Search

Enhancers regulate multiple genes via higher-order chromatin structures, and they further affect cancer progression. Epigenetic changes in cancer cells activate several cancer-specific enhancers that are silenced in normal cells. These cancer-specific enhancers are potential therapeutic targets of cancer. However, the functions and regulation networks of colorectal-cancer-specific enhancers are still unknown. In this study, we profile colorectal-cancer-specific enhancers and reveal their regulation network through the analysis of HiChIP data that were derived from a colorectal cancer cell line and Hi-C and RNA-seq data that were derived from tissue samples by in silico analysis and in vitro experiments. Enhancer–promoter loops in colorectal cancer cells containing colorectal-cancer-specific enhancers are involved in more than 50% of the topological associated domains (TADs) changed in colorectal cancer cells compared to normal colon cells. In addition, colorectal-cancer-specific enhancers interact with 152 genes that are significantly and highly expressed in colorectal cancer cells. These colorectal-cancer-specific enhancer target genes include ITGB4, RECQL4, MSLN, and GDF15. We propose that the regulation network of colorectal-cancer-specific enhancers plays an important role in the progression of colorectal cancer.

Chromatin domains and loops are important elements of chromatin structure and dynamics, but much remains to be learned about their exact biological role and nature. Topological associated domains and functional loops are key to gene expression and hold the answer to many questions regarding developmental decisions and diseases. Here, we discuss new findings, which have linked chromatin conformation with development, differentiation and diseases and hypothesized on various models while integrating all recent findings on how chromatin architecture affects gene expression during development, evolution and disease.

Topologically associating domains (TAD) are a key structure of the 3D mammalian genomes. However, the prevalence and dynamics of TAD-like domains in single cells remain elusive. Here we develop a new algorithm, named deTOKI, to decode TAD-like domains with single-cell Hi-C data. By non-negative matrix factorization, deTOKI seeks regions that insulate the genome into blocks with minimal chance of clustering. deTOKI outperforms competing tools and reliably identifies TAD-like domains in single cells. Finally, we find that TAD-like domains are not only prevalent, but also subject to tight regulation in single cells. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02435-7.

El uso de microtornillos e implantes en ortodoncia como método para obtener anclaje absoluto está hoy en boga, a pesar de haber transcurrido ya más de cuarenta años desde su descubrimiento. Estos dispositivos han demostrado ser uno de los avances más significativos en la historia moderna de la ortodoncia. Este sistema tiene una singularidad: su uso temporal, el cual, aunque transitorio, aporta ese anclaje absoluto, evitando efectos recíprocos indeseados generados en el transcurso del tratamiento. Las numerosas indicaciones de estos dispositivos ofrecen al ortodoncista un amplio abanico de posibilidades para corregir casos que, hasta hace poco, no se podrían solucionar sin pasar por quirófano y/o llevando aparatología extraoral. La necesidad de colaboración del paciente y la reducción del tiempo de tratamiento, son unas de las principales ventajas. Su eficacia probada, además de su fácil colocación, aportan seguridad y satisfacción en los resultados de los tratamientos, haciendo que cada día sean más populares Objetivo: El propósito de este trabajo es realizar una revisión sistemática de la literatura para cuantificar la capacidad de movimiento sagital de los microtornillos, mostrar que ventajas tienen estos dispositivos frente a los tratamientos convencionales en este plano. The use of miniscrews has become, nowadays, a feasible option to treat several cases that requires absolute anchorage. These devices, have been proven to be one of the most significant developments in the modern history of orthodontics, since its invention, more than forty years ago. They have a distinctive characteristic: its temporary use, which, albeit is transitory, provides that simple absolute anchorage that dentists seek, avoiding the reciprocal effects that are commonly produced over the course of almost every treatment. These devices offer the orthodontist a wide range of possibilities to approach many cases which, until very recently, could only been corrected with major surgery or wearing extraoral appliances. All of the above diminish the necessity of cooperation with the patient, and the overall treatment time decrease too. Its proven efficacy, but also the ease with which it is placed, that doesn’t require any surgery beyond the dentist’s capacity, bring secure results and satisfaction, making them increasingly popular. Aim: The purpose of this systematic review is to quantify the capacity of sagittal movement of the miniscrews, and the advantages that these devices can offer against traditional ways of treatments used in this plane. Universidad de Sevilla. Grado en Odontología

Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.

