HCT-116 wt and double knockout for DNMT1 and DNMT3b (DKO) cells revealed 34 proteins overexpressed in the condition of DNMTs depletion. From five genes with higher transcript lavels in DKO cells, comparing with HCT-116 wt. oniy AKR1B1, UCHLl and VIM are melhylated in HCT-116. As expected. the DNA methvlation 1s lost in DKO cells. The rneth,vl ation of VIM and UCHLl promoters in some cancer samples has already been repaired, thus further studies has been focused on AKRlBI. AKR1B1 expression due lo DNA methyiaton of promoter region seems to occur specilfically in the colon cancer cell Iines. which was confirmed in the DNA rnethylation status and expression analyses. performed on 32 different cancer cell lines (including colon, breast, lymphoma, leukemia, neuroblastoma, glioma and lung cancer cell Iines) as well as normal colon and normal lymphocytes samples. AKRIBI expression after treatments with DNA demethvlating agent (AZA) was rescued in 5 coloncancer cell lines (including genetic regulation of the candidate gene. The methylation status of the rest of the genes identified in proteomic analysis was checked by methylation specific PCR (MSP) experiment and all appeared to be unmethylated. The similar research has been done also bv means of Mecp2-null mouse model For 14 selected candidate genes the analyses of expression leveis, methylation Status and MeCP2 interaction with promoters are currently being performed.