Metilación diferencial en el genoma humano y su asociación con la transcripción

In this Doctoral Thesis the reliability in detecting the methylation levels of individual cytosines from WGBS reads has been significantly improved, taking into account all the sources of error known today. This has allowed to test the hypothesis which argues that the sign of the association between methylation and transcription depends on the genomic context in which methylation occurs and the type of transcription factors that are involved. In the light of the obtained results, it has not been possible to refute this hypothesis. An unexpected finding was that the positive association between methylation and transcription appears to be more frequent than it had been previously described, being even more frequent than the negative association. In relation to this, in transcription factors binding sites with greater affinity for methylated sites, green CpG-TLs are over-represented, but red CpG-TLs are underrepresented. These positive associations may be due to a hitherto unknown transcription regulation mechanism, but there are also likely to be cases where hydroxymethylation is positively associated with transcription, as the WGBS method is unable to discriminate between methylation and hydroxymethylation. In further studies, OxBS-seq or TAB-seq methods should be used in order to clarify the true nature of green CpG-TLs.En esta Tesis Doctoral se ha mejorado notablemente la fiabilidad en la detección de los niveles de metilación de las citosinas individuales a partir de lecturas de WGBS, tomando en cuenta todas fuentes de error conocidas en la actualidad. Esto ha permitido poner a prueba la hipótesis de que el signo de la asociación entre la metilación y la transcripción depende del contexto genómico en que se produce la metilación y del tipo de factores de transcripción implicados. A la vista de los resultados obtenidos, no ha sido posible refutar esta hipótesis. Un hallazgo inesperado fue que la asociación positiva entre la metilación y la transcripción parece ser más frecuente de lo que previamente se había descrito, llegando incluso a ser más frecuente que la asociación negativa. En relación a esto, los sitios de unión a factores de transcripción con mayor afinidad por sitios metilados son ricos en CpGTLs verdes pero pobres en CpG-TLs rojos. Estas asociaciones positivas podrían deberse a un mecanismo de regulación de la transcripción hasta ahora desconocido, pero también es probable que en realidad se trate de casos en los que la hidroximetilación se asocia positivamente con la transcripción, ya que el método WGBS es incapaz de discriminar entre metilación e hidroximetilación. En futuros estudios, se deberían utilizar los métodos OxBS-seq o TAB-seq para tratar de esclarecer la verdadera naturaleza de los CpG-TLs verdes.Tesis Univ. Granada.Financiado por la Junta de Andalucía, a través del Programa de Ayudas a Grupos de Investigación (Grupo PAI BIO-162) y de dos proyectos del Ministerio de Economía, Industria y Competitividad, a través del Programa Estatal de Investigación, Desarrollo e Innovación Orientada a los Retos de la Sociedad (AGL2013-49090-C2-2-R y AGL2017-88702-C2-2-R)

Functional characterization of the tomato HAIRPLUS gene reveals the implication of the epigenome in the control of glandular trichome formation

This research was supported by the Spanish Ministry of Science, Innovation and Universities (grants AGL2017-88702-C2-1-R and AGL2017-88702-C2-2-R). Funding was also received from the BRESOV (Breeding for resilient, efficient, and sustainable organic vegetable production) project. BRESOV was funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No. 774244. We would also like to thank research facilities provided by the Campus de Excelencia Internacional Agroalimentario (CeiA3). PhD fellowships were funded by the FPU (R.F., R.Le.) Programmes of the Ministerio de Ciencia e Innovacion and the LASPAU (J.L.Q.).Trichomes are specialised epidermal cells developed in the aerial surface of almost every terrestrial plant. These structures form physical barriers, which combined with their capability of synthesis of complex molecules, prevent plagues from spreading and confer trichomes a key role in the defence against herbivores. In this work, the tomato gene HAIRPLUS (HAP) that controls glandular trichome density in tomato plants was characterised. HAP belongs to a group of proteins involved in histone tail modifications although some also bind methylated DNA. HAP loss of function promotes epigenomic modifications in the tomato genome reflected in numerous differentially methylated cytosines and causes transcriptomic changes in hap mutant plants. Taken together, these findings demonstrate that HAP links epigenome remodelling withmulticellular glandular trichome development and reveal that HAP is a valuable genomic tool for pest resistance in tomato breeding.Spanish Government AGL2017-88702-C2-1-R AGL2017-88702-C2-2-REuropean Commission 774244FPU Programmes of the Ministerio de Ciencia e InnovacionLASPAUBRESOV (Breeding for resilient, efficient, and sustainable organic vegetable production) projec

liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies

MiRNAs are important regulators of gene expression and are frequently deregulated under pathologic conditions. They are highly stable in bodily fluids which makes them feasible candidates to become minimally invasive biomarkers. In fact, several studies already proposed circulating miRNA-based biomarkers for different types of neoplastic, cardiovascular and degenerative diseases. However, many of these studies rely on small RNA sequencing experiments that are based on different RNA extraction and processing protocols, rendering results incomparable. We generated liqDB, a database for liquid biopsy small RNA sequencing profiles that provides users with meaningful information to guide their small RNA liquid biopsy research and to overcome technical and conceptual problems. By means of a user-friendly web interface, miRNA expression profiles from 1607 manually annotated samples can be queried and explored at different levels. Result pages include downloadable expression matrices, differential expression analysis, most stably expressed miRNAs, cluster analysis and relevant visualizations by means of boxplots and heatmaps. We anticipate that liqDB will be a useful tool in liquid biopsy research as it provides a consistently annotated large compilation of experiments together with tools for reproducible analysis, comparison and hypothesis generation.European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [grant agreement ELBA, 765492 to M.H. and D.K.L.]; Spanish Government [AGL2017-88702-C2-2-R to M.H.]; Instituto de Salud Carlos III, FEDER funds [PIE16/00045 to J.A.M.]; Chair ‘Doctors Galera-Requena in cancer stem cell research’ (to J.A.M.); Ministry of Education of Spain [FPU13/05662 to R.L. and IFI16/00041 to E.A.]. Funding for open access charge: Instituto de Salud Carlos III (FEDER funds) [PIE16/00045]

Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.)

The authors want to thank the research facilities provided by the Campus de Excelencia Internacional Agroalimentario (CeiA3).Pod maturation of common bean relies upon complex gene expression changes, which in turn are crucial for seed formation and dispersal. Hence, dissecting the transcriptional regulation of pod maturation would be of great significance for breeding programs. In this study, a comprehensive characterization of expression changes has been performed in two common bean cultivars (ancient and modern) by analyzing the transcriptomes of five developmental pod stages, from fruit setting to maturation. RNA-seq analysis allowed for the identification of key genes shared by both accessions, which in turn were homologous to known Arabidopsis maturation genes and furthermore showed a similar expression pattern along the maturation process. Gene- expression changes suggested a role in promoting an accelerated breakdown of photosynthetic and ribosomal machinery associated with chlorophyll degradation and early activation of alpha-linolenic acid metabolism. A further study of transcription factors and their DNA binding sites revealed three candidate genes whose functions may play a dominant role in regulating pod maturation. Altogether, this research identifies the first maturation gene set reported in common bean so far and contributes to a better understanding of the dynamic mechanisms of pod maturation, providing potentially useful information for genomic-assisted breeding of common bean yield and pod quality attributes.Ministerio de Ciencia, Innovacion y Universidades (MCIU/AEI/FEDER, UE) AGL2017-88174-R RTC2017-6198-2 AGL2017-88702-C2-2-RJunta de Andalucia 612

Driven progressive evolution of genome sequence complexity in Cyanobacteria

Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species’ biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven—the minimum, ancestor– descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.Generalitat Valenciana Prometeo/2018/A/133European Union (EU)Fulbright fellowship (Spanish Minister of Science, Innovation and Universities)SAF2015-65878-RAGL2017-88702-C2-2-RPGC2018-099344-B-I0

sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression

Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well asmicroRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNAseq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency.European Union [765492 to M.H.]; Spanish Government [AGL2017-88702-C2-2-R to M.H., J.L.O.]; Instituto de Salud Carlos III, FEDER funds [PIE16/00045 to J.A.M.]; Chair ‘Doctors Galera-Requena in cancer stem cell research’ to JMA and by the Ministry of Education of Spain [FPU13/05662 to R.L., IFI16/00041 to E.A.]; Strategic Research Area (SFO) program of the Swedish Research Council (to V.R.) through Stockholm University (to B.F.). Funding for open access charge: SpanishGovernment [AGL2017-88702-C2-2-R]

Tomato POLLEN DEFICIENT 2 encodes a G-Type lectin receptor kinase required for viable pollen grain formation

