All episodes of PaperPlayer biorxiv genomics

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Genome wide efficiency profiling reveals modulation of maintenance and de novo methylation by Tets

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.06.236307v1?rss=1 Authors: Giehr, P., Kyriakopoulos, C., Karl Nordström, K., Salhab, A., Müller, F., von Meyenn, F., Ficz, G., Reik, W., Wolf, V., Walter, J. Abstract: Background: DNA methylation is an essential epigenetic modification which is set and maintained by DNA methyl transferases (Dnmts) and removed via active and passive mechanisms involving Tet mediated oxidation. While the molecular mechanisms of these...

Published 08/07/20

Ubiquitous selfish toxin-antidote elements in Caenorhabditis species

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.06.240564v1?rss=1 Authors: Ben-David, E., Pliota, P., Widen, S. A., Koreshova, A., Lemus-Vergara, T., Verpukhovskiy, P., Mandali, S., Braendle, C., Burga, A., Kruglyak, L. Abstract: Toxin-antidote elements (TAs) are selfish genetic dyads that spread in populations by selectively killing non-carriers. TAs are common in prokaryotes, but few examples are known in animals. We discovered five maternal-effect TAs in the...

Published 08/07/20

Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the coffee wilt pathogen Fusarium xylarioide

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.07.241695v1?rss=1 Authors: Peck, L., Barraclough, T., Nowell, R., Flood, J., Ryan, M. Abstract: Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimated coffee production in west and central Africa following an initial 1920s outbreak. After successful management, it...

Published 08/07/20

Targeted Transcriptome Analysis using Synthetic Long Read Sequencing Uncovers Isoform Reprograming in the Progression of Colon Cancer

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.07.240069v1?rss=1 Authors: Liu, S., Wu, I., Yu, Y.-P., Balamotis, M., Ren, B.-G., Yehezkel, T. B., Luo, J.-H. Abstract: Diversity in human gene expression stems, to a large extent, from splicing exons into multiple mRNA isoforms. Characterization of isoforms requires accurate long-read sequencing. However, read lengths, high error rates, low throughput and large input requirements are some of the challenges that remain to...

Published 08/07/20

Multiomics analysis reveals extensive epigenome remodeling during cortical development

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.07.241828v1?rss=1 Authors: Noack, F., Vangelisti, S., Carido, M., Chong, F., Bonev, B. Abstract: Despite huge advances in stem-cell, single-cell and epigenetic technologies, the precise molecular mechanisms that determine lineage specification remain largely unknown. Applying an integrative multiomics approach, e.g. combining single-cell RNA-seq, single-cell ATAC-seq together with cell-type-specific DNA methylation and 3D...

Published 08/07/20

Genome Diversity in Ukraine

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.07.238329v1?rss=1 Authors: Oleksyk, T. K., Wolfsberger, W. W., Weber, A., Shchubelka, K., Oleksyk, O. T., Levchuk, O., Patrus, A., Lazar, N., Castro-Marquez, S. O., Boldyzhar, P., Urbanovych, A., Stakhovska, V., Malyar, K., Chervyakova, S., Podoroha, O., Kovalchuk, N., Hasynets, Y., Rodriguez-Flores, J. L., Medley, S., Battistuzzi, F. U., Liu, R., Hou, Y., Chen, S., Yang, H., Yeager, M., Dean, M., Mills, R. E., Smolanka,...

Published 08/07/20

Multi-omics approach highlights differences between functional RLP classes in Arabidopsis thaliana

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.07.240911v1?rss=1 Authors: Steidele, C. E., Stam, R. Abstract: The receptor-like protein (RLP) family is a complex gene family with 57 members in Arabidopsis thaliana. Some members of the RLP family are known to be involved in basal developmental processes, whereas others have found to be involved in defence responses. However, functional data is to date, only available for a small subset of RLPs, leaving the remaining...

Published 08/07/20

Genomic evolutionary analysis in R with geaR.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.06.240754v1?rss=1 Authors: Ward, C. M., Ludington, A. J., Breen, J., Baxter, S. W. Abstract: The analysis and interpretation of datasets generated through sequencing large numbers of individual genomes is becoming commonplace in population and evolutionary genetic studies. Here we introduce geaR, a modular R package for evolutionary analysis of genome-wide genotype data. The package leverages the Genomic Data Structure...

