All episodes of PaperPlayer biorxiv genomics

Episodes

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.249870v1?rss=1 Authors: Halstead, M. M., Kern, C., Saelao, P., Wang, Y., Chanthavixay, G., Medrano, J. F., Van Eenennaam, A. L., Korf, I., Tuggle, C. K., Ernst, C. W., Zhou, H., ROSS, P. J. Abstract: Background: Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This...

Published 08/14/20

DREAM represses distinct targets by cooperating with different THAP domain proteins

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.249698v1?rss=1 Authors: Gal, C., Carelli, F. N., Appert, A., Cerrato, C., Huang, N., Dong, Y., Murphy, J., Ahringer, J. Abstract: The DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle and other genes, but its mechanism of action is unclear. Here we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function...

Published 08/14/20

Scarless engineering of the Drosophila genome near any site-specific integration site

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.249656v1?rss=1 Authors: Feng, S., Lu, S., Grueber, W. B., Mann, R. S. Abstract: We describe a simple and efficient technique that allows scarless engineering of Drosophila genomic sequences near any landing site containing an inverted attP cassette, such as a MiMIC insertion. This 2-step method combines phiC31 integrase mediated site-specific integration and homing nuclease mediated resolution of local duplications,...

Published 08/14/20

Conditional resampling improves sensitivity and specificity of single cell CRISPR regulatory screens

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.250092v1?rss=1 Authors: Katsevich, E., Roeder, K. Abstract: Mapping gene-enhancer regulatory relationships is key to unraveling molecular disease mechanisms based on GWAS associations in non-coding regions. Recently developed CRISPR regulatory screens (CRSs) based on single cell RNA-seq (scRNA-seq) are a promising high-throughput experimental approach to this problem. However, the analysis of these screens presents...

Published 08/14/20

Suv39h-catalysed H3K9me3 is critical for euchromatic genome organisation and the maintenance of gene transcription

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.249078v1?rss=1 Authors: Keenan, C. R., Coughlan, H. D., Iannarella, N., Johanson, T. M., Chan, W. F., Garnham, A. L., Smyth, G. K., Allan, R. S. Abstract: H3K9me3-dependent heterochromatin is critical for the silencing of repeat-rich pericentromeric regions and also has key roles in repressing lineage-inappropriate protein-coding genes in differentiation and development. Here, we investigate the molecular consequences...

Published 08/14/20

Mitogenomic Phylogeny of Callithrix with Special Focus on Human Transferred Taxa

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.247692v1?rss=1 Authors: Malukiewicz, J., Cartwright, R. A., Curi, N. H., Dergam, J. A., Igayara, C. S., Moreira, S. B., Molina, C. V., Nicola, P. A., Noll, A., Passamani, M., Pereira, L. C., Pissinatti, A., Ruiz-Miranda, C. R., Silva, D. L., Stone, A. C., Zinner, D., Roos, C. Abstract: Background Callithrix marmosets are a relatively young non-human primate radiation, whose phylogeny is not yet fulllly resolved. These...

Published 08/14/20

Systematic evaluation of genome sequencing as a first-tier diagnostic test for prenatal and pediatric disorders

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.248526v1?rss=1 Authors: Lowther, C., Valkanas, E., Giordano, J. L., Wang, H. Z., Currall, B. B., O'Keefe, K., Collins, R. L., Zhao, X., Austin-Tse, C. A., Evangelista, E., Aggarwal, V., Lucente, D., Gauthier, L. D., Tolonen, C., Sahakian, N., An, J.-Y., Dong, S., Norton, M. E., MacKenzie, T., Devlin, B., Gilmore, K., Powell, B., Brandt, A., Vetrini, F., DiVito, M., Goldstein, D. B., Sanders, S. J., MacArthur, D. G.,...

Published 08/13/20

Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.247528v1?rss=1 Authors: Wang, S., Tao, Z., Wu, T., Liu, X.-S. Abstract: Summary: Mutational signatures are recurring DNA alteration patterns caused by distinct mutational events during the evolution of cancer. In recent years, several bioinformatics tools are available for mutational signature analysis. However, most of them focus on specific type of mutation, or have limited scope of application. A pipeline tool for...

Published 08/13/20

Gene expression associated with disease resistance and long-term growth in a reef-building coral

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.248286v1?rss=1 Authors: Kelley, E. R., Sleith, R. S., Matz, M. V., Wright, R. M. Abstract: Rampant coral disease, exacerbated by climate change and other anthropogenic stressors, threatens reefs worldwide, especially in the Caribbean. Physically isolated yet genetically connected reefs such as Flower Garden Banks National Marine Sanctuary (FGBNMS) may serve as potential refugia for degraded Caribbean reefs. However,...

