https://hdl.handle.net/10481/31028 Sat, 11 Apr 2026 14:16:35 GMT 2026-04-11T14:16:35Z https://hdl.handle.net/10481/111323 sRNAtoolbox: an integrated collection of small RNA research tools Rueda, Antonio; Barturen, Guillermo; Lebrón, Ricardo; Gómez Martín, Cristina; Alganza, Ángel; Oliver Jiménez, José Lutgardo; Hackenberg, Michael Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and plants. MicroRNAs are important in host-microbe interactions and parasite microRNAs might modulate the innate immunity of the host. Furthermore, small RNAs can be detected in bodily fluids making them attractive non-invasive biomarker candidates. Given the general broad interest in small RNAs, and in particular microRNAs, a large number of bioinformatics aided analysis types are needed by the scientific community. To facilitate integrated sRNA research, we developed sRNAtoolbox, a set of independent but interconnected tools for expression profiling from high-throughput sequencing data, consensus differential expression, target gene prediction, visual exploration in a genome context as a function of read length, gene list analysis and blast search of unmapped reads. All tools can be used independently or for the exploration and downstream analysis of sRNAbench results. Workflows like the prediction of consensus target genes of parasite microRNAs in the host followed by the detection of enriched pathways can be easily established. The web-interface interconnecting all these tools is available at http://bioinfo5.ugr.es/srnatoolbox Ministerio de Economía y Competitividad from the Spanish Government [AGL2013-49090-C2-2-R to J.L.O.]. Conflict of interest statement. https://hdl.handle.net/10481/111323 https://hdl.handle.net/10481/111321 High-level organization of isochores into gigantic superstructures in the human genome Carpena, Pedro; Oliver Jiménez, José Lutgardo; Hackenberg, Michael; Coronado, Ana V.; Barturen Briñas, Guillermo; Bernaola-Galván, Pedro Human DNA shows a complex structure with compositional features at many scales; the isochores—long DNA segments (~105 bp) of relatively homogeneous guanine-cytosine (G + C) content—are the largest well-documented and well-analyzed compositional structures. However, we report here on the existence of a high-level compositional organization of isochores in the human genome. By using a segmentation algorithm incorporating the long-range correlations existing in human DNA, we find that every chromosome is composed of a few huge segments (~ 107 bp) of relatively homogeneous G + C content, which become the largest compositional organization of the genome. Finally, we show evidence of the biological relevance of these superstructures, pointing to a large-scale functional organization of the human genome. We thank the Spanish Government (Grant BIO2008-01353 to J.L.O., P.C., and P.B., mobilities PR2009-0285 to P.C. and JC2009-00067 to A.V.C., and Juan de la Cierva Grant to M.H.), the Spanish Junta de Andalucía (Grants P07-FQM3163, P06-FQM1858), and the Basque Country (Programa de formación de investigadores grant to G.B.). Departamento de Física Aplicada II, Universidad de Málaga, ES-29071, Málaga, Spain Division of Sleep Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA Departamento de Genética, Instituto de Biotecnología, Universidad de Granada, ES-18071 Granada, Spain https://hdl.handle.net/10481/111321 https://hdl.handle.net/10481/111318 Clustering of DNA words and biological function: A proof of principle Hackenberg, Michael; Rueda, Antonio; Carpena, Pedro; Bernaola-Galván, Pedro; Barturen, Guillermo; Oliver Jiménez, José Lutgardo Relevant words in literary texts (key words) are known to be clustered, while common words are randomly distributed. Given the clustered distribution of many functional genome elements, we hypothesize that the biological text per excellence, the DNA sequence, might behave in the same way: k-length words (k-mers) with a clear function may be spatially clustered along the one-dimensional chromosome sequence, while less-important, non-functional words may be randomly distributed. To explore this linguistic analogy, we calculate a clustering coefficient for each k-mer (k=2–9 bp) in human and mouse chromosome sequences, then checking if clustered words are enriched in the functional part of the genome. First, we found a positive general trend relating clustering level and word enrichment within exons and Transcription Factor Binding Sites (TFBSs), while a much weaker relation exists for repeats, and no relation at all exists for introns. Second, we found that 38.45% of the 200 top-clustered 8-mers, but only 7.70% of the non-clustered words, are represented in known motif databases. Third, enrichment/depletion experiments show that highly clustered words are significantly enriched in exons and TFBSs, while they are depleted in introns and repetitive DNA. Considering exons and TFBSs together, 1417 (or 72.26%) in human and 1385 (or 72.97%) in mouse of the top-clustered 8-mers showed a statistically significant association to either exons or TFBSs, thus strongly supporting the link between word