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Centromeres are epigenetically specified by the histone H3 variant CENP-A. Although mammalian centromeres are typically associated with satellite DNA, we previously demonstrated that the centromere of horse chromosome 11 (ECA11) is completely devoid of satellite DNA. We also showed that the localization of its CENP-A binding domain is not fixed but slides within an about 500 kb region in different individuals, giving rise to positional alleles. These epialleles are inherited as Mendelian traits but their position can move in one generation. It is still unknown whether centromere sliding occurs during meiosis or during development. Here, we first improve the sequence of the ECA11 centromeric region in the EquCab3.0 assembly. Then, to test whether centromere sliding may occur during development, we map the CENP-A binding domains of ECA11 using ChIP-seq in five tissues of different embryonic origin from the four horses of the equine FAANG (Functional Annotation of ANimal Genomes) consortium. Our results demonstrate that the centromere is localized in the same region in all tissues, suggesting that the position of the centromeric domain is maintained during development. Sequence improvement of the centromeric region of horse chromosome 11 and mapping of the histone H3 variant CENP-A binding domains show that the centromere is localized in the same region in horse tissues from different embryonic origin.

As institutions committed to society, universities communicate their responsible behavior and their impacts on the environment and community through University Social Responsibility (USR) and sustainability reports. This paper analyzes USR management in the 50 higher education institutions that belong to the Spanish public university system and their commitment to the Sustainable Development Goals (SDGs) of the 2030 Agenda. A descriptive methodology was followed to carry out a document review and content analysis of their social responsibility and sustainability reports, as well as their institutional development plans. The results show that both the conceptualization and management of USR as a policy is very heterogeneous between universities and by regions. There is little evidence that USR policies are deeply rooted in a government framework and that the contribution of public universities to the 2030 Agenda is incipient. Although the relationship with internal and external audiences is represented in the documents, there are weaknesses in the relationship with mixed interest groups. Responsible communication is presented as a mechanism for the integration and promotion of the SDGs in universities and as a manifestation of their relationships with stakeholders.

Abstract Centromeres are epigenetically specified by the histone H3 variant CENP-A and typically associated with highly repetitive satellite DNA. We previously discovered natural satellite-free neocentromeres in Equus caballus and Equus asinus. Here, through ChIP-seq with an anti-CENP-A antibody, we found an extraordinarily high number of centromeres lacking satellite DNA in the zebras Equus burchelli (15 of 22) and Equus grevyi (13 of 23), demonstrating that the absence of satellite DNA at the majority of centromeres is compatible with genome stability and species survival and challenging the role of satellite DNA in centromere function. Nine satellite-free centromeres are shared between the two species in agreement with their recent separation. We assembled all centromeric regions and improved the reference genome of E. burchelli. Sequence analysis of the CENP-A binding domains revealed that they are LINE-1 and AT-rich with four of them showing DNA amplification. In the two zebras, satellite-free centromeres emerged from centromere repositioning or following Robertsonian fusion. In five chromosomes, the centromeric function arose near the fusion points, which are located within regions marked by traces of ancestral pericentromeric sequences. Therefore, besides centromere repositioning, Robertsonian fusions are an important source of satellite-free centromeres during evolution. Finally, in one case, a satellite-free centromere was seeded on an inversion breakpoint. At 11 chromosomes, whose primary constrictions seemed to be associated with satellite repeats by cytogenetic analysis, satellite-free neocentromeres were instead located near the ancestral inactivated satellite-based centromeres; therefore, the centromeric function has shifted away from a satellite repeat containing locus to a satellite-free new position.

Interstitial telomeric sequences (ITSs) are stretches of telomeric-like repeats located at internal chromosomal sites. We previously demonstrated that ITSs have been inserted during the repair of DNA double-strand breaks in the course of evolution and that some rodent ITSs, called TERC-ITSs, are flanked by fragments retrotranscribed from the telomerase RNA component (TERC). In this work, we carried out an extensive search of TERC-ITSs in 30 vertebrate genomes and identified 41 such loci in 22 species, including in humans and other primates. The fragment retrotranscribed from the TERC RNA varies in different lineages and its sequence seems to be related to the organization of TERC. Through comparative analysis of TERC-ITSs with orthologous empty loci, we demonstrated that, at each locus, the TERC-like sequence and the ITS have been inserted in one step in the course of evolution. Our findings suggest that telomerase participated in a peculiar pathway of DNA double-strand break repair involving retrotranscription of its RNA component and that this mechanism may be active in all vertebrate species. These results add new evidence to the hypothesis that RNA-templated DNA repair mechanisms are active in vertebrate cells.

