All episodes of PaperPlayer biorxiv molecular biology

Episodes

Assembly and symmetry of the fungal E3BP-containing core of the Pyruvate Dehydrogenase Complex

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.232140v1?rss=1 Authors: Forsberg, B. O., Aibara, S., Howard, R. J., Mortezaei, N., Lindahl, E. Abstract: The pyruvate dehydrogenase complex (PDC) is a central component of all aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Despite its central metabolic role, its precise composition and means of regulation re- main unknown. To explain the variation in stoichiometry reported for the...

Published 08/14/20

A Strategy to Assess the Cellular Activity of E3 Ligases against Neo-Substrates using Electrophilic Probes

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.249482v1?rss=1 Authors: Pinch, B. J., Buckley, D. L., Gleim, S., Brittain, S. M., Tandeske, L., D'Alessandro, P. L., Harvey, E. P., Hauseman, Z. J., Schirle, M., Sprague, E. R., Forrester, W. C., Dovala, D., McGregor, L. M., Thoma, C. R. Abstract: Targeted protein degradation is a rapidly developing therapeutic modality that promises lower dosing and enhanced selectivity as compared to traditional occupancy-driven...

Published 08/14/20

The RNA-binding protein Puf5 buffers mRNA levels against chromatin-mediated changes in nascent transcription

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.249912v1?rss=1 Authors: Kochan, D. Z., Mawer, J. S. P., Tishinov, K., Parekh, S., Maassen, J., Graef, M., Spang, A., Tessarz, P. Abstract: Gene expression is a dynamic process regulated at all stages, starting with opening of chromatin, transcription, and continuing with mRNA export, translation and, finally, degradation. While there are feedback mechanisms within the system, it is not clear whether these extend to...

Published 08/14/20

The Macerprep: a minimalist kit- and enzyme-free high-yield miniprep utilising alkaline lysis and alkaline hydrolysis principles

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.249607v1?rss=1 Authors: Hu, I. Abstract: The commercialisation of miniprep kits supplanted the original alkaline lysis method for plasmid DNA preparation, and had remained relatively unchanged for almost two decades. The Miraprep substantially improved the yields of miniprep kits. However, the method still relies on commercial kits, which can be a burden financially to certain projects. Additionally, Pronobis et al....

Published 08/14/20

Maternal high fat diet alters lactation-specific miRNA expression and programs the DNA methylome in the amygdala of female offspring

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.249300v1?rss=1 Authors: Abuaish, S., Wijenayake, S., de Vega, W. C., Lum, C. M. W., Sasaki, A., McGowan, P. Abstract: Adverse maternal diets high in saturated fats are associated with impaired neurodevelopment and epigenetic modifications in offspring. Maternal milk, the primary source of early life nutrition in mammals, contains lactation-specific microRNAs (miRNAs). Lactation-specific miRNAs have been found in...

Published 08/14/20

Homologous recombination defects in Shwachman-Diamond syndrome and Diamond-Blackfan anemia

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.250068v1?rss=1 Authors: Asik, E., Chatterjee, N., Bertuch, A. A. Abstract: Shwachman-Diamond syndrome (SDS) and Diamond-Blackfan anemia (DBA) are ribosomopathies characterized by impaired hematopoiesis and cancer predisposition. The mechanisms underlying cancer predisposition in these disorders are not well understood. We found that LCLs derived from patients with SDS or DBA had a prolonged DNA damage response and...

Published 08/14/20

UPRmt scales mitochondrial network expansion with protein synthesis via mitochondrial import

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.248161v1?rss=1 Authors: Shpilka, T., Du, Y., Yung, Q., Melber, A., Uma Naresh, N., Lavelle, J., Liu, P., Weidberg, H., Li, R., Yu, J., Zhu, L. J., Strittmatter, L., Haynes, C. M. Abstract: As organisms develop, individual cells generate mitochondria to fulfill physiologic requirements. However, it remains unknown how mitochondrial network expansion is scaled to cell growth and impacted by environmental cues. The...

Published 08/14/20

Structure Basis of Cav1.1 Modulation by Dihydropyridine Compounds

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.13.250340v1?rss=1 Authors: Gao, S., Yan, N. Abstract: 1,4-Dihydropyridines (DHP), the most commonly used antihypertensives, function by inhibiting the L-type voltage-gated Ca2+ (Cav) channels. DHP compounds exhibit chirality-specific antagonistic or agonistic effects. Recent structural elucidation of rabbit Cav1.1 bound to an achiral drug nifedipine reveals the general binding mode for DHP drugs, but the molecular basis...