In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. The class of transcription factors that carry a cluster of C2H2-type zinc fingers consisting of five or more domains (C2H2 proteins) is widely represented in all groups of animals. The functions of most C2H2 proteins still remain unknown. This review presents data on the structure and possible functions of these proteins, using the example of the vertebrate CTCF protein and several well- characterized C2H2 proteins in Drosophila and mammals.

Myofibres (primary and secondary myofibre) are the basic structure of muscle and the determinant of muscle mass. To explore the skeletal muscle developmental processes from primary myofibres to secondary myofibres in pigs, we conducted an integrative three-dimensional structure of genome and transcriptomic characterization of longissimus dorsi muscle of pig from primary myofibre formation stage [embryonic Day 35 (E35)] to secondary myofibre formation stage (E80). In the hierarchical genomic structure, we found that 11.43% of genome switched compartment A/B status, 14.53% of topologically associating domains are changed intradomain interactions (D-scores) and 2,730 genes with differential promoter–enhancer interactions and (or) enhancer activity from E35 to E80. The alterations of genome architecture were found to correlate with expression of genes that play significant roles in neuromuscular junction, embryonic morphogenesis, skeletal muscle development or metabolism, typically, NEFL, MuSK, SLN, Mef2D and GCK. Significantly, Sox6 and MATN2 play important roles in the process of primary to secondary myofibres formation and increase the regulatory potential score and genes expression in it. In brief, we reveal the genomic reorganization from E35 to E80 and construct genome-wide high-resolution interaction maps that provide a resource for studying long-range control of gene expression from E35 to E80.

Development of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art ‘HPV integrated site capture’ (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a ‘looping’ mechanism by which flanking host regions become amplified. Furthermore, using our ‘HPV16-specific Region Capture Hi-C’ technique, we have determined that three-dimensional (3D) interactions between the integrated virus genome and host chromosomes, both at short- (500 kbp), appear to drive host gene dysregulation through the disruption of local host:host 3D interactions known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a ‘cancer-causing gene’ is not essential to influence such genes within an entire TAD and that these modifications to 3D interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression.