In mammals, centromeres are epigenetically specified by the histone H3 variant CENP-A and are typically associated with satellite DNA. We previously described the first example of a natural satellite-free centromere on Equus caballus chromosome 11 (ECA11) and, subsequently, on several chromosomes in other species of the genus Equus. We discovered that these satellite-free neocentromeres arose recently during evolution through centromere repositioning and/or chromosomal fusion, after inactivation of the ancestral centromere, where, in many cases, blocks of satellite sequences were maintained. Here, we investigated by FISH the chromosomal distribution of satellite DNA families in Equus przewalskii (EPR), demonstrating a good degree of conservation of the localization of the major horse satellite families 37cen and 2PI with the domestic horse. Moreover, we demonstrated, by ChIP-seq, that 37cen is the satellite bound by CENP-A and that the centromere of EPR10, the ortholog of ECA11, is devoid of satellite sequences. Our results confirm that these two species are closely related and that the event of centromere repositioning which gave rise to EPR10/ECA11 centromeres occurred in the common ancestor, before the separation of the two horse lineages.

In mammals, centromeres are epigenetically specified by the histone H3 variant CENP-A and are typically associated with satellite DNA. We previously described the first example of a natural satellite-free centromere on Equus caballus chromosome 11 (ECA11) and, subsequently, on several chromosomes in other species of the genus Equus. We discovered that these satellite-free neocentromeres arose recently during evolution through centromere repositioning and/or chromosomal fusion, after inactivation of the ancestral centromere, where, in many cases, blocks of satellite sequences were maintained. Here, we investigated by FISH the chromosomal distribution of satellite DNA families in Equus przewalskii (EPR), demonstrating a good degree of conservation of the localization of the major horse satellite families 37cen and 2PI with the domestic horse. Moreover, we demonstrated, by ChIP-seq, that 37cen is the satellite bound by CENP-A and that the centromere of EPR10, the ortholog of ECA11, is devoid of satellite sequences. Our results confirm that these two species are closely related and that the event of centromere repositioning which gave rise to EPR10/ECA11 centromeres occurred in the common ancestor, before the separation of the two horse lineages.

La preocupación por las cuestiones relacionadas con la seguridad de los menores ha impulsado la puesta en marcha de diversas iniciativas a cargo del Gobierno de España en colaboración con las Fuerzas y Cuerpos de Seguridad del Estado. Así, con el acuerdo de los sindicatos de enseñanza, las organizaciones de los centros educativos y las asociaciones de padres y madres de alumnos, el Gobierno español aprobó en marzo de 2006 el “Plan para la Mejora de la Convivencia Escolar” con la finalidad de fomentar hábitos y conductas que promovieran la concordia en estos entornos. En el marco de la ejecución de este Plan Director no han pasado inadvertidas las posibilidades de Internet y las Redes Sociales. Describir las acciones emprendidas por los Ministerios del Interior, de Educación y Ciencia e Igualdad del Gobierno de España en colaboración con las Fuerzas y Cuerpos de Seguridad del Estado en materia de seguridad escolar a través de las Redes Sociales es, precisamente, el objetivo de este trabajo. 

