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Genomics & Functional Genomics

  • A novel <em>canis lupus familiaris</em> reference genome improves variant resolution for use in breed-specific GWAS
    Open Access
    A novel canis lupus familiaris reference genome improves variant resolution for use in breed-specific GWAS

    Robert A Player, Ellen R Forsyth, Kathleen J Verratti, David W Mohr, Alan F Scott, Christopher E Bradburne

    Robert A Player ... Christopher E Bradburne

    Published 29 January 2021

    This paper describes the economical optimization of DNA extraction, short and long read sequencing, and bioinformatic assembly, which in turn improves mapping and variant resolution of short-read sequenced, same-breed dogs for association studies. This methodology is applicable for any investigators planning a genome-wide association study.

  • The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells
    Open Access
    The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells

    Li Ding, Maciej Paszkowski-Rogacz, Jovan Mircetic, Debojyoti Chakraborty, Frank Buchholz

    Li Ding ... Frank Buchholz

    Published 29 December 2020

    Using ChIP-seq and functional genomic analyses, the study shows that the Paf1 complex occupies transcriptional enhancers and positively regulates their activity.

  • The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells
    Open Access
    The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells

    Maria Inês Alvelos, Mirko Brüggemann, FX Reymond Sutandy, Jonàs Juan-Mateu, Maikel Luis Colli, Anke Busch, Miguel Lopes, Ângela Castela, Annemieke Aartsma-Rus, Julian König, Kathi Zarnack, Décio L Eizirik

    Maria Inês Alvelos ... Décio L Eizirik

    Published 29 December 2020

    The RNA-binding protein SRSF6 recognizes a purine-rich consensus motif consisting of GAA triplets, and its downregulation in human pancreatic β-cells affects alternative splicing in a position-dependent manner.

  • Polycomb mutant partially suppresses DNA hypomethylation–associated phenotypes in Arabidopsis
    Open Access
    Polycomb mutant partially suppresses DNA hypomethylation–associated phenotypes in Arabidopsis

    Martin Rougée, Leandro Quadrana, Jérôme Zervudacki, Valentin Hure, Vincent Colot, Lionel Navarro, Angélique Deleris

    Martin Rougée ... Angélique Deleris

    Published 21 December 2020

    A mutation in Arabidopsis polycomb repressive complex 2 partially suppresses the transposon activity observed in a DNA methylation mutant, challenging expectations.

  • Single-cell RNA sequencing of human breast tumour-infiltrating immune cells reveals a γδ T-cell subtype associated with good clinical outcome
    Open Access
    Single-cell RNA sequencing of human breast tumour-infiltrating immune cells reveals a γδ T-cell subtype associated with good clinical outcome

    Katerina Boufea, Víctor González-Huici, Marcus Lindberg, Stefan Symeonides, Olga Oikonomidou, Nizar N Batada

    Katerina Boufea ... Nizar N Batada

    Published 2 December 2020

    Single-cell sequencing of γδ-T cells from human blood and tumours revealed novel markers of subtypes with distinct effector functions and a subtype that is associated with favourable clinical outcome.

  • Characterization of ori and parS-like functions in secondary genome replicons in <em>Deinococcus radiodurans</em>
    Open Access
    Characterization of ori and parS-like functions in secondary genome replicons in Deinococcus radiodurans

    Ganesh K Maurya, Hari S Misra

    Ganesh K Maurya ... Hari S Misra

    Published 16 November 2020

    An array of direct repeats upstream to parAB operon helps in secondary genome elements’ maintenance independent of primary chromosome in multipartite genome harboring bacterium Deinococcus radiodurans.

  • Incipient sympatric speciation in wild barley caused by geological-edaphic divergence
    Open Access
    Incipient sympatric speciation in wild barley caused by geological-edaphic divergence

    Kexin Li, Xifeng Ren, Xiaoying Song, Xiujuan Li, Yu Zhou, Eli Harlev, Dongfa Sun, Eviatar Nevo

    Kexin Li ... Eviatar Nevo

    Published 20 October 2020

    Sympatric speciation is still contentious but here based on genome-wide analysis; we show incipient sympatric speciation of an emerging new wild barley species from Hordeum spontaneum, the progenitor of all cultivated barleys at “Evolution Plateau” (EP), Upper Galilee, Israel.

  • Predicting gene regulatory networks from cell atlases
    Open Access
    Predicting gene regulatory networks from cell atlases

    Andreas Fønss Møller, Kedar Nath Natarajan

    Andreas Fønss Møller ... Kedar Nath Natarajan

    Published 21 September 2020

    Integrated single-cell gene regulatory network from three mouse cell atlases captures global and cell type–specific regulatory modules and crosstalk, important for cellular identity.

  • multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets
    Open Access
    multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets

    Aditya M Bhagwat, Johannes Graumann, Rene Wiegandt, Mette Bentsen, Jordan Welker, Carsten Kuenne, Jens Preussner, Thomas Braun, Mario Looso

    Aditya M Bhagwat ... Mario Looso

    Published 9 September 2020

    A bioinformatics R package for a fast and generic guideRNA design, optimized for large-scale perturbation assays.

  • Peptide-based quorum sensing systems in <em>Paenibacillus polymyxa</em>
    Open Access
    Peptide-based quorum sensing systems in Paenibacillus polymyxa

    Maya Voichek, Sandra Maaß, Tobias Kroniger, Dörte Becher, Rotem Sorek

    Maya Voichek ... Rotem Sorek

    Published 6 August 2020

    Discovery of conserved communication systems in the agriculturally important Paenibacillus bacteria. These systems are widespread, and some species encode more than 25 different peptide-receptor pairs.

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