FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces

28 Pags.- 8 Figs. The definitive version is available at: http://link.springer.com/bookseries/7651 and http://link.springer.com/book/10.1007/978-1-4939-6396-6.FootprintDB is a database and search engine that compiles regulatory sequences from open access libraries of curated DNA cis-elements and motifs, and their associated transcription factors (TFs). It systematically annotates the binding interfaces of the TFs by exploiting protein-DNA complexes deposited in the Protein Data Bank. Each entry in footprintDB is thus a DNA motif linked to the protein sequence of the TF(s) known to recognize it, and in most cases, the set of predicted interface residues involved in specific recognition. This chapter explains step-by-step how to search for DNA motifs and protein sequences in footprintDB and how to focus the search to a particular organism. Two real-world examples are shown where this software was used to analyze transcriptional regulation in plants. Results are described with the aim of guiding users on their interpretation, and special attention is given to the choices users might face when performing similar analyzes.This work was funded by grant Euroinvestigación EUI2008-03612 under the framework of the Transnational (Germany, France, Spain) Cooperation within the PLANT-KBBE Initiative.Peer reviewe

Macromoléculas biológicas: proteínas, DNA y RNA

27 Pags.- 14 Figs. Licencia Creative Commons BY-NC-SA 4.0Peer reviewe

Macromoléculas biológicas: proteínas, DNA y RNA

27 Pags.- 14 Figs. Licencia Creative Commons BY-NC-SA 4.0Peer reviewe

OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors

17 pags., 8 Figs.High salinity causes remarkable losses in rice productivity worldwide mainly because it inhibits growth and reduces grain yield. To cope with environmental changes, plants evolved several adaptive mechanisms, which involve the regulation of many stress-responsive genes. Among these, we have chosen OsRMC to study its transcriptional regulation in rice seedlings subjected to high salinity. Its transcription was highly induced by salt treatment and showed a stress-dose-dependent pattern. OsRMC encodes a receptor-like kinase described as a negative regulator of salt stress responses in rice. To investigate how OsRMC is regulated in response to high salinity, a salt-induced rice cDNA expression library was constructed and subsequently screened using the yeast one-hybrid system and the OsRMC promoter as bait. Thereby, two transcription factors (TFs), OsEREBP1 and OsEREBP2, belonging to the AP2/ERF family were identified. Both TFs were shown to bind to the same GCC-like DNA motif in OsRMC promoter and to negatively regulate its gene expression. The identified TFs were characterized regarding their gene expression under different abiotic stress conditions. This study revealed that OsEREBP1 transcript level is not significantly affected by salt, ABA or severe cold (5 °C) and is only slightly regulated by drought and moderate cold. On the other hand, the OsEREBP2 transcript level increased after cold, ABA, drought and high salinity treatments, indicating that OsEREBP2 may play a central role mediating the response to different abiotic stresses. Gene expression analysis in rice varieties with contrasting salt tolerance further suggests that OsEREBP2 is involved in salt stress response in rice.This work was supported by Fundação para a Ciência e a Tecnologia (FCT) through national funds allocated to research projects [POCI/BIA-BCM/56063/2004 and PTDC/BIA-BCM/099836/2008] and PhD scholarships [SFRH/BD/31011/2006 to TS, SFRH/BD/29258/2006 to DF, SFRH/BD/74946/2010 to AC, SFRH/BD/65229/2009 to DA, SFRH/BPD/34943/2007 to TL]. NS and IA were supported by Programa Ciência 2007, financed by POPH (QREN). AS and BCM work was supported by funding from Programa Euroinvestigación 2008 [EUI2008-03612].Peer reviewe

"Bioinformática con Ñ v1.0": a collaborative project of young Spanish scientists to write a complete book about Bioinformatics

Here we present a project aiming to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The idea of writing a book in Spanish language covering the most important topics in the field of Bioinformatics was born in the XIth Spanish Symposium on Bioinformatics in Barcelona two years ago. Different scientists have been involved in the project, from senior scientists to PhD students from different countries. The book intends to be the beginning of an open project, where all the chapters are susceptible of being updated and new topics can be incorporated in future versions. Current book version can be accessed online at http://goo.gl/UYG0o7.Peer Reviewe

FootprintDB: A database of transcription factors with annotated cis elements and binding interfaces

24 Pags., 5 figs., 8 suppl. figs., 2 tabls., 7 suppl. tabls. Available online 14 November 2013. This is a pre-copyedited, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version [Bioinformatics 30 (2): 258-265 (2014)] is available online at: http://bioinformatics.oxfordjournals.org/content/30/2/258.fullMotivation: Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases. Results: FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value.Funding: Programa Euroinvestigación/Plant KBBE 2008 (EUI2008-03612). Results have been achieved under the framework of the Transnational (Germany, France, Spain) Cooperation within the PLANT-KBBE Initiative, with Funding from Ministerio de Ciencia e Innovación, Agence Nationale de la Recherce (ANR) and BMBF.Peer reviewe

The twilight zone of cis element alignments

12 Pags., 8 Figs.Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein–DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein–DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.Funding for open access charge: Programa Euroinvestigación/Plant KBBE 2008 [EUI2008-03612].Peer reviewe

Protein-DNA interface dissection

Atomic interactions within protein-DNA interfaces are responsible for direct readout. This video highlights a few such interactions found in the PDB structure 1JE8, that describes the NarL transcription factor from Escherichia coli, produced by Maris et al.programa Euroinvestigación [EUI2008-03612

RSAT mirror for plants integrated with DB of transcription factors of known DNA motifs

A .pdf copy with 16 Pags.- Figs.- Tabls. from the original presentation by authors at Training Event. Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0).Peer reviewe

RSAT: Plants a regulatory sequence nalysis tools mirror for plant genome analysis

Peer Reviewe