Informationen des Genoms werden nicht nur mit der Sequenz oder epigenetischen Modifikation codiert, sondern auch in ihrer Faltung im 3D-Raum gefunden. Jüngste Entwicklungen bei der Konformationserfassung von Chromosomen ermöglichten es uns, die räumliche Positionierung des Genoms in verschiedenen Maßstäben aufzudecken. Die Bildung selbstinteragierender Genomregionen, die als Topologically Associated Domains (TADs) bezeichnet werden, wird von Hi-C als Schlüsselmerkmal der Genomorganisation jenseits der Nukleosomenebene entdeckt. Jedes TAD ist eine isolierte lokale Packungseinheit, in der Intra-TADWechselwirkungen bevorzugt und Inter-TAD-Wechselwirkungen isoliert werden. Bei Tieren wird gezeigt, dass mehrere Architekturproteine zur Struktur und Funktion der tierischen TADs beitragen. Im Gegensatz zu Tieren sind TAD-Bildung, - Funktion und -Proteine, die bei diesen Prozessen in Pflanzen eine Rolle spielen, eher unbekannt. Unsere vorläufige Hi-C-Analyse zeigte, dass das Genom von Marchantia polymorpha, einem Mitglied einer basalen Landpflanzenlinie, eine evolutionär konservierte 3DLandschaft mit dem höheren Pflanzen teilt. Das Marchantia-Genom ist in Hunderte von TADs unterteilt und ihre Grenzen sind mit der TCP1-Proteinbindung verbunden. Eine genomweite epigenetische Analyse ergab, dass ein beträchtlicher Teil der Marchantia-TADs interstitielles Heterochromatin darstellt und mit repressiven epigenetischen Markierungen verziert ist. Wir identifizieren auch einen neuartigen TAD-Typ, den wir TCP1-reiches TAD nennen, bei dem genomische Regionen gut zugänglich und durch TCP1-Proteine dicht gebunden sind. TCP1- gebundene Gene, die sich in TCP1-reichen TADs befinden, weisen im Vergleich zu TCP1-gebundenen Genen an anderen Stellen niedrigere Genexpressionsniveaus auf. In tcp1-Mutanten änderten sich die TAD-Muster in der Hi-C-Karte nicht, was darauf hinweist, dass das TCP1-Protein für die TAD-Bildung und -Struktur nicht wesentlich ist. Wir stellen jedoch fest, dass in tcp1-Mutanten Gene, die in TCP1-reichen TADs leben, eine größere Veränderung der Expressionsfalte aufweisen als Gene, die nicht zu diesen TADs gehören. Unsere Ergebnisse zeigen, dass Pflanzen-TADs nicht nur als räumliche Chromatin-Packungsmodule stehen, sondern auch als nukleare Mikrokompartimente fungieren, die die Aktivitäten des Transkriptionsfaktors korrelieren. Information of the genome is not only encoded to its sequence or epigenetic modifications but also found in its folding in 3D space. Recent developments in Chromosome Conformation Capture techniques enabled us to unveil spatial positioning of the genome at different scales. The formation of self-interacting genomic regions, named Topologically Associated Domains (TADs), are discovered by Hi-C, as a key feature of genome organization beyond the nucleosomal level. Each TAD is an isolated local packing unit in which intra-TAD interactions are favoured and inter-TAD interactions are insulated. In animals several architectural proteins are shown to contribute the structure and the function of the animal TADs. Unlike those in animals, TAD formation, function and proteins that play a role in these processes in plants are rather unknown. Our Hi-C analyses show that the genome of Marchantia polymorpha, a member of a basal land plant lineage, shares an evolutionary conserved 3D landscape with that of higher plants. The Marchantia genome is subdivided into hundreds of TADs and their borders are associated with TCP1 protein binding. Genome-wide epigenetic analysis reveals that a considerable fraction of Marchantia TADs represent interstitial heterochromatin and are decorated with repressive epigenetic marks. We also identify a novel type of TAD that we name TCP1-rich TAD, in which genomic regions are highly accessible and densely bound by TCP1 proteins. TCP1-bound genes residing in TCP1-rich TADs exhibit lower gene expression levels compared to the TCP1- bound genes in other locations. In tcp1 mutants, TAD patterns in the Hi-C map do not change, indicating that TCP1 protein is not essential for TAD formation and structure. However, we find that in tcp1 mutants, genes residing in TCP1-rich TADs have a greater extent in expression fold change compared to genes not belonging to these TADs. Our results indicate that, besides standing as spatial chromatin packing modules, plant TADs function as nuclear micro-compartments that correlate transcription factor activities.

Graphical abstract, Highlights • N-terminal domain of SpTad2/3 is a putative kinase but not functional. • N-SpTad2 does not bind tRNA but its deletion renders the deaminase inactive. • Structure of N-SpTad2 was solved, revealing it may bind phosphates. • Incapable of binding to DNA, N-SpTad2 may enhance the stability of the holoenzyme., Editing is a post-transcriptional process that changes the content of nucleic acids occurring on both DNA and RNA levels. Inosine at position 34 in tRNA is one such example, commonly produced via the deamination of A34, catalyzed by adenosine deaminase acting on tRNA (ADAT or Tad). The formation of inosine is essential for cell viability. The eukaryotic deaminases normally consist of the catalytic subunit Tad2 and the structural subunit Tad3, but the catalytic process is poorly understood. Despite the conservation of the (pseudo-) catalytic domains, the heterodimeric enzyme Tad2/3 also possesses additional domains that could exhibit novel functions. Here we present the structure of the N-terminal domain of the Schizosaccharomyces pombe Tad2/3 heterodimeric tRNA(A34) deaminase (N-SpTad2), which shares ~30% sequence identities with uridine-cytidine or pantothenate kinases, but lacks the predicted kinase functions. While biochemical assays indicated that the domain is not a nucleic-acid binder, it is able to significantly influence the A34-tRNA deamination activity of the holoenzyme. Through co-expression and purification analyses, we deduce that N-SpTad2 plays a role in mediating protein-protein contacts and enhancing the stability and solubility of SpTad2/3, without which the deaminase is not functional. Taken together, our structural and biochemical studies highlighted the importance of the additional domains to the intrinsic deaminase functions of heterodimeric Tad2/3 enzymes and promoted our understanding on this essential post-transcriptional tRNA modification.