Published 08/13/20

Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.245308v1?rss=1 Authors: Du, X., Li, L., Liang, F., Liu, S., Zhang, W., Sun, S., Sun, Y., Fan, F., Wang, L., Liang, X., Qiu, W., Fan, G., Wang, O., Yang, W., Zhang, J., Xiao, Y., Wang, Y., Wang, D., Qu, S., Chen, F., Huang, J. Abstract: The importance of structural variants (SVs) on phenotypes and human diseases is now recognized. Although a variety of SV detection platforms and strategies that vary in sensitivity and...

Published 08/12/20

The Contributions of the Allopolyploid Parents of the Mesopolyploid Brassiceae are Evolutionarily Distinct but Functionally Compatible

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.245258v1?rss=1 Authors: Hao, Y., Mabry, M. E., Edger, P., Freeling, M., Zheng, C., Jin, L., VanBuren, R., Colle, M., An, H., Abrahams, R. S., Qi, X., Barry, K., Daum, C., Shu, S., Schmutz, J., Sankoff, D., Barker, M. S., Lyons, E., Pires, J. C., Conant, G. C. Abstract: The members of the tribe Brassiceae share an ancient whole genome triplication (WGT), and plants in this tribe display extraordinarily high...

Published 08/12/20

A combined RAD-Seq and WGS approach reveals the genomic basis of yellow colour variation in bumble bee Bombus terrestris

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.248740v1?rss=1 Authors: Rahman, S. R., Cnaani, J., Kinch, L. N., Grishin, N. V., Hines, H. M. Abstract: Background: In the model bumble bee species B. terrestris, both males and females exhibit black coloration on the third thoracic and first metasomal segments. We discovered a fortuitous lab-generated mutant in which this typical black coloration is replaced by yellow. As this same color variant is found in several...

Published 08/12/20

A cohesin-independent mechanism modulates recombination activity along meiotic chromosomes

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.11.247122v1?rss=1 Authors: Heldrich, J., Markowitz, T. E., Vale-Silva, L. A., Hochwagen, A. Abstract: Meiotic chromosomes organize around a cohesin-dependent axial element, which promotes meiotic recombination and fertility. In the absence of cohesin, axial-element proteins instead accumulate in poorly understood genomic regions. Here, we show in S. cerevisiae that these regions are particularly enriched for axis proteins...

Published 08/12/20

Novel effector genes revealed by the genomic analysis of the phytopathogenic fungus Fusarium oxysporum f. sp. physali (Foph) that infects cape gooseberry plants

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.235309v1?rss=1 Authors: Simbaqueba, J., Rodriguez, E. A., Burbano, D. M., Gonzalez, C., Caro, A. Abstract: The vascular wilt disease caused by the fungus Fusarium oxysporum f. sp. physali (Foph) is one of the most limiting factors for the production and export of cape gooseberry (Physalis peruviana) in Colombia. A previous study of the transcriptomic profile of a highly virulent strain of F. oxysporum in cape...

Published 08/11/20

Biodiversity genomics of small metazoans: high quality de novo genomes from single specimens of field-collected and ethanol-preserved springtails

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.244541v1?rss=1 Authors: Schneider, C., Woehle, C., Greve, C., D'Haese, C. A., Wolf, M., Janke, A., Balint, M., Hüttel, B. Abstract: Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in evolutionary sciences, ecology, systematics and in biodiversity-related applied fields such as environmental management and natural product research. Advances in DNA sequencing technologies make genome...

Published 08/11/20

ViruSurf: an integrated database to investigate viral sequences

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.244624v1?rss=1 Authors: Canakoglu, A., Pinoli, P., Bernasconi, A., Alfonsi, T., Melidis, D. P., Ceri, S. Abstract: ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf...

Published 08/11/20

Genetic-substructure and complex demographic history of South African Bantu speakers

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.11.243840v1?rss=1 Authors: Sengupta, D., Choudhury, A., Fortes-Lima, C., Aron, S., Whitelaw, G., Bostoen, K., Gunnink, H., Chousou-Polydouri, N., Delius, P., Tollman, S., Casas, F. G.-O., Norris, S., Mashinya, F., Alberts, M., Hazelhurst, S., Schlebusch, C. M., Ramsay, M. Abstract: South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic...