Published 08/07/20

Genomic investigation of a suspected multi-drug resistant Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.06.236117v1?rss=1 Authors: Cornick, J. E., Musicha, P., Peno, C., Saeger, E., Iroh-Tam, P.-Y., Bennett, A., Kennedy, N., Feasey, N., Heniz, E., Cain, A. K. Abstract: A suspected outbreak of multi-drug resistant (MDR) Klebsiella pneumoniae in a Malawian neonatal unit was investigated using whole-genome sequencing. Strain-types, virulence and resistance genes of K. pneumoniae isolated from patients in the hospital over a...

Published 08/07/20

Dissecting mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.04.234245v1?rss=1 Authors: Zou, X., Koh, G. C. C., Nanda, A. S., Degasperi, A., Urgo, K., Roumeliotis, T., Agu, C. A., Side, L., Brice, G., Perez-Alonso, V., Rueda, D., Badja, C., Young, J., Gomez, C., Bushell, W., Harris, R., Choudhary, J., Jiricny, J. I., Skarnes, W. C., Nik-Zainal, S. Abstract: Mutational signatures are imprints of pathophysiological processes arising through tumorigenesis. Here, we generate isogenic...

Published 08/06/20

Automatic inference of demographic parameters using Generative Adversarial Networks

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.237834v1?rss=1 Authors: Wang, Z., Wang, J., Kourakos, M., Hoang, N., Lee, H. H., Mathieson, I., Mathieson, S. Abstract: Population genetics relies heavily on simulated data for validation, inference, and intuition. In particular, since real data is always limited, simulated data is crucial for training machine learning methods. Simulation software can accurately model evolutionary processes, but requires many...

Published 08/06/20

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Published 08/06/20

Diversity of sea star-associated densoviruses and transcribed endogenized viral elements of densovirus origin

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.239004v1?rss=1 Authors: Jackson, E. W., Wilhelm, R. C., Johnson, M. R., Lutz, H. L., Danforth, I., Gaydos, J. K., Hart, M. H., Hewson, I. H. Abstract: A viral etiology of Sea Star Wasting Syndrome (SSWS) has been largely explored using metagenomics leading to the conclusion that a densovirus is the predominant DNA virus associated with this syndrome, and, thus, the most promising viral candidate pathogen....

Published 08/06/20

Modified base-binding EVE and DCD Domains Implicated in the Origins of Programmed Cell Death and the piRNA Pathway

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.06.240630v1?rss=1 Authors: Bell, R., Wolf, Y. I., Koonin, E. V. Abstract: Background: DNA and RNA of most cellular life forms and many viruses contain an expansive repertoire of modified bases. The modified bases play diverse biological roles that include both regulation of transcription and translation, and protection against restriction endonucleases and antibiotics. Modified bases are often recognized by dedicated...

Published 08/06/20

The mutational load in natural populations is significantly affected by high primary rates of retroposition

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.06.239277v1?rss=1 Authors: Zhang, W., Xie, C., Ullrich, K. K., Zhang, Y. E., Tautz, D. Abstract: Gene retroposition is known to contribute to patterns of gene evolution and adaptations. However, possible negative effects of gene retroposition remain largely unexplored, since most previous studies have focussed on between-species comparisons where negatively selected copies are mostly not observed, as they are quickly lost...

Published 08/06/20

QTL mapping in an interspecific sorghum population uncovers plasma-membrane intrinsic proteins as key regulators of salinity tolerance

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.238972v1?rss=1 Authors: Henderson, A. N., Govindarajulu, R., Hawkins, J. S. Abstract: Soil salinity impedes crop production via both osmotic and ionic stress and is an intensifying problem affecting lands used to produce agronomically important crops.. Such stress slows plant growth and disrupts normal metabolic processes, resulting in decreased biomass and increased leaf senescence. Therefore, the ability to maintain...

Published 08/06/20

Bayesian estimation of cell-type-specific gene expression per bulk sample with prior derived from single-cell data

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.238949v1?rss=1 Authors: Wang, J., Roeder, K., Devlin, B. Abstract: When assessed over a large number of samples, bulk RNA sequencing provides reliable data for gene expression at the tissue level. Single-cell RNA sequencing (scRNA-seq) deepens those analyses by evaluating gene expression at the cellular level. Both data types lend insights into disease etiology. With current technologies, however, scRNA-seq data are...