Background The three-dimensional spatial organization of the genome plays important roles in chromatin accessibility and gene expression in multiple biological processes and has been reported to be altered in response to environmental stress. However, the functional changes in spatial genome organization during environmental changes in crop plants are poorly understood. Results Here we perform Hi-C, ATAC-seq, and RNA-seq in two agronomically important rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica), to report a comprehensive profile of nuclear dynamics during heat stress (HS). We show that heat stress affects different levels of chromosome organization, including A/B compartment transition, increase in the size of topologically associated domains, and loss of short-range interactions. The chromatin architectural changes were associated with chromatin accessibility and gene expression changes. Comparative analysis revealed that 93-11 exhibited more dynamic gene expression and chromatin accessibility changes, including HS-related genes, consistent with observed higher HS tolerance in this cultivar. Conclusions Our data uncovered higher-order chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in rice.

This study was designed to demonstrate the effects of surgical skills of final-year veterinary medicine students relating to total surgery time and skin incision length on postoperative stress, oxidative stress and pain in bitches undergoing ovariohysterectomy under identical anaesthesia and surgical procedures. The control group (n=12) consisted of bitches that were operated on by an experienced surgeon, while the ovariohysterectomies in the experiment group (n=12) were performed by final-year veterinary medicine students. Blood samples were taken 24 hours before the surgery, during premedication, at the end of surgery and 30 minutes, 1, 2, 4 and 6 hours after surgery for the analysis of cortisol, total oxidant status (TOS), total antioxidant status (TAS) and for the calculation of the oxidative stress index (OSI). Modified Melbourne Pain Scale was used for pain assessment. It was observed that the total surgery time and length of skin incision in the experiment group were significantly higher (p, SSunulan çalışmada, veteriner hekimliği eğitiminin son sınıfında olan öğrencilerin, toplam operasyon süresi ve deri ensizyonu uzunluğu ile ilişkili olan cerrahi becerilerinin operasyon sonrası stres, oksidatif stres ve ağrı üzerine etkilerinin aynı anestezi ve cerrahi prosedürler altında ortaya konulması amaçlandı. Tecrübeli bir hekimin opere ettiği köpekler kontrol grubunu (n=12) oluştururken, veteriner fakültesi son sınıfta eğitim gören öğrenciler tarafından opere edilen köpekler (n=12) deneme grubunu oluşturdu. Operasyondan 24 saat önce, premedikasyon sırasında, operasyon sonunda ve operasyondan 30 dakika, 1, 2, 4 ve 6 saat sonra kan örnekleri toplanarak kortizol, toplam oksidant durum (TOD), toplam antioksidant durum (TAD) ölçüldü ve oksidatif stress indeksi (OSI) hesaplandı. Modifiye edilmiş Melbourne Ağrı Skalası ağrı değerlendirilmesi için kullanıldı. Deneme grubundaki köpeklerde, toplam operasyon süresi ve deri ensizyon uzunluğunun kontrol grubundaki köpeklerden istatistiksel olarak (p