Published 08/14/20

Creb5 establishes the competence for Prg4 expression in articular cartilage

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.248609v1?rss=1 Authors: Zhang, C.-H., Gao, Y., Jadhav, U., Hung, H.-H., Holton, K. M., Grodzinsky, A. J., Shivdasani, R. A., Lassar, A. B. Abstract: A hallmark of cells comprising the superficial zone of articular cartilage is their expression of lubricin, encoded by the Prg4 gene, that lubricates the joint and protects against the development of arthritis. Here, we identify Creb5 as a transcription factor that is...

Published 08/12/20

KIAA1841, a novel SANT and BTB domain-containing protein, inhibits class switch recombination

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.247809v1?rss=1 Authors: Zheng, S., Matthews, A. J., Rahman, N., Herrick-Reynolds, K., Choi, J. E., Sible, E., Ng, Y. K., Rhodes, D., Elledge, S. J., Vuong, B. Q. Abstract: Class switch recombination (CSR) enables B cells to produce different immunoglobulin isotypes and mount an effective immune response against pathogens. Timely resolution of CSR prevents damage due to an uncontrolled and prolonged immune response....

Published 08/12/20

TRIM28 regulates SARS-CoV-2 cell entry by targeting ACE2

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.247825v1?rss=1 Authors: Wang, Y., Fan, Y., Huang, Y., Du, T., Liu, Z., Huang, D., Wang, Y., Wang, N., Zhang, P. Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19), it binds to angiotensin-converting enzyme 2 (ACE2) to enter into human cells. The expression level of ACE2 potentially determine the susceptibility and severity of COVID-19, it is thus...

Published 08/12/20

Transcriptome profiling of ulcerative colitis mouse model suggests biomarkers and therapeutic targets for human colitis

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.12.225458v1?rss=1 Authors: Yarani, R., Palasca, O., Doncheva, N. T., Anthon, C., Pilecki, B., Svane, C. A. S., Mirza, A. H., Litman, T., Holmskov, U., Bang-Berthelsen, C. H., Vilien, M., Jensen, L. J., Gorodkin, J., Pociot, F. Abstract: BACKGROUND & AIMS: Ulcerative colitis (UC) is an inflammatory bowel disorder with unknown etiology. Given its complex nature, in vivo studies to investigate its pathophysiology is...

Published 08/12/20

A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.11.242081v1?rss=1 Authors: Arrastia, M. V., Jachowicz, J. W., Ollikainen, N., Curtis, M. S., Lai, C., Quinodoz, S., Selck, D. A., Guttman, M., Ismagilov, R. F. Abstract: In eukaryotes, the nucleus is organized into a three dimensional structure consisting of both local interactions such as those between enhancers and promoters, and long-range higher-order structures such as nuclear bodies. This organization is central to...

Published 08/12/20

Structural and molecular basis for protein-stimulated ribosomal frameshifting in Theiler's murine encephalomyelitis virus

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.11.245068v1?rss=1 Authors: Hill, C. H., Cook, G., Napthine, S., Kibe, A., Brown, K., Caliskan, N., Firth, A. E., Graham, S. C., Brierley, I. Abstract: The 2A protein of Theiler's murine encephalomyelitis virus (TMEV) is required for stimulating programmed -1 ribosomal frameshifting (PRF) during infection. However, the amino acid sequence of TMEV 2A shares only 27% identity with the 2A orthologue from the related...

Published 08/11/20

Structural studies of Cardiovirus 2A protein reveal the molecular basis for RNA recognition and translational control

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.11.245035v1?rss=1 Authors: Hill, C. H., Napthine, S., Pekarek, L., Kibe, A., Firth, A. E., Graham, S. C., Caliskan, N., Brierley, I. Abstract: Encephalomyocarditis virus 2A protein is a multi functional virulence factor essential for efficient virus replication with roles in stimulating programmed -1 ribosomal frameshifting (PRF), inhibiting cap-dependent translational initiation, interfering with nuclear import and...

Published 08/11/20

The RAD51 recombinase protects mitotic chromatin in human cells

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.11.246231v1?rss=1 Authors: Wassing, I. E., Saayman, X., Rampazzo, L., Ralf, C., Bassett, A., Esashi, F. Abstract: The RAD51 recombinase plays critical roles in safeguarding genome integrity, which is fundamentally important for all living cells. While interphase functions of RAD51 in repairing broken DNA and protecting stalled replication forks are well characterised, its role in mitosis remains contentious. In this...

