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Next-generation sequencing technologies expedited research to develop efficient computational tools for the identification of structural variants (SVs) and their use to study human diseases. As deeper data is obtained, the existence of higher complexity SVs in some genomes becomes more evident, but the detection and definition of most of these complex rearrangements is still in its infancy. The full characterization of SVs is a key aspect for discovering their biological implications. Here we present a pipeline (PeSV-Fisher) for the detection of deletions, gains, intra- and inter-chromosomal translocations, and inversions, at very reasonable computational costs. We further provide comprehensive information on co-localization of SVs in the genome, a crucial aspect for studying their biological consequences. The algorithm uses a combination of methods based on paired-reads and read-depth strategies. PeSV-Fisher has been designed with the aim to facilitate identification of somatic variation, and, as such, it is capable of analysing two or more samples simultaneously, producing a list of non-shared variants between samples. We tested PeSV-Fisher on available sequencing data, and compared its behaviour to that of frequently deployed tools (BreakDancer and VariationHunter). We have also tested this algorithm on our own sequencing data, obtained from a tumour and a normal blood sample of a patient with chronic lymphocytic leukaemia, on which we have also validated the results by targeted re-sequencing of different kinds of predictions. This allowed us to determine confidence parameters that influence the reliability of breakpoint predictions. This work was supported by AGAUR (Generalitat de Catalunya, 2009 SGR 1502) (X.E.); CIBERESP (Instituto de Salud Carlos III) (G.E.); ESGI (European Commission, 262055_ESGI) (R.R., X.E.), ENGAGE (European Commission, ENGAGE_201413), TECHGENE (European Commission, TECHGENE_223143), and GEUVADIS (European Commission, 261123_GEUVADIS) (X.E.); NOVADIS (Ministerio de Ciencia y Technologia, SAF2008-00357) (X.E.); Galicia Government Xunta de Galicia (Spain) through the project number 10PXIB918057 (J.M.C.T.); MAEC-AEC1 Predoctoral Fellowship (Ministerio de Asuntos Exteriores y Cooperación, Spain) (A.M.F.); and Ramón y Cajal position and grant BFU2007-60930 (Ministerio de Educación y Ciencia) (M.C.).

The intrinsic dynamic nature of chromosomes is emerging as a fundamental component in regulating DNA transcription, replication, and damage-repair among other nuclear functions. With this increased awareness, reinforced over the last ten years, many new experimental techniques, mainly based on microscopy and chromosome conformation capture, have been introduced to study the genome in space and time. Owing to the increasing complexity of these cutting-edge techniques, computational approaches have become of paramount importance to interpret, contextualize, and complement such experiments with new insights. Hence, it is becoming crucial for experimental biologists to have a clear understanding of the diverse theoretical modeling approaches available and the biological information each of them can provide. M.A.M-R. acknowledges support from the European Union’s Seventh Framework Programme through the ERC (grant agreement 609989), European Union’s Horizon 2020 research and innovation programme (grant agreement 676556), and the Spanish Ministerio de Ciencia, Innovación y Universidades (BFU2017-85926-P). M.D.S. acknowledges support from the ORION project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement (grant agreement 741527). D.J. acknowledges Agence Nationale de la Recherche (ANR-18-CE12-0006-03, ANR-18-CE45-0022-01) for funding. CRG acknowledges support from ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 and the CERCA Programme/Generalitat de Catalunya as well as support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the EMBL partnership, the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement, and the Co-financing with funds from the European Regional Development Fund (ERDF) by the Spanish Ministery of Science and Innovation coresponding to the Programa Opertaivo FEDER Plurirregional de España (POPE) 2014-2020 and by the Secretaria d'Universitats i Recerca, Departament d'Empresa i Coneixement of the Generalitat de Catalunya corresponding to the programa Operatiu FEDER Catalunya 2014-2020. Open Access fees paid from COST Action INC (CA18127), supported by COST (European Cooperation in Science and Technology)

Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent playground to evaluate different assembly methods. Here, we compare the structure of satellites found in three different assemblies of the Caenorhabditis elegans genome: the original sequence obtained by Sanger sequencing, an assembly based on PacBio technology, and an assembly using Nanopore sequencing reads. In general, satellites were found in equivalent genomic regions, but the new long-read methods (PacBio and Nanopore) tended to result in longer assembled satellites. Important differences exist between the assemblies resulting from the two long-read technologies, such as the sizes of long satellites. Our results also suggest that the lengths of some annotated genes with internal repeats which were assembled using Sanger sequencing are likely to be incorrect.

Heterozygous mutations in the melanocortin-4 receptor (MC4R) gene represent the most frequent cause of monogenic obesity in humans. MC4R mutation analysis in a cohort of 77 children with morbid obesity identified previously unreported heterozygous mutations (P272L, N74I) in two patients inherited from their obese mothers. A rare polymorphism (I251L, allelic frequency: 1/100) reported to protect against obesity was found in another obese patient. When expressed in neuronal cells, the cell surface abundance of wild-type MC4R and of the N74I and I251L variants and the cAMP generated by these receptors in response to exposure to the agonist, α-MSH, were not different. Conversely, MC4R P272L was retained in the endoplasmic reticulum and had reduced cell surface expression and signaling (by ≈3-fold). The chemical chaperone PBA, which promotes protein folding of wild-type MC4R, had minimal effects on the distribution and signaling of the P272L variant. In contrast, incubation with UBE-41, a specific inhibitor of ubiquitin activating enzyme E1, inhibited ubiquitination of MC4R P272L and increased its cell surface expression and signaling to similar levels as wild-type MC4R. UBE41 had much less profound effects on MC4R I316S, another obesity-linked MC4R variant trapped in the ER. These data suggest that P272L is retained in the ER by a propensity to be ubiquitinated in the face of correct folding, which is only minimally shared by MC4R I316S. Thus, studies that combine clinical screening of obese patients and investigation of the functional defects of the obesity-linked MC4R variants can identify specific ways to correct these defects and are the first steps towards personalized medicine, This work has been funded by Fondo de Investigación Sanitaria (PI09/91060, PI10/02512, PI01/00747), CIBERobn Instituto de Salud Carlos III (ISCIII), Fundación Mutua Madrileña (AP2561/2008), Fundación Endocrinología y Nutrición, the National Institutes of Health (R01DK080424 to GB), and the Arkansas Tobacco Settlement (to GB). CS-J and GAM-M were recipients of fellowships from ISCIII (FI08/00365 and CM05/00100, respectively)

A current problem in deoxyribonucleic acid (DNA) sequence analysis is to determine the exact locations of the genes and also in eukaryotes, the protein-coding regions in the mRNA primary transcript (pre-mRNA).The conversion into discrete numerical values of the symbols associated to the nucleotides of these sequences allows for a signal to address the problems related to localization and annotation of genes. In this work, thermodynamic data of free energy changes (#G°) on the formation of a duplex structure of DNA or RNA are used to convert the symbols into numerical values associated with the nucleotide sequence pre-mRNA. This study presents an analysis, based on techniques of time-frequency representation of a large number of gene sequences, in order to find variables related to pre-mRNA that could best characterize and discriminate coding regions from non-coding regions. It has been found that instantaneous frequency variables and instantaneous spectral energy variables in different frequency bands, allowed exons and introns to be correctly classified with more than 85%.

1) The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp 2) Article espanyol més citat de la dècada 1999-2009, segons ScienceWatch (Set. 2010) DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allows, 1) handling big data sets (~5 Mbp per sequence); 2) conducting a large number of coalescent- based tests by Monte Carlo computer simulations; 3) extensive analyses of the genetic differentiation and gene flow among populations; 4) analysing the evolutionary pattern of preferred and unpreferred codons; 5) generating graphical outputs for an easy visualization of results. Peer Reviewed Award-winning