(1) Background: Miniscrew insertion, using a surgical guide, aims to avoid possible adverse effects or complications. With the higher availability of both 3D imaging and printing, 3D surgical guides have been used more frequently in orthodontics. The aim of the present systematic review was to find scientific clinical evidence concerning the precision of the 3D guided insertion of miniscrews for temporary orthodontic anchorage. (2) Methods: Literature searches were performed in the following five search engines: Pubmed (Medline), Pubmed Central, Scopus, Web of Science and Embase on 10 September 2021 (articles from 1950 to 10 September 2021). A meta-analysis was performed using the random-effect model, with Standardized Mean Differences (SMD) and 95% confidence intervals (95% CI) calculated as effect estimates. The heterogeneity was assessed quantitatively. (3) Results: The search strategy identified 671 potential articles. After the removal of duplicates, 530 articles were analyzed. Subsequently, 487 papers were excluded, because they were not associated with the subject of the study. Of the remaining 43 papers, 34 were excluded because they did not meet the methodological criteria. Finally, only nine papers were subjected to a qualitative analysis. (4) Conclusions: The current literature concerning guided miniscrew insertion reveals, for the most part, a low methodological level. High-quality clinical trials are in the minority. The use of surgical guides increases insertion accuracy, stability and reduces the failure rate of orthodontic miniscrews. Tooth-borne insertion guides supported on the edges of the teeth ensure a higher insertion precision compared to mucosa-borne ones. The study protocol was registered in PROSPERO under the number CRD42021267248.

Precise spatiotemporal gene expression during embryonic developmental is controlled by cis- regulatory elements (CREs) such as enhancers and promoters. Their physical chromatin proximity is correlated with active transcription and thought to be restricted to topologically associated domains (TADs) that help establish interactions between CREs and limit inappropriate contacts. Accordingly, TADs frequently overlap with gene regulatory landscapes, in which are contained diverse enhancers that transmit their activity across the domain towards their target promoter. Large structural variants reorganizing TADs were shown to cause gene misexpression and disease thereby linking gene regulation to chromatin structure. Recently, several studies revealed controversial results questioning the importance of TADs for transcriptional control. Acute depletion of CTCF and other architectural proteins in vitro led to loss of TAD structures with surprisingly modest effects on gene expression. However, the cytotoxicity of such depletion assays hindered analysis of more complex gene regulatory scenarios and their effect during development. This study specifically addresses the connection between TADs and developmental gene regulation through two projects using the murine limb as a model system. First, we took advantage of the Sox9/Kcnj2-locus that is subdivided into two adjacent TADs with distinct expression patterns of Sox9 and Kcnj2. The systematic deletion of individual CTCF binding sites at the TAD boundary and within the TAD resulted in gradual fusion of the neighboring domains without major effects on gene expression. TAD rearrangement by TAD-spanning inversions and repositioning of the boundary, however, redirected the regulatory activity and resulted in pathogenic gene misexpression. Thus, TAD structures may not be essential for developmental gene regulation, yet CTCF-dependent rearrangement of TADs can lead to the redirection of enhancer–promoter contacts and gene misexpression. In the second project, we studied how enhancer position relative to its TAD influences the function of an individual enhancer at the Shh-locus. Therefore, we repositioned the Shh-limb enhancer ZRS to five alternative locations inside and outside of its TAD. As expected, the enhancer lost all function in the positions outside of the Shh-TAD. Interestingly, the new positions inside the TAD also displayed decreased enhancer activity, albeit to varying degrees. Further analysis suggests that CTCF likely functions in some positions as a facilitator of enhancer-promoter contacts, while insulating short-range contacts in others. Ultimately, the ZRS is only able to ectopically activate some genes if repositioned to novel TADs, displaying strong enhancer-promoter selectivity. In summary, the results demonstrate that TADs provide robustness and precision to gene regulation, guiding enhancer-promoter interaction without being essential. The findings in this work build a basis for future studies aiming to understand enhancer-promoter interaction and can help in contextualizing potential disease-causing mutations disrupting TADs.