Published 08/06/20

Photomap of the polythenic chromosomes of Drosophila malerkotliana and in situ mapping of the Hsp83 locus

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.238600v1?rss=1 Authors: Felix, P. T., dos Santos, J. F. Abstract: A photomap of the polythenic chromosomes of D. malerkotliana was constructed to facilitate the identification of the chromosomal arms and their sections, in order to allow the identification of the breaking points of inversions and the location of the bands marked by in situ hybridization. The photomap included the six chromosome arms corresponding to...

Published 08/06/20

Identification of pituitary thyrotrope signature genes and regulatory elements

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.238253v1?rss=1 Authors: Daly, A. Z., Dudley, L. A., Peel, M. T., Liebhaber, S. A., Parker, S. C., Camper, S. A. Abstract: Pituitary thyrotropes are specialized cells that produce thyroid stimulating hormone, a critical factor for growth and maintenance of metabolism. The transcription factors POU1F1 and GATA2 have been implicated in thyrotrope fate and regulation of Tshb transcription, but no transcriptomic or...

Published 08/06/20

Low Quantity single strand CAGE (LQ-ssCAGE) maps regulatory enhancers and promoters

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.04.231969v1?rss=1 Authors: Takahashi, H., Nishiyori-Sueki, H., Ramilowski, J. A., Itoh, M., Carninci, P. Abstract: The Cap Analysis of Gene Expression (CAGE) is a powerful method to identify the Transcription Start Sites (TSSs) of capped RNAs while simultaneously measuring transcripts expression level. CAGE allows mapping at single nucleotide resolution at all active promoters and enhancers. Large CAGE datasets have been...

Published 08/05/20

Incorporation of DNA methylation into eQTL mapping in African Americans.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.238030v1?rss=1 Authors: Singh, A., Zhong, Y., Park, C. S., Nahlawi, L., Alarcon, C., De, T., Perera, M. Abstract: Epigenetics is a reversible molecular mechanism that plays a critical role in many developmental, adaptive, and disease processes. DNA methylation has been shown to regulate gene expression and the advent of high throughput technologies has made genome-wide DNA methylation analysis possible. We investigated...

Published 08/05/20

Analysis of the potential impact of genomic variants in SARS-CoV-2 genomes from India on molecular diagnostic assays

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.238618v1?rss=1 Authors: Jain, A., Rophina, M., Mahajan, S., Krishnan, B. B., Sharma, M., Mandal, S., Fernandez, T., Sultanji, S., Mathew, S., Sivasubbu, S., Scaria, V. Abstract: An isolated epidemic of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causing Coronavirus Diseases (C0VID-19) originating in Wuhan, China has now rapidly emerged into a global pandemic affecting millions of people worldwide....

Published 08/05/20

IFN-γ and TNF-α drive a CXCL10+ CCL2+ macrophage phenotype expanded in severe COVID-19 and other diseases with tissue inflammation

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.238360v1?rss=1 Authors: Zhang, F., Mears, J. R., Shakib, L., Beynor, J. I., Shanaj, S., Korsunsky, I., Nathan, A., Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus,, Donlin, L. T., Raychaudhuri, S. Abstract: Immunosuppressive and anti-cytokine treatment may have a protective effect for patients with COVID-19. Understanding the immune cell states shared between COVID-19 and other...

Published 08/05/20

Analysis of single nucleotide polymorphisms between 2019-nCoV genomes and its impact on codon usage

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.05.237404v1?rss=1 Authors: Gupta, S., Singh, R., Paul, P. Abstract: The spread of COVID-19 is a global concern that has taken a toll on entire human health. Researchers across the globe has been working in devising the strategies to combat this dreadful disease. Studies focused on genetic variability helps design effective drugs and vaccines. Considering this, the present study entails the information regarding the...

Published 08/05/20

Genome-Wide Screening Reveals CSDE1 as a Novel Regulator of the LDL Receptor

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.03.235028v1?rss=1 Authors: Smith, G. A., Pampana, A., Natarajan, P., Shokat, K., Chorba, J. S. Abstract: In humans, clearance of LDL cholesterol, which causes atherosclerotic heart disease, is mediated by the hepatic LDL receptor (LDLR). As a result, therapies that upregulate the LDLR are highly effective treatments for atherosclerosis. Since cardiovascular disease remains the leading cause of death in Western countries,...

Published 08/04/20