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Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 118,476 papers from 511,089 authors.

Most downloaded biology preprints, all time

in category molecular biology

3,576 results found. For more information, click each entry to expand.

81: NgAgo-enhanced homologous recombination in E. coli is mediated by DNA endonuclease activity
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Posted 04 Apr 2019

NgAgo-enhanced homologous recombination in E. coli is mediated by DNA endonuclease activity
2,938 downloads bioRxiv molecular biology

Kok Zhi Lee, Michael A Mechikoff, Archana Kikla, Arren Liu, Paula Pandolfi, Frederick S Gimble, Kevin V. Solomon

Prokaryotic Argonautes (pAgos) have been proposed as more flexible tools for gene-editing as they do not require sequence motifs adjacent to their targets for function, unlike popular CRISPR/Cas systems. One promising pAgo candidate, from the halophilic archaeon Natronobacterium gregoryi (NgAgo), however, has been subject to intense debate regarding its potential in eukaryotic systems. Here, we revisit this enzyme and characterize its function in prokaryotes. NgAgo expresses poorly in non-halophilic hosts with the majority of protein being insoluble and inactive even after refolding. However, we report that the soluble fraction does indeed act as a DNA endonuclease. Structural homology modelling revealed that NgAgo shares canonical domains with other catalytically active pAgos but also contains a previously unrecognized single stranded DNA binding domain (repA). Both repA and the canonical PIWI domain participate in DNA cleavage activities. We also found that these endonuclease activities are essential for enhanced NgAgo-guided homologous recombination, or gene-editing, in E. coli. Collectively, our results provide insight into the poorly characterized NgAgo for subsequent gene-editing tool development and sheds new light on seemingly contradictory reports.

82: ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs
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Posted 15 May 2019

ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs
2,892 downloads bioRxiv molecular biology

Ronen Sadeh, Israa Sharkia, Gavriel Fialkoff, Ayelet Rahat, Jenia Gutin, Alon Chappleboim, Mor Nitzan, Ilana Fox-Fisher, Daniel Neiman, Guy Meler, Zahala Kamari, Dayana Yaish, Tamar Peretz, Ayala Hubert, Jonatan E Cohen, Salach Azzam, Mark Temper, Albert Grinshpun, Myriam Maoz, Samir Abu-Gazala, Ami Ben Ya’acov, Eyal Shteyer, Rifaat Safadi, Tommy Kaplan, Ruth Shemer, David Planer, Eithan Galun, Benjamin Glaser, