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DNA replication timing (RT), reflecting the temporal order of origin activation, is known as a robust and conserved cell-type specific process. Upon low replication stress, the slowing of replication forks induces well-documented RT delays associated to genetic instability, but it can also generate RT advances that are still uncharacterized. In order to characterize these advanced initiation events, we monitored the whole genome RT from six independent human cell lines treated with low doses of aphidicolin. We report that RT advances are cell-type-specific and involve large heterochromatin domains. Importantly, we found that some major late to early RT advances can be inherited by the unstressed next-cellular generation, which is a unique process that correlates with enhanced chromatin accessibility, as well as modified replication origin landscape and gene expression in daughter cells. Collectively, this work highlights how low replication stress may impact cellular identity by RT advances events at a subset of chromosomal domains This work was supported by “la Ligue nationale contre le cancer” (LNCC labellisation to JSH and VB and the grants RS16/75-108 and RS17/75-135 to JCC), the “Institut National du Cancer” (INCA, PLBIO2016-10493 to JSH, VB and JCC), the “Centre de Recherches en Cancérologie de Toulouse” to VB, the “Laboratoire d’excellence Toulouse Cancer—TOUCAN” to JSH, the “Groupement des Entreprises Françaises contre le Cancer” (GEFLUC) to JCC, the “IdEx Université de Paris” (ANR-18-IDEX-0001) to JCC, the generous legacy from Ms Suzanne Larzat to JCC, and “la Fondation pour la Recherche Médicale” to LC. MM and VP were funded by INSERM, the “Fondation Toulouse Cancer Santé” and “Pierre Fabre Research Institute” as part of the Chair of Bioinformatics in Oncology of the CRCT.

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.

We present 42 new Y-chromosomal sequences from diverse Indian tribal and non-tribal populations, including the Jarawa and Onge from the Andaman Islands, which are analysed within a calibrated Y-chromosomal phylogeny incorporating South Asian (in total 305 individuals) and worldwide (in total 1286 individuals) data from the 1000 Genomes Project. In contrast to the more ancient ancestry in the South than in the North that has been claimed, we detected very similar coalescence times within Northern and Southern non-tribal Indian populations. A closest neighbour analysis in the phylogeny showed that Indian populations have an affinity towards Southern European populations and that the time of divergence from these populations substantially predated the Indo-European migration into India, probably reflecting ancient shared ancestry rather than the Indo-European migration, which had little effect on Indian male lineages. Among the tribal populations, the Birhor (Austro-Asiatic-speaking) and Irula (Dravidian-speaking) are the nearest neighbours of South Asian non-tribal populations, with a common origin in the last few millennia. In contrast, the Riang (Tibeto-Burman-speaking) and Andamanese have their nearest neighbour lineages in East Asia. The Jarawa and Onge shared haplogroup D lineages with each other within the last ~7000 years, but had diverged from Japanese haplogroup D Y-chromosomes ~53000 years ago, most likely by a split from a shared ancestral population. This analysis suggests that Indian populations have complex ancestry which cannot be explained by a single expansion model. Funding was provided by the joint Spain–India bilateral grant PRI-PIBIN-2011-0942 and BFU2016-77961-P (AEI/ FEDER, UE) both awarded by the Ministerio de Economía y Competitividad (Spain) and with the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2014 SGR 866). Anders Bergström, YaliXue and Chris Tyler-Smith were supported by The Wellcome Trust (Grant 098051)

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)

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