clustering and biological function. Lastly, we identified a subset of clustered, diagnostic words that are enriched in exons but depleted in introns, and therefore might help to discriminate between these two gene regions. The clustering of DNA words thus appears as a novel principle to detect functionality in genome sequences. As evolutionary conservation is not a prerequisite, the proof of principle described here may open new ways to detect species-specific functional DNA sequences and the improvement of gene and promoter predictions, thus contributing to the quest for function in the genome. This work was supported by the Ministry of Innovation and Science of the Spanish Government [BIO2008-01353 to JLO and BIO2010-20219 to MH], ‘Juan de la Cierva’ grant (M.H.) and Basque country ‘AE’ grant (G.B.). We gratefully acknowledge the valuable comments of two anonymous referees, which significantly improved the manuscript. We thank Ángel M. Alganza for help with system administration and database support. https://hdl.handle.net/10481/111318 https://hdl.handle.net/10481/110767 NGSmethDB 2017: enhanced methylomes and differential methylation Lebrón, Ricardo; Gómez Martín, Cristina; Carpena, Pedro; Bernaola-Galván, Pedro; Barturen, Guillermo; Hackenberg, Michael; Oliver Jiménez, José Lutgardo The 2017 update of NGSmethDB stores whole genome methylomes generated from short-read data sets obtained by bisulfite sequencing (WGBS) technology. To generate high-quality methylomes, stringent quality controls were integrated with third-part software, adding also a two-step mapping process to exploit the advantages of the new genome assembly models. The samples were all profiled under constant parameter settings, thus enabling comparative downstream analyses. Besides a significant increase in the number of samples, NGSmethDB now includes two additional data-types, which are a valuable resource for the discovery of methylation epigenetic biomarkers: (i) differentially methylated single-cytosines; and (ii) methylation segments (i.e. genome regions of homogeneous methylation). The NGSmethDB back-end is now based on MongoDB, a NoSQL hierarchical database using JSONformatted documents and dynamic schemas, thus accelerating sample comparative analyses. Besides conventional database dumps, track hubs were implemented, which improved database access, visualization in genome browsers and comparative analyses to third-part annotations. In addition, the database can be also accessed through a RESTful API. Lastly, a Python client and a multiplatform virtual machine allow for program-driven access from user desktop. This way, private methylation data can be compared to NGSmethDB without the need to upload them to public servers. Database website: http://bioinfo2.ugr.es/NGSmethDB. https://hdl.handle.net/10481/110767 https://hdl.handle.net/10481/110324 Impaired Sertoli-Spermatogonia interactions contribute to oligospermia and infertility in F1 captive-bred male Solea senegalensis Barturen, Guillermo; Robledo, Diego; Robles Rodríguez, Francisca; Ruiz Daniels, Rose; Carballeda, Maialen; Torres Sabino, Dorinda; Navajas Pérez, Rafael; Martínez, Paulino; Ruiz Rejón, Carmelo; Herrán Moreno, Roberto De La Reproductive dysfunction of captive-bred males of the Senegalese sole (Solea senegalensis) represents a significant bottleneck for its aquaculture, as these fish exhibit reduced sperm production and impaired fertility compared to wild-bred counterparts acclimated to farm conditions. To elucidate the cellular and molecular mechanisms underlying this phenomenon, single-nuclei RNA sequencing was performed on gonadal tissue from adult captive-bred and wild-bred males. The analysis yielded a high-quality dataset comprising ∼80.000 cells, which were grouped into eleven distinct clusters representing all major germline and somatic cell types, including spermatogonial stem cells, differentiating spermatogonia, spermatocytes, spermatids, Sertoli cells, Leydig cells, immune cells, and peritubular myoid cells. It is noteworthy that captive-bred males exhibited a marked overrepresentation of proliferative spermatogonia and a significant reduction in mature spermatids, suggesting a disruption in the progression of spermatogenesis. Differential expression and functional enrichment analyses revealed that spermatogonial cells in captive-bred males displayed heightened translational activity alongside downregulation of pathways related to cell-cell communication and interaction. Focused in-silico cell-cell communication analyses further suggested potential defective Sertoli-spermatogonia interactions as a key factor contributing to oligospermia and infertility of captive-bred males. This study provides the first single-nuclei transcriptomic atlas of the Senegalese sole male gonad, offering valuable insights into the molecular basis of reproductive failure in captivity related to gonadal development. The findings of the study will inform future strategies to enhance selective breeding and improve aquaculture productivity for this economically important species. https://hdl.handle.net/10481/110324