Javier Fernández-Chamorro

Universidad Autónoma de Madrid

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Encarnación Martı́nez-Salas

Universidad Autónoma de Madrid

Rosario Francisco‐Velilla

Centro de Biología Molecular Severo Ochoa

Jorge Ramajo

Centro de Biología Molecular Severo Ochoa

Gloria Lozano

Centro de Biología Molecular Severo Ochoa

Robert J. Weatheritt

UNSW Sydney

Nesli Avgan

St Vincent's Hospital Sydney

Juli Wang

University of Alberta

Iván Dotú

United Nations Children's Fund

Juan Antonio García-Martín

Centro Nacional de Biotecnología

Peter Clote

Boston College

Cooperative Institutions

Consejo Superior de Investigaciones Científicas

Centro de Biología Molecular Severo Ochoa

Universidad Autónoma de Madrid

Instituto de Salud Carlos III

Boston College

Centro de Astrobiología

Centro de Investigación Biomédica en Red

Garvan Institute of Medical Research

EMBL Australia

Institució Catalana de Recerca i Estudis Avançats

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

Additional file 3: of Multilayered control of exon acquisition permits the emergence of novel forms of regulatory control

Figshare (2019)

Nesli Avgan Juli Wang Javier Fernández-Chamorro Robert J. Weatheritt

Table S2. GO terms results for genes with exonization events. (XLSX 109 kb)

10.6084/m9.figshare.8947802

Cite

Citations (0)

Rab1b and ARF5 are novel RNA-binding proteins involved in FMDV IRES–driven RNA localization

Life Science Alliance (2019)

Javier Fernández-Chamorro Rosario Francisco‐Velilla Jorge Ramajo Encarnación Martínez‐Salas

Internal ribosome entry site (IRES) elements are organized in domains that guide internal initiation of translation. Here, we have combined proteomic and imaging analysis to study novel foot-and-mouth disease virus IRES interactors recognizing specific RNA structural subdomains. Besides known picornavirus IRES–binding proteins, we identified novel factors belonging to networks involved in RNA and protein transport. Among those, Rab1b and ARF5, two components of the ER-Golgi, revealed direct binding to IRES transcripts. However, whereas Rab1b stimulated IRES function, ARF5 diminished IRES activity. RNA-FISH studies revealed novel features of the IRES element. First, IRES-RNA formed clusters within the cell cytoplasm, whereas cap-RNA displayed disperse punctate distribution. Second, the IRES-driven RNA localized in close proximity with ARF5 and Rab1b, but not with the dominant-negative of Rab1b that disorganizes the Golgi. Thus, our data suggest a role for domain 3 of the IRES in RNA localization around ER-Golgi, a ribosome-rich cellular compartment.

10.26508/lsa.201800131

Cite

Citations (16)

RNA-Binding Proteins Impacting on Internal Initiation of Translation

International Journal of Molecular Sciences (2013)

Encarnación Martínez‐Salas Gloria Lozano Javier Fernández-Chamorro Rosario Francisco‐Velilla Alfonso Galan

RNA-binding proteins (RBPs) are pivotal regulators of all the steps of gene expression. RBPs govern gene regulation at the post-transcriptional level by virtue of their capacity to assemble ribonucleoprotein complexes on certain RNA structural elements, both in normal cells and in response to various environmental stresses. A rapid cellular response to stress conditions is triggered at the step of translation initiation. Two basic mechanisms govern translation initiation in eukaryotic mRNAs, the cap-dependent initiation mechanism that operates in most mRNAs, and the internal ribosome entry site (IRES)-dependent mechanism activated under conditions that compromise the general translation pathway. IRES elements are cis-acting RNA sequences that recruit the translation machinery using a cap-independent mechanism often assisted by a subset of translation initiation factors and various RBPs. IRES-dependent initiation appears to use different strategies to recruit the translation machinery depending on the RNA organization of the region and the network of RBPs interacting with the element. In this review we discuss recent advances in understanding the implications of RBPs on IRES-dependent translation initiation.

Eukaryotic translation

Translational regulation

Eukaryotic initiation factor

10.3390/ijms141121705

Cite

Citations (62)

RNA–protein interaction methods to study viral IRES elements

Methods (2015)

Rosario Francisco‐Velilla Javier Fernández-Chamorro Gloria Lozano Rosa Díaz-Toledano Encarnación Martínez‐Salas

RNA Silencing

Nucleic acid structure

10.1016/j.ymeth.2015.06.023

Cite

Citations (25)

A Combined ELONA-(RT)qPCR Approach for Characterizing DNA and RNA Aptamers Selected against PCBP-2

Molecules (2019)

Miguel Moreno María Fernández-Algar Javier Fernández-Chamorro Jorge Ramajo Encarnación Martínez‐Salas