Moving past learning just algorithms and code is a key challenge of bioinformatics education: the ideal goal is for students to acquire higher-order knowledge such as the ability to solve biological problems with the appropriate tools, and more importantly learn to interpret the results in the broader context where bioinformatics is needed. To design such a teaching and learning experience, data simulations play a key role: however, there is a massive barrier to adoption. Different data types are produced by different tools, requiring educators to learn each of them and adapt their workflow to the necessary dependencies, requirements and input files. Additionally, most existing data simulation solutions are meant for benchmarking and methods development rather than education and cannot provide the context needed to teach students the critical interpretation skills they need to move beyond problem-based learning to what we call storyline-based learning. A significant effort must be placed also when many datasets with the same characteristics are needed, such as in tutoring or assessment in higher education. Here, we present eduomics: a Nextflow pipeline meant to automate the simulation workflow for both genomic and transcriptomic next-generation sequencing data, and to produce realistic clinical scenarios to provide students with clues and a biomedical story necessary for the interpretation of their results. Eduomics removes barriers to adoption, by requiring the user to just decide which chromosome datasets should be simulated on, and which type of data they would like to simulate. There is no need to learn specific tools and resolve their dependencies. The use of Gemini API provides an innovative approach to generate plausible clinical scenarios, consistent with the genes where either a pathological mutation or differential expression has been simulated. With eduomics, we offer an accessible and scalable solution to design comprehensive learning experiences and innovate bioinformatics education. Modern bioinformatics education faces a dual challenge: students must learn how to analyse data and interpret results within the biological problems they aim to solve, while instructors who wish to design such a comprehensive learning experience should introduce appropriately simulated data in their teaching. However, the complexity of existing simulation tools is an often daunting barrier to overcome: current solutions require different software for different data types and provide no support for teaching interpretation skills. Most available simulators were designed for benchmarking and method development, not for education: therefore they lack the biological and clinical context needed to move beyond the traditional problem-based learning. To address these challenges, we developed eduomics, a Nextflow-based end-to-end pipeline that automates the simulation of genomic and transcriptomic data in a fully automated manner for educational use. Educators only need to choose the type of data to simulate, while the pipeline handles all underlying tools and dependencies. As a groundbreaking element, we integrated the Google Gemini API to generate patient-inspired clinical scenarios that gives students realistic clues and a biomedical narrative in which to interpret the results. This approach complements the traditional problem-based learning by offering a more complete, storyline-based learning experience. By combining automated data simulation and clinical storytelling, eduomics provides an accessible and scalable solution that support an engaging and immersive learning experience for both educators and students.

The transcription of human telomeres gives rise to a family of long noncoding RNAs, named TERRA. We previously showed that TERRA transcription is driven by CpG island promoters that are composed by stretches of three types of repeats. Using the human genome assembly that was available at that time, putative promoter sequences were localized at several subtelomeres. In this work, using the T2T-CHM13v2.0 human reference genome, we found that 39 out of 46 subtelomeres contain TERRA promoters and grouped them in classes depending on their organization. We then discovered 106 intrachromosomal TERRA-like promoters, adjacent to interstitial telomeric sequences (ITSs) or far away from them. Fortyseven of these promoters are flanked and may regulate the transcription of coding genes, ncRNAs or pseudogenes. Comparative sequence analysis showed that interstitial and subtelomeric promoters belong to a previously undescribed family of segmental duplications deriving from common ancestral sequences. RT-PCR experiments in seven cell lines demonstrated that TERRA transcripts can be synthesized from ITSs. TERRA expression was always low in primary fibroblasts and HeLa cells while highly variable in the other two telomerase positive (HT1080 and HEK293) and in the three telomerase negative ALT cell lines (GM847, U2OS and VA13). The analysis of RNA-seq data from U2OS, HeLa and HEK293 cells showed that 205 ITSs were transcribed in at least one cell lines. The fraction of transcribed ITSs and the level of their transcription increased with the length of the telomeric repeat stretch. Given the large number of transcribed ITSs, we propose that these loci contribute significantly to the production of the TERRA pool.

Centromeres are epigenetically specified by the histone H3 variant CENP-A and typically associated to highly repetitive satellite DNA. We previously discovered natural satellite-free neocentromeres in Equus caballus and E. asinus. Here, through ChIP-seq with an anti-CENP-A antibody, we found an extraordinarily high number of centromeres lacking satellite DNA in the zebras E. burchelli (15 of 22) and E. grevyi (13 of 23), demonstrating that the absence of satellite DNA at the majority of centromeres is compatible with genome stability and species survival and challenging the role of satellite DNA in centromere function. Nine neocentromeres are shared between the two species in agreement with their recent separation. We de novo assembled all neocentromeric regions and improved the reference genome of E. burchelli. Sequence analysis of the CENP-A binding domains revealed that they are LINE-1 and AT-rich with four of them showing DNA amplification. In the two zebras, satellite-free centromeres emerged from centromere repositioning or following Robertsonian fusion. In five chromosomes, the centromeric function arose near the fusion points, which are located within regions marked by traces of ancestral pericentromeric sequences. Therefore, besides centromere repositioning, Robertsonian fusions are an important source of satellite-free centromeres during evolution. Finally, in one case, a neocentromere was seeded on an inversion breakpoint. At eleven chromosomes, whose primary constrictions seemed to be associated to satellite repeats by cytogenetic analysis, neocentromeres were instead located near the ancestral inactivated satellite-based centromeres, therefore, the centromeric function has shifted away from a satellite repeat containing locus to a satellite-free new position. Competing Interest Statement The authors have declared no competing interest.