Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA

Recent studies have revealed that the DNA cross-inversion mechanism of topoisomerase II (topo II) not only removes DNA supercoils and DNA replication intertwines, but also produces small amounts of DNA knots within the clusters of nucleosomes that conform to eukaryotic chromatin. Here, we examine how transcriptional supercoiling of intracellular DNA affects the occurrence of these knots. We show that although (-) supercoiling does not change the basal DNA knotting probability, (+) supercoiling of DNA generated in front of the transcribing complexes increases DNA knot formation over 25-fold. The increase of topo II-mediated DNA knotting occurs both upon accumulation of (+) supercoiling in topoisomerase-deficient cells and during normal transcriptional supercoiling of DNA in TOP1 TOP2 cells. We also show that the high knotting probability (Pkn 65 0.5) of (+) supercoiled DNA reflects a 5-fold volume compaction of the nucleosomal fibers in vivo. Our findings indicate that topo II-mediated DNA knotting could be inherent to transcriptional supercoiling of DNA and other chromatin condensation processes and establish, therefore, a new crucial role of topoisomerase II in resetting the knotting-unknotting homeostasis of DNA during chromatin dynamics

Sharing, Living Together and Understanding. A Journey Through our Experiences

S’exposen les metodologies i objectius d’un recull d’experiències educatives que ajuden als infants a comprendre el món mitjançant l’ús d’eines i recursos culturals matemàtics. Aquestes experiències s’han realitzat amb nins d’Educació Infantil de diferents escoles públiques de les Illes Balears. Així mateix, dues experiències, Xishun i Codi de barres, s’han realitzat amb alumnat de primer cicle d’Educació PrimàriaSe exponen las metodologías y objetivos de una recopilación de experiencias educativas que ayudan a los niños a comprender el mundo mediante el uso de herramientas y recursos culturales matemáticos. Estas experiencias se han realizado con niños de Educación Infantil de diferentes escuelas públicas de las Illes Balears. Asimismo, dos experiencias: Xishun y Código de barras, se han realizado con alumnado de primer ciclo de Educación Primaria.This paper presents the methodologies and objectives of a collection of educational experiences that help children understand the world and ourselves through the use of mathematical and cultural tools and resources. These experiences were implemented with 3, 4 and 5-year-old preschool children in different Balearic schools and two of them, “Xishun” and “Codi de Barres”, were implemented with first-cycle primary school students

Tobacco cessation among smokers under substance use treatment for alcohol and/or cannabis: study protocol and pilot study

Background: Approximately 80% of people with a substance use disorder (SUD) are smokers. Starting SUD treatment offers the opportunity to also quit smoking. The ACT-ATAC project aims to identify the predictors associated with smoking cessation among persons treated for alcohol and/or cannabis use disorder in Barcelona. This manuscript reports its methodology and the experience of carrying it out during the COVID-19 pandemic. Methods: Mixed methods project with three substudies. Substudy 1 (S1) comprises heterogeneous discussion groups among clinicians. S2 has two prospective cohorts composed of smokers under treatment for alcohol and/or cannabis use disorder and the clinicians in charge of these patients. Participating smokers will be followed for 12 months and interviewed about their substance use and the tobacco cessation services received using the Spanish version of the users' Knowledge, Attitudes, and Services (S-KAS) scale. The clinicians will be asked about their self-reported practices in smoking cessation using the Knowledge, Attitudes, and Practices (S-KAP) scale. S3 comprises heterogeneous discussion groups with smokers. Data will be triangulated using qualitative and quantitative analyses. To facilitate the recruitment process, the researchers have introduced several strategies (design clear protocols, set monthly online meetings, extend the project, provide gift cards, etc.). Discussion: The results of S1 were used to develop the questionnaires. S2 required some adjustments due to the COVID-19 pandemic, particularly the follow-up interviews being conducted by phone instead of face-to-face, and the recruitment rhythm was lower than expected. Recruitment will last until reaching at least 200-250 users. The fieldwork could not have been possible without the collaboration of the ACT-ATAC team and the introduction of several strategies