Mammalian and Drosophila genomes are partitioned into topologically associating domains (TADs). Although this partitioning has been reported to be functionally relevant, it is unclear whether TADs represent true physical units located at the same genomic positions in each cell nucleus or emerge as an average of numerous alternative chromatin folding patterns in a cell population. Here, we use a single-nucleus Hi-C technique to construct high-resolution Hi-C maps in individual Drosophila genomes. These maps demonstrate chromatin compartmentalization at the megabase scale and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which closely resembles the TAD profile in the bulk in situ Hi-C data. Over 40% of TAD boundaries are conserved between individual nuclei and possess a high level of active epigenetic marks. Polymer simulations demonstrate that chromatin folding is best described by the random walk model within TADs and is most suitably approximated by a crumpled globule build of Gaussian blobs at longer distances. We observe prominent cell-to-cell variability in the long-range contacts between either active genome loci or between Polycomb-bound regions, suggesting an important contribution of stochastic processes to the formation of the Drosophila 3D genome., Genomes are partitioned into topologically associating domains (TADs). Here the authors present single-nucleus Hi-C maps in Drosophila at 10 kb resolution, demonstrating the presence of chromatin compartments in individual nuclei, and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which resembles population TAD profiles.

El secado a través de aire es comúnmente usado en la industria de papel Tissue y es un proceso con un alto consumo de energía. Un modelo teórico fue desarrollado para predecir la velocidad de los ventiladores principales y el consumo de gas en el quemador, basados en una tasa de producción. El modelo mostro un buen ajuste con los datos reales, permitiendo de esta manera optimizar el proceso real y obtener ahorros alrededor de US 250.000/año., Through Air Drying (TAD) commonly used in tissue paper manufacture is an energy intensive process. A theoretical model was developed to predict the fans’ speed and the burner duty based on the type of product and operating parameters. The model showed good agreement to the industrial plant behavior and allowed insight of the drying system. This study, and the associated industrial implementation resulting from it, has led to savings of around of 250.000 USD associated with energy consumption