Pollen development is a crucial biological process indispensable for seed set in flowering plants and for successful crop breeding. However, little is known about the molecular mechanisms regulating pollen development in crop species. This study reports a novel male-sterile tomato mutant, pollen deficient 2 (pod2), characterized by the production of non-viable pollen grains and resulting in the development of small parthenocarpic fruits. A combined strategy of mapping-by-sequencing and RNA interference-mediated gene silencing was used to prove that the pod2 phenotype is caused by the loss of Solanum lycopersicum G-Type lectin receptor kinase II.9 (SlG-LecRK-II.9) activity. In situ hybridization of floral buds showed that POD2/SlG-LecRK-II.9 is specifically expressed in tapetal cells and microspores at the late tetrad stage. Accordingly, abnormalities in meiosis and tapetum programmed cell death in pod2 occurred during microsporogenesis, resulting in the formation of four dysfunctional microspores leading to an aberrant microgametogenesis process. RNA-seq analyses supported the existence of alterations at the final stage of microsporogenesis, since we found tomato deregulated genes whose counterparts in Arabidopsis are essential for the normal progression of male meiosis and cytokinesis. Collectively, our results revealed the essential role of POD2/SlG-LecRK-II.9 in regulating tomato pollen development.This work was supported by research grants PID2019-110833RB-C31, PID2019-110833RB-C32, and PID2020-113324GB-100 funded by the Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033), and the Research and Innovation Programme of the European Union Horizon 2020 (BRESOV Project, ID 774244). A PhD fellowship to MGA was funded by the FPU Programme of the Spanish Ministry of Education and Culture (ref. AP2010-4528). RLe was supported by a Junta de Andalucía and FEDER research contract (DOC_01129)

Resilient Response to Combined Heat and Drought Stress Conditions of a Tomato Germplasm Collection, Including Natural and Ethyl Methanesulfonate-Induced Variants

Agricultural systems are currently facing significant issues, primarily due to population growth rates in the context of global climate change. Rising temperatures cause plant heat stress and impact crop yield, which in turn compromises global food production and safety. Climate change is also having a significant impact on water availability around the world, and droughts are becoming more frequent and severe in many regions. The combined effect of both heat and drought stresses increases plant damage, resulting in reduced plant development and productivity loss. Therefore, developing heat–drought-tolerant crop varieties is crucial for enhancing yield under these challenging conditions. Tomato (Solanum lycopersicum L.), a major vegetable crop highly appreciated for its nutritional qualities, is particularly sensitive to extreme temperatures, which have a significant negative impact on tomato fruit setting and cause male gametophyte abortion. In this work, a classical genetic approach was employed to identify tomato genotypes showing a resilient response to combined heat and drought stress conditions. A phenotype screening of a natural germplasm collection and an ethyl methanesulfonate (EMS) mutagenized population resulted in the identification of a significant number of tomato lines tolerant to combined heat and drought conditions, specifically 161 EMS lines and 24 natural accessions as tolerant. In addition, TILLING and Eco-TILLING analyses were used as proof-of-concept to isolate new genetic variants of genes previously reported as key regulators of abiotic stress responses in different species. The identification of these variants holds the potential to provide suitable plant material for breeding programs focused on enhancing tomato resilience to adverse climate conditions

Decoding gene expression signatures underlying vegetative to inflorescence meristem transition in the common bean

The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean

Progressive genome evolution in Cyanobacteria

Resumen del trabajo presentado a la VII Biennial Congress of Sociedad Española de Biología Evolutiva (SEBE), celebrada en Sevilla (España) del 5 al 7 de febrero de 2020.Progressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires the proper measurement of complexity. To address this challenge, we consider that genomes are the best entities to measure complexity because they record the history and information gain of organisms in their ongoing biotic and environmental interactions. By recurring to six metrics that measure genome complexity, which are not primarily associated to functionality, we report the existence of progressive evolution towards higher genome complexity in the evolution of the Cyanobacteria phylum. We show that these complexity metrics plus three additional genome parameters present statistically significant phylogenetic signal in Cyanobacteria. Moreover, a ridge regression of genome complexity metrics against evolutionary age shows that three out of six present a positively driven evolutionary trend towards higher complexity. These findings support the existence of progressive genome evolution in this ancient and diverse group of organisms.Peer reviewe