Nutrición parenteral domiciliaria en España, 2019: informe del Grupo de Nutrición Artificial Domiciliaria y Ambulatoria NADYA

RESUMEN Objetivo: comunicar los datos de nutrición parenteral domiciliaria (NPD) obtenidos del registro del grupo NADYA-SENPE (www.nadyasenpe.com) del año 2019. Material y métodos: análisis descriptivo de los datos recogidos de pacientes adultos y pediátricos con NPD en el registro NADYA-SENPE desde el 1 de enero al 31 de diciembre de 2019. Resultados: se registraron 283 pacientes (51,9 %, mujeres), 31 niños y 252 adultos procedentes de 47 hospitales españoles, lo que representa una tasa de prevalencia de 6,01 pacientes/millón de habitantes/año 2019. El diagnóstico más frecuente en los adultos fue “oncológico paliativo” y “otros” (21,0 %). En los niños fue la enfermedad de Hirschsprung junto a la enterocolitis necrotizante, las alteraciones de la motilidad intestinal y la pseudoobstrucción intestinal crónica, con 4 casos cada uno (12,9 %). El primer motivo de indicación fue el síndrome del intestino corto tanto en los niños (51,6 %) como en los adultos (37,3 %). El tipo de catéter más utilizado fue el tunelizado tanto en los niños (75,9 %) como en los adultos (40,8 %). Finalizaron 68 episodios, todos en adultos: la causa más frecuente fue el fallecimiento (54,4 %). Pasaron a la vía oral el 38,2 %. Conclusiones: el número de centros y profesionales colaboradores con el registro NADYA va incrementándose. Se mantienen estables las principales indicaciones y los motivos de finalización de la NPD

Nutrición parenteral domiciliaria en España 2018. Informe del Grupo de Nutrición Artificial Domiciliaria y Ambulatoria NADYA

Aim: to communicate home parenteral nutrition (HPN) data obtained from the HPN registry of the NADYA-SENPE group (www.nadya-senpe. com) for the year 2018. Material and methods: descriptive analysis of the data collected from adult and pediatric patients with HPN in the NADYA-SENPE group registry from January 1st, 2018 to December 31st, 2018. Results: there were 278 patients from 45 Spanish hospitals (54.7 % women), 23 children and 255 adults, which represent a prevalence rate of 5.95 patients/million inhabitants/year 2018. The most frequent diagnosis in adults was " palliative cancer" (22.0 %), followed by "others". In children it was Hirschsprung's disease together with necrotizing enterocolitis, with four cases (17.4 %). The first indication was short bowel syndrome in both children (60.9 %) and adults (35.7 %). The most frequently used type of catheter was tunneled in both children (81.0 %) and adults (41.1 %). Ending 75 episodes, the most frequent cause was death (52.0 %) and change to oral feeding (33.3 %). Conclusions: the number of centers and collaborating professionals in the registry of patients receiving HPN remains stable, as well as the main indications and reasons for termination of HPN

DNA knots occur in intracellular chromatin

In vivo DNA molecules are narrowly folded within chromatin fibers and self-interacting chromatin domains. Therefore, intra-molecular DNA entanglements (knots) might occur via DNA strand passage activity of topoisomerase II. Here, we assessed the presence of such DNA knots in a variety of yeast circular minichromosomes. We found that small steady state fractions of DNA knots are common in intracellular chromatin. These knots occur irrespective of DNA replication and cell proliferation, though their abundance is reduced during DNA transcription. We found also that in vivo DNA knotting probability does not scale proportionately with chromatin length: it reaches a value of ∼0.025 in domains of ∼20 nucleosomes but tends to level off in longer chromatin fibers. These figures suggest that, while high flexibility of nucleosomal fibers and clustering of nearby nucleosomes facilitate DNA knotting locally, some mechanism minimizes the scaling of DNA knot formation throughout intracellular chromatin. We postulate that regulation of topoisomerase II activity and the fractal architecture of chromatin might be crucial to prevent a potentially massive and harmful self-entanglement of DNA molecules in vivo.Plan Estatal de Investigacion Científica y Tecnica of Spain ´ [BFU2015-67007-P and MDM-2014-0435-02 to J.R., BES2015-071597 to. A.V.]. Funding for open access charge: Plan Estatal de Investigacion Científica y Tecnica of Spain.Peer reviewe

Keeping intracellular DNA untangled: A new role for condensin?