The phenotypic diversity found in vertebrates is closely related to modifications in the transcription patterns of developmental genes. Developmental genes often participate in several patterning processes and are thus very well conserved. In contrast, their associated cis-regulatory elements (CREs) function in a mostly time and tissue specific manner. Genetic modifications within CREs may thus alter the pattern of expression of their target developmental gene in a spatiotemporal limited manner. Consequently, they may lead to morphological changes with less probability of associated lethality than mutations affecting coding sequences. For this reason, understanding the mechanisms of CREs evolution is key to gain insight into vertebrate diversification. In vertebrate genomes, the multiple CREs controlling the activity of common developmental target gene(s) are generally found in large genomic regions called ‘regulatory landscapes'. In addition, the limits of these regulatory landscapes often correspond to the boundaries of Topologically Associating Domains (TADs), suggesting a functional link between regulatory activities and chromatin organization. The mouse HoxD locus represents an excellent system to study evolution of gene regulation because it is conserved and used in multiple tissue types through development. In addition, the different regulatory mechanisms controlling Hoxd gene expression are physically divided by function into several regulatory landscapes, C-DOM and T-DOM; where the T-DOM is further subdivided. Remarkably, the different regulatory domains appear to match the sub-compartmentalization of the 3D genome. This correspondence provided an entrance to systematically test the relationship between genomic organization and gene regulation in an evolutionary perspective. In this work, we started by comparing some aspects of the Hox genomic organization in different chordate species and at different mouse Hox loci. This analysis created a framework for the interpretation and contextualization of the ensuing experiments. Then, we turned to an analysis of the transcription of anterior Hoxd genes in the mouse primordia of vibrissae follicles and somites, which we compared to the corresponding chicken tissues, the primordia of feather follicles and somites respectively. These structures arose independently over an enormous amount of time – approximately 300 million years separates the appearance of somites (chordates) and the evolution of the first skin appendages (tetrapods). Yet, we found that the transcription of Hoxd genes is controlled by regulatory elements located in the T-DOM that are sometimes common between the two tissue types. In addition, we show that CREs regulating Hoxd1 are systematically found in the same genomic region, which establish frequent interactions with its promoter, no matter the species (mouse, chicken) or the tissue analysed (skin primordia, somites). These findings are detailed in a first manuscript for publication, which is attached to this thesis. Our analysis about Hoxd1 regulation in mouse embryos led to a collaboration with the group of Aurélien Capitan (INRAE), which is attached to this thesis as an annex (Allais-Bonnet et al. 2021, Annex 1). This work showed that the presence of supernumerary horns in goats and sheep (polyceraty) was linked to alterations of HOXD1 function. The mapping of POLYCERATE alleles in four-horned goats revealed that the mutation responsible for this morphological alteration is a large deletion located in the T-DOM, complementing our findings about the evolution of Hoxd1 regulation. Altogether, our results highlight the deep conservation of the HoxD cluster topology throughout vertebrates, despite divergent nucleotide sequences and regulatory activities. They support and reinforce the proposal that 3D chromatin organization both facilitates the emergence of new enhancers and limit their range of action., La diversité phénotypique des vertébrés est fortement liée à des variations dans les patterns de transcription des gènes du développement. Ces gènes sont généralement impliqués dans plusieurs processus d'organogenèse et ont par conséquent été fortement conservés au cours de l'évolution. En revanche, leurs séquences régulatrices, appelées cis-regulatory elements (CREs), ont une activité majoritairement spécifique aux tissus et aux stades de développement. Ainsi, certaines modifications de ces séquences de régulation affectent le pattern d'expression de leur gène cible de manière limitée dans le temps et dans l'espace. De ce fait, elles sont plus susceptibles de provoquer des altérations morphologiques non létales que des modifications des séquences codantes. Une compréhension accrue des mécanismes entraînant l'évolution des séquences régulatrices permettrait donc d'améliorer nos déductions quant aux raisons de l'incroyable diversité biologique des vertébrés. Les génomes de ces animaux présentent des domaines de chromatine particuliers, appelés ‘paysages de régulation'. Ces paysages rassemblent une multitude de séquences régulatrices qui contrôlent à distance l'activité d'un ou plusieurs gènes de manière coordonnée. L'étendue des paysages de régulation coïncide souvent avec celle de structures topologiques d'interactions préférentielles (TADs pour ‘topological associating domains') au sein desquelles les séquences ont une probabilité accrue de se retrouver proches les unes des autres. Cette correspondance a conduit à l'idée que l'organisation fonctionnelle de la régulation génique à distance et l'organisation physique de la chromatine dans l'espace du noyau forment deux aspects interdépendants du génome. Le locus HoxD de la souris constitue un système adéquat pour étudier l'évolution de la régulation génique parce qu'il est fortement conservé et parce qu'il est actif dans de nombreux processus développementaux. Par ailleurs, les différents mécanismes de régulation qui contrôlent l'expression des gènes Hoxd sont compartimentés en différents paysages de régulation, le C-DOM (pour domaine centromérique) et deux domaines imbriqués plus petits formant le T-DOM (pour domaine télomérique). Chacun de ces paysages présente une structure topologique en TAD, formant un ensemble génomique qui permet de tester de manière systématique la corrélation entre l'organisation de la chromatine et la régulation génique dans une perspective évolutive. Pour ce travail, nous avons d'abord comparé certains aspects de l'organisation génomique entre des complexes Hox de différentes espèces de chordés, ainsi qu'entre les différents clusters Hox chez la souris. Cette analyse nous a permis de formuler un cadre théorique pour l'interprétation et la contextualisation des expériences suivantes. Nous avons ensuite analysé la transcription des gènes Hoxd antérieurs dans les primordia de vibrisses et les somites chez la souris que nous avons comparés aux tissus correspondant chez le poulet, à savoir les primordia de plumes et les somites. Les somites (chordés) et les premiers appendices cutanés (tétrapodes) sont apparus indépendamment sur terre il y a plus de 300 millions d'années. Nous avons pourtant montré que la transcription des gènes Hoxd dans ces structures est contrôlée par des éléments de régulation situés dans le T-DOM, et qui sont parfois communs entre les deux tissus. Nous montrons également que la régulation à distance de Hoxd1 dépend systématiquement d'une région génomique commune qui établit de fréquentes interactions avec son promoteur, indépendamment du type de tissus ou de l'espèce considérée. Les résultats de cette recherche sont détaillés dans un premier manuscrit pour publication, attaché à cette thèse. L'analyse de la régulation de Hoxd1 dans l'embryon de souris a conduit à une collaboration avec le groupe de recherche d'Aurélien Capitan (INRAE), qui est annexée à cette thèse (Allais-Bonnet et al. 2021, Annex 1). Ce travail montre que la présence de cornes surnuméraires chez les chèvres et les moutons, des animaux qualifiés de polycérates, est associée à des défaillances dans la fonction du gène HOXD1. La cartographie des allèles POLYCERATE chez la chèvre a permis de localiser la mutation responsable de cette anomalie anatomique au sein du T-DOM, ce qui complémente nos résultats quant à l'évolution de la régulation de Hoxd1. Nos résultats de recherche, considérés dans leur ensemble, mettent en évidence la forte conservation du complexe HoxD chez les vertébrés, et ce malgré de fortes divergences dans les séquences ADN ainsi que dans les activités régulatrices. Nos résultats soutiennent et renforcent l'hypothèse que l'organisation de la chromatine au sein du noyau facilite l'émergence de nouvelles régulations, tout en limitant leur portée.