Published 08/11/20

Anti-pausing activity of region 4 of the RNA polymerase σ subunit and its regulation by σ-remodeling factors

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.11.244855v1?rss=1 Authors: Brodolin, K., Morichaud, Z. Abstract: The basal transcription factors of cellular RNA polymerases (RNAPs) stimulate the initial RNA synthesis via poorly understood mechanisms. Here, we explored the mechanism employed by the bacterial factor {sigma} in promoter-independent initial transcription. We found that the RNAP holoenzyme lacking the promoter-binding domain {sigma}4 is ineffective in de...

Published 08/11/20

Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identifies disease-relevant transcripts containing G-rich motifs.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.11.246249v1?rss=1 Authors: Pashler, A. L., Towler, B. P., Jones, C. I., Burgess, T., Newbury, S. F. Abstract: XRN1 is a highly conserved exoribonuclease which degrades uncapped RNAs in a 5'-3' direction. Degradation of RNAs by XRN1 is important in many cellular and developmental processes and is relevant to human disease. Studies in D. melanogaster demonstrate that XRN1 can target specific RNAs, which have important...

Published 08/11/20

KinPred: A unified approach and resource for human kinase-substrate predictions

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.244426v1?rss=1 Authors: Xue, B., Jordan, B., Rizvi, S., Naegle, K. M. Abstract: Tyrosine and serine/threonine kinases are essential regulators of cell processes and are important targets for human therapies. Unfortunately, very little is known about specific kinase-substrate relationships, making it difficult to infer meaning from dysregulated phosphoproteomic datasets or for researchers to identify possible kinases...

Published 08/10/20

The secret of VDAC isoforms is in their gene regulation? Characterization of human VDAC genes expression profile, promoter activity, and transcriptional regulators.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.244327v1?rss=1 Authors: Zinghirino, F., Pappalardo, X. G., Messina, A., Guarino, F., De Pinto, V. Abstract: Background: VDACs (Voltage Dependent Anion selective Channels) are pore forming proteins of the outer mitochondrial membrane, whose permeability is primarily due to their presence. In higher eukaryotes three isoforms raised during the evolution: they have the same exon-intron organization and the proteins show...

Published 08/10/20

The inner membrane protein YhdP modulates the rate of anterograde phospholipid flow in Escherichia coli

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.09.213157v1?rss=1 Authors: Grimm, J., Shi, H., Wang, W., Mitchell, A. M., Wingreen, N. S., Huang, K. C., Silhavy, T. J. Abstract: The outer membrane (OM) of Gram-negative bacteria is a selective permeability barrier that allows uptake of nutrients while simultaneously protecting the cell from harmful compounds. The basic pathways and molecular machinery responsible for transporting lipopolysaccharides (LPS), lipoproteins,...

Published 08/10/20

Genome-wide analysis of DNA replication and DNA double strand breaks by TrAEL-seq

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.243931v1?rss=1 Authors: Kara, N., Krueger, F., Rugg-Gunn, P., Houseley, J. Abstract: Understanding the distribution of sites at which replication forks stall, and the ensuing fork processing events, requires genome-wide methods sensitive to both changes in replication fork structure and the formation of recombinogenic DNA ends. Here we describe Tr ansferase- A ctivated E nd L igation seq uencing (TrAEL-seq), a method...

Published 08/10/20

A human cancer cell line initiates DNA replication normally in the absence of ORC5 and ORC2 proteins

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.245076v1?rss=1 Authors: Shibata, E., Dutta, A. Abstract: The six-subunit Origin Recognition Complex (ORC) binds to origins of replication as a ring-shaped heterohexameric ATPase that is essential to recruit MCM2-7 and initiate DNA replication. We now report that human HCT116 colon cancer cells survive with a mutation in the initiator ATG of the ORC5 gene that abolishes the expression of ORC5 protein. Even if an...

Published 08/10/20

The PNUTS-PP1 axis regulates endothelial aging and barrier function via SEMA3B suppression

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.10.243170v1?rss=1 Authors: Lozano-Vidal, N., Stanicek, L., Bink, D. I., Kremer, V., MacInnes, A. W., Dimmeler, S., Boon, R. A. Abstract: Age-related diseases pose great challenges to health care systems worldwide. During aging, endothelial senescence increases the risk for cardiovascular disease. Recently, it was described that Phosphatase 1 Nuclear Targeting Subunit (PNUTS) has a central role in cardiomyocyte aging and...

Published 08/10/20

Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.09.243451v1?rss=1 Authors: Yuan, S., Peng, L., Park, J. J., Hu, Y., Devarkar, S. C., Dong, M. B., Wu, S., Chen, S., Lomakin, I., Xiong, Y. Abstract: The COVID-19 pandemic affects millions of people worldwide with a rising death toll. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), uses its nonstructural protein 1 (Nsp1) to redirect host translation machinery to the viral RNA by binding...

Published 08/10/20