A new chromosome-assigned Mongolian gerbil genome allows characterization of complete centromeres and a fully heterochromatic chromosome

This is the final version. Available on open access from Oxford University Press via the DOI in this recordData Availability: All sequencing data and the genome are available under SRA BioProject PRJNA397533. Specific accession numbers can be found in supplementary material S1, Supplementary Material online. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAODIK000000000. The version described in this paper is version JAODIK010000000. The genetic map, a vcf of the genetic markers and their genotypes in the mapping panel, the gff of the gene annotations, the gff of the repetitive element annotations, and “Supplemental_Material 3_codebase.zip”, can be found in the Dryad repository here: Brekke, Thomas D. (2022), Data for “The origin of a new chromosome in gerbils”, Dryad, Dataset, https://doi.org/10.5061/dryad.1vhhmgqws.Chromosome-scale genome assemblies based on ultralong-read sequencing technologies are able to illuminate previously intractable aspects of genome biology such as fine-scale centromere structure and large-scale variation in genome features such as heterochromatin, GC content, recombination rate, and gene content. We present here a new chromosome-scale genome of the Mongolian gerbil (Meriones unguiculatus), which includes the complete sequence of all centromeres. Gerbils are thus the one of the first vertebrates to have their centromeres completely sequenced. Gerbil centromeres are composed of four different repeats of length 6, 37, 127, or 1,747 bp, which occur in simple alternating arrays and span 1-6 Mb. Gerbil genomes have both an extensive set of GC-rich genes and chromosomes strikingly enriched for constitutive heterochromatin. We sought to determine if there was a link between these two phenomena and found that the two heterochromatic chromosomes of the Mongolian gerbil have distinct underpinnings: Chromosome 5 has a large block of intraarm heterochromatin as the result of a massive expansion of centromeric repeats, while chromosome 13 is comprised of extremely large (>150 kb) repeated sequences. In addition to characterizing centromeres, our results demonstrate the importance of including karyotypic features such as chromosome number and the locations of centromeres in the interpretation of genome sequence data and highlight novel patterns involved in the evolution of chromosomes.Leverhulme TrustNatural Environment Research Council (NERC)Ministerio de Economía y Competitivida

Primitive shape fitting in point clouds for enabling autonomous underwater grasping

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Engaging with media – a matter of literacy?

This article considers the continued relevance of critical research on audience reception and audience ethnography to today’s study of complex media and communications environment. Although much of the work addressing people’s engagement with new media is now framed not in terms of audiences but rather in terms of literacies, there are many parallels between the critical analysis of literacy and of audiences. Both examine the interface between the interpretative activities of ordinary people and the powerful institutions, texts and technologies they engage with. Both identify forms of stratification and exclusion while recognising the micro-tactics of marginalised audiences/ the digitally excluded. On the one hand, the notion of literacy offers some advantages over that of audiences, for it draws on a long history of theorising knowledge in relation to emancipation and democratisation. On the other hand, literacy occasions critical scrutiny, particularly when, as today, it is mobilised in support of by neo-liberal, deregulatory policies in the media and communications sector. Insofar as audience research directs its energies towards the analysis of new media literacies, it is vital to follow the principles of critical analysis, explicating research assumptions, scrutinising how our work is used, and asking whose interests are thereby served

Three-dimensional genomic structure and cohesin occupancy correlate with transcriptional activity during spermatogenesis

Mammalian gametogenesis involves dramatic and tightly regulated chromatin remodeling, whose regulatory pathways remain largely unexplored. Here, we generate a comprehensive high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ chromosome conformation capture sequencing (Hi-C), RNA sequencing (RNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) of CCCTC-binding factor (CTCF) and meiotic cohesins, coupled with confocal and super-resolution microscopy. Spermatogonia presents well-defined compartment patterns and topological domains. However, chromosome occupancy and compartmentalization are highly re-arranged during prophase I, with cohesins bound to active promoters in DNA loops out of the chromosomal axes. Compartment patterns re-emerge in round spermatids, where cohesin occupancy correlates with transcriptional activity of key developmental genes. The compact sperm genome contains compartments with actively transcribed genes but no fine-scale topological domains, concomitant with the presence of protamines. Overall, we demonstrate how genome-wide cohesin occupancy and transcriptional activity is associated with three-dimensional (3D) remodeling during spermatogenesis, ultimately reprogramming the genome for the next generation.This work was supported by the Ministry of Economy and Competitiveness (BFU2017-89408-R to A.M.P.; BFU2013-47736-P and BFU2017-85926-P to M.A.M.-R.; and CGL2014-54317-P and CGL2017-83802-P to A.R.-H.) and the Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR) (DI2015 to A.R.-H. and R.A.C., as well as SGR468 to M.A.M-R.). Work at CRG, BIST, and UPF was in part funded by the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ (SEV-2012-0208), and ‘Centro de Excelencia María de Maeztu 2016-2019.’ CIC-IBMCC is supported by the Programa de Apoyo a Planes Estratégicos de Investigación de Estructuras de Investigación de Excelencia, co-funded by Junta de Castilla y León (CSI239P18) and the European Regional Development Fund (CLC–2017–01). C.V. is supported by a FPI predoctoral fellowship from the Ministry of Economy and Competitiveness (BES-2015-072924). A.P.-G. is supported by a ‘Doctorats Industrials’ predoctoral fellowship (AGAUR). H.H. is a Miguel Servet (CP14/00229) researcher funded by the Spanish Institute of Health Carlos III (ISCIII), the Agencia Estatal de Investigación (AEI), and FEDER (SAF2017-89109-P). C.M. is an Asociación Española Contra el Cáncer (AECC) postdoctoral fellow. M.A.M.-R. acknowledges support by the European Research Council under the 7th Framework Program FP7/2007-2013 (ERC grant agreement 609989) and the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement 676556). A.M.P. and A.R.-H. also acknowledge support from MeioNet (BFU2015-71786-REDT)

Three-dimensional genomic structure and cohesin occupancy correlate with transcriptional activity during spermatogenesis

Altres ajuts: Agaur SGR468 to M.A.M-R. A.P.-G. is supported by a 'Doctorats Industrials' predoctoral fellowship (AGAUR). H.H. is a Miguel Servet (CP14/00229) researcher funded by the Spanish Institute of Health Carlos III (ISCIII)Mammalian gametogenesis involves dramatic and tightly regulated chromatin remodeling, whose regulatory pathways remain largely unexplored. Here, we generate a comprehensive high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ chromosome conformation capture sequencing (Hi-C), RNA sequencing (RNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) of CCCTC-binding factor (CTCF) and meiotic cohesins, coupled with confocal and super-resolution microscopy. Spermatogonia presents well-defined compartment patterns and topological domains. However, chromosome occupancy and compartmentalization are highly re-arranged during prophase I, with cohesins bound to active promoters in DNA loops out of the chromosomal axes. Compartment patterns re-emerge in round spermatids, where cohesin occupancy correlates with transcriptional activity of key developmental genes. The compact sperm genome contains compartments with actively transcribed genes but no fine-scale topological domains, concomitant with the presence of protamines. Overall, we demonstrate how genome-wide cohesin occupancy and transcriptional activity is associated with three-dimensional (3D) remodeling during spermatogenesis, ultimately reprogramming the genome for the next generation