The DNA-passage activity of topoisomerase II accidentally produces DNA knots and interlinks within and between chromatin fibers. Fortunately, these unwanted DNA entanglements are actively removed by some mechanism. Here we present an outline on DNA knot formation and discuss recent studies that have investigated how intracellular DNA knots are removed. First, although topoisomerase II is able to minimize DNA entanglements in vitro to below equilibrium values, it is unclear whether such capacity performs equally in vivo in chromatinized DNA. Second, DNA supercoiling could bias topoisomerase II to untangle the DNA. However, experimental evidence indicates that transcriptional supercoiling of intracellular DNA boosts knot formation. Last, cohesin and condensin could tighten DNA entanglements via DNA loop extrusion (LE) and force their dissolution by topoisomerase II. Recent observations indicate that condensin activity promotes the removal of DNA knots during interphase and mitosis. This activity might facilitate the spatial organization and dynamics of chromatin.Prospects & Overviews; Plan Estatal de Investigación Científica y Técnica of Spain

Condensin minimizes topoisomerase II-mediated entanglements of DNA in vivo

© 2020 The Authors.The juxtaposition of intracellular DNA segments, together with the DNA-passage activity of topoisomerase II, leads to the formation of DNA knots and interlinks, which jeopardize chromatin structure and gene expression. Recent studies in budding yeast have shown that some mechanism minimizes the knotting probability of intracellular DNA. Here, we tested whether this is achieved via the intrinsic capacity of topoisomerase II for simplifying the equilibrium topology of DNA; or whether it is mediated by SMC (structural maintenance of chromosomes) protein complexes like condensin or cohesin, whose capacity to extrude DNA loops could enforce dissolution of DNA knots by topoisomerase II. We show that the low knotting probability of DNA does not depend on the simplification capacity of topoisomerase II nor on the activities of cohesin or Smc5/6 complexes. However, inactivation of condensin increases the occurrence of DNA knots throughout the cell cycle. These results suggest an in vivo role for the DNA loop extrusion activity of condensin and may explain why condensin disruption produces a variety of alterations in interphase chromatin, in addition to persistent sister chromatid interlinks in mitotic chromatin.This research was supported by the Plan Estatal de Investigación Científica y Técnica of Spain, with grants BFU2015-67007-P and PID2019-109482GB-I00 to J.R; and research fellowships BES-2016-077806 to S.D., BES-2012-061167 to J.S., and BES-2015-071597 to A.V

In vivo DNA topology and conformations of chromatin

Trabajo presentado en el EMBO Workshop: DNA topoisomerases and DNA topology, celebrado en Les Diablerets (Suiza), del 17 al 21 de septiembre de 2017In contrast to our approximated view of the topology and conformations of naked DNA molecules in vitro, we can hardly picture the topology and spatial configurations of DNA in vivo. Chromatin architecture and its enzymatic activities determine how twist and writhe deformations of DNA are constrained or unconstrained, and how DNA supercoiling energy is generated, buffered or dissipated at each genomic site. Understanding the topology of nucleosomal DNA and nucleosomal fibers is therefore a fundamental prerequisite to evaluate the DNA topology outcomes of more complex chromatin structures. In this regard, we have revisited the "linking number paradox" of nucleosomal DNA, which states that the 1.7 lefthanded turns of DNA around a histone octamer results in the apparent stabilization of only one negative DNA supercoil (∆Lk ≈ -1). In order to assess how nucleosomal fibers are packaged in vivo, we have also conducted a first analysis of the probability of DNA knot formation in eukaryotic chromatin. We found that steady state fractions of trefoils and more complex knot species are maintained by topoisomerase II activity. We uncovered also that the knotting probability of intracellular DNA does not scale proportionally to chromatin length. On the basis of our experimental observations, we inferred novel traits of the nucleosomal DNA topology and the chromatin architecture in vivo.N