Published 08/11/20

Different mutant RUNX1 oncoproteins program alternate haematopoietic differentiation trajectories

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.244657v1?rss=1 Authors: Kellaway, S. G., Keane, P., Edginton-White, B., Kakkad, R., Kennett, E., Bonifer, C. Abstract: Mutations of the hematopoietic master regulator RUNX1 cause acute myeloid leukaemia, familial platelet disorder and other haematological malignancies whose phenotypes and prognoses depend upon the class of RUNX1 mutation. The biochemical behaviour of these oncoproteins and their ability to cause unique...

Published 08/11/20

Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.243543v1?rss=1 Authors: Tian, L., Jabbari, J. S., Thijssen, R., Gouil, Q., Amarasinghe, S. L., Kariyawasam, H., Su, S., Dong, X., Law, C. W., Lucattini, A., Chung, J. D., Naim, T., Chan, A., Ly, C. H., Lynch, G. S., Ryall, J. G., Anttila, C. J. A., Peng, H., Anderson, M. A., Roberts, A. W., Huang, D. C. S., Clark, M. B., Ritchie, M. E. Abstract: Alternative splicing shapes the phenotype of cells in development and...

Published 08/10/20

Susceptibility to gingipains and transcriptomic response to P. gingivalis highlights the ribosome, hypothalamus, and cholinergic neurons

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.09.243402v1?rss=1 Authors: Patel, S., Howard, D., French, L. Abstract: Porphyromonas gingivalis, a keystone species in the development of periodontal disease, is a suspected cause of Alzheimer's disease. This bacterium is reliant on gingipain proteases, which cleave host proteins after arginine and lysine residues. To characterize gingipain susceptibility, we performed enrichment analyses of arginine and lysine proportion...

Published 08/10/20

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.09.243378v1?rss=1 Authors: Williams, A. M., Itgen, M. W., Broz, A. K., Carter, O. G., Sloan, D. B. Abstract: The angiosperm genus Silene is a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic...

Published 08/10/20

Refinement of Genome assemblies of Pigeonpea (Cajanus cajan)

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.243949v1?rss=1 Authors: Marla, S. S., Mishra, P., Maurya, R., Singh, M., Wankhade, D. P., Gupta, A. K., N, S. R., Singh, S. K., Kumar, R. Abstract: Recent developments in genome sequencing of several important crops helped to enrich our understanding of basic biology and immensely contributed to crop improvement. However, assembly of short reads from large plant genomes remains a challenge in computational biology...

Published 08/10/20

Somatic mosaicism in the mature brain reveals clonal cellular distributions during cortical development

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.244814v1?rss=1 Authors: Breuss, M. W., Yang, X., Antaki, D., Schlachetzki, J. C. M., Lana, A. A., Xu, X., Chai, G., Stanley, V., Song, Q., Fang Newmeyer, T., Nguyen, A., Cao, B., Nott, A., McEvoy-Venneri, J., Pasillas, M. P., Nahas, S., Van Der Kraan, L., Ding, Y., NIMH Brain Somatic Mosaicism Network,, Glass, C. K., Gleeson, J. G. Abstract: The structure of the human neocortex underlies species-specific features and...

Published 08/10/20

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.242677v1?rss=1 Authors: Bhoyar, R. C., Jain, A., Sehgal, P., Divakar, M. K., Sharma, D., Imran, M., Jolly, B., Ranjan, G., Rophina, M., Sharma, S., Siwach, S., Pandhare, K., Sahoo, S., Sahoo, M., Nayak, A., Mohanty, J. N., Das, J., Bhandari, S., Mathur, S. K., Kumar, A., Sahlot, R., Rojarani, P., Vijaya Lakshmi, J., Surekha, A., Sekhar, P. C., Mahajan, S., Masih, S., Singh, P., Kumar, V., Jose, B., Mahajan, V., Gupta,...

Published 08/10/20

Early Alpine human occupation backdates westward human migration in Late Glacial Europe

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.241430v1?rss=1 Authors: Bortolini, E., Pagani, L., Oxilia, G., Posth, C., Fontana, F., Badino, F., Saupe, T., Montinaro, F., Margaritora, D., Romandini, M., Lugli, F., Papini, A., Boggioni, M., Perrini, N., Oxilia, A., Aiese Cigliano, R., Barcelona, R., Visentin, D., Fasser, N., Arrighi, S., Figus, C., Marciani, G., Silvestrini, S., Bernardini, F., Menghi Sartorio, J. C., Fiorenza, L., Moggi Cecchi, J., Tuniz, C.,...

Published 08/10/20