Improvements in Systematic Evolution of Ligands by EXponential enrichment (SELEX) technology and DNA sequencing methods have led to the identification of a large number of active nucleic acid molecules after any aptamer selection experiment. As a result, the search for the fittest aptamers has become a laborious and time-consuming task. Herein, we present an optimized approach for the label-free characterization of DNA and RNA aptamers in parallel. The developed method consists in an Enzyme-Linked OligoNucleotide Assay (ELONA) coupled to either real-time quantitative PCR (qPCR, for DNA aptamers) or reverse transcription qPCR (RTqPCR, for RNA aptamers), which allows the detection of aptamer-target interactions in the high femtomolar range. We have applied this methodology to the affinity analysis of DNA and RNA aptamers selected against the poly(C)-binding protein 2 (PCBP-2). In addition, we have used ELONA-(RT)qPCR to quantify the dissociation constant (Kd) and maximum binding capacity (Bmax) of 16 high affinity DNA and RNA aptamers. The Kd values of the high affinity DNA aptamers were compared to those derived from colorimetric ELONA performed in parallel. Additionally, Electrophoretic Mobility Shift Assays (EMSA) were used to confirm the binding of representative PCBP-2-specific RNA aptamers in solution. We propose this ELONA-(RT)qPCR approach as a general strategy for aptamer characterization, with a broad applicability in biotechnology and biomedicine.

Aptamer

SELEX Aptamer Technique

10.3390/molecules24071213

Cite

Citations (14)

RNAiFold2T: Constraint Programming design of thermo-IRES switches

Bioinformatics (2016)

Juan Antonio García-Martín Iván Dotú Javier Fernández-Chamorro Gloria Lozano Jorge Ramajo

Abstract Motivation: RNA thermometers (RNATs) are cis -regulatory elements that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting potential resource in synthetic biology, where engineered RNATs could prove to be useful tools in biosensors and conditional gene regulation. Results: Solving the 2-temperature inverse folding problem is critical for RNAT engineering. Here we introduce RNAiFold2T, the first Constraint Programming (CP) and Large Neighborhood Search (LNS) algorithms to solve this problem. Benchmarking tests of RNAiFold2T against existent programs (adaptive walk and genetic algorithm) inverse folding show that our software generates two orders of magnitude more solutions, thus allowing ample exploration of the space of solutions. Subsequently, solutions can be prioritized by computing various measures, including probability of target structure in the ensemble, melting temperature, etc. Using this strategy, we rationally designed two thermosensor internal ribosome entry site ( thermo -IRES) elements, whose normalized cap-independent translation efficiency is approximately 50% greater at 42 °C than 30 °C, when tested in reticulocyte lysates. Translation efficiency is lower than that of the wild-type IRES element, which on the other hand is fully resistant to temperature shift-up. This appears to be the first purely computational design of functional RNA thermoswitches, and certainly the first purely computational design of functional thermo-IRES elements. Availability: RNAiFold2T is publicly available as part of the new release RNAiFold3.0 at https://github.com/clotelab/RNAiFold and http://bioinformatics.bc.edu/clotelab/RNAiFold , which latter has a web server as well. The software is written in C ++ and uses OR-Tools CP search engine. Contact: clote@bc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Folding (DSP implementation)

10.1093/bioinformatics/btw265

Cite

Citations (8)

Additional file 6: of Multilayered control of exon acquisition permits the emergence of novel forms of regulatory control

Figshare (2019)

Nesli Avgan Juli Wang Javier Fernández-Chamorro Robert J. Weatheritt

Table S5. GO terms results from GProfiler for exonization events identified depleted in cancer samples. (XLSX 254 kb)

10.6084/m9.figshare.8947820

Cite

Citations (0)

Insights into Structural and Mechanistic Features of Viral IRES Elements

Frontiers in Microbiology (2018)

Encarnación Martínez‐Salas Rosario Francisco‐Velilla Javier Fernández-Chamorro Azman M. Embarek

Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of protein synthesis using cap-independent mechanisms. However, distinct types of IRES elements present in the genome of various RNA viruses perform the same function despite lacking conservation of sequence and secondary RNA structure. Likewise, IRES elements differ in host factor requirement to recruit the ribosomal subunits. In spite of this diversity, evolutionarily conserved motifs in each family of RNA viruses preserve sequences impacting on RNA structure and RNA-protein interactions important for IRES activity. Indeed, IRES elements adopting remarkable different structural organizations contain RNA structural motifs that play an essential role in recruiting ribosomes, initiation factors and/or RNA-binding proteins using different mechanisms. Therefore, given that a universal IRES motif remains elusive, it is critical to understand how diverse structural motifs deliver functions relevant for IRES activity. This will be useful for understanding the molecular mechanisms beyond cap-independent translation, as well as the evolutionary history of these regulatory elements. Moreover, it could improve the accuracy to predict IRES-like motifs hidden in genome sequences. This review summarizes recent advances on the diversity and biological relevance of RNA structural motifs for viral IRES elements.

Nucleic acid structure

Structural motif

Eukaryotic translation

10.3389/fmicb.2017.02629

Cite

Citations (130)

Additional file 5: of Multilayered control of exon acquisition permits the emergence of novel forms of regulatory control

Figshare (2019)

Nesli Avgan Juli Wang Javier Fernández-Chamorro Robert J. Weatheritt

Table S4. Datasets used in paper including description and relevant figures information plus PubMed ID and SRA ID. (XLSX 54 kb)

10.6084/m9.figshare.8947817

Cite