En este trabajo se reportan resultados parciales de una investigación que se ubica en la problemática de la formación de estudiantes de profesorado en lógica matemática. Como referencial teórico se adopta a la Teoría Antropológica de lo Didáctico. El estudio se llevó a cabo en dos grupos en los que se orientó un mismo curso a estudiantes de un programa universitario en una institución colombiana; cada grupo fue dirigido por un docente distinto. Los principales resultados indican que los docentes formadores de estudiantes de profesorado se concentran en interpretar tareas y resolverlas mediante una única técnica, así como en formular preguntas que no resultan problemáticas. En el proceso de estudio los estudiantes mantienen una actitud neutral o comunican respuestas que se restringen a las preguntas planteadas por los docentes. Fil: Cardona Hurtado, Oscar Abel. Universidad del Tolima; Colombia Fil: Corica, Ana Rosa. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Núcleo de Investigación en Educacion Ciencia y Tecnologia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; Argentina

Dosage compensation between the sexes results in one X chromosome being inactivated during female mammalian development. Chromosome-wide transcriptional silencing from the inactive X chromosome (Xi) in mammalian cells is erased in a process termed X-chromosome reactivation (XCR), which has emerged as a paradigm for studying the reversal of chromatin silencing. XCR is linked with germline development and induction of naive pluripotency in the epiblast, and also takes place upon reprogramming somatic cells to induced pluripotency. XCR depends on silencing of the long non-coding RNA (lncRNA) X inactive specific transcript (Xist) and is linked with the erasure of chromatin silencing. Over the past years, the advent of transcriptomics and epigenomics has provided new insights into the transcriptional and chromatin dynamics with which XCR takes place. However, multiple questions remain unanswered about how chromatin and transcription related processes enable XCR. Here, we review recent work on establishing the transcriptional and chromatin kinetics of XCR, as well as discuss a model by which transcription factors mediate XCR not only via Xist repression, but also by direct targeting of X-linked genes. ispartof: Cells vol:9 issue:12 ispartof: location:Switzerland status: published

Topologically associating domains (TADs) are the structural and functional units of the genome. However, the functions of protein-coding genes existing in the same or different TADs have not been fully investigated. We compared the functional similarities of protein-coding genes existing in the same TAD and between different TADs, and also in the same gap region (the region between two consecutive TADs) and between different gap regions. We found that the protein-coding genes from the same TAD or gap region are more likely to share similar protein functions, and this trend is more obvious with TADs than the gap regions. We further created two types of gene–gene spatial interaction networks: the first type is based on Hi-C contacts, whereas the second type is based on both Hi-C contacts and the relationship of being in the same TAD. A graph auto-encoder was applied to learn the network topology, reconstruct the two types of networks, and predict the functions of the central genes/nodes based on the functions of the neighboring genes/nodes. It was found that better performance was achieved with the second type of network. Furthermore, we detected long-range spatially-interactive regions based on Hi-C contacts and calculated the functional similarities of the gene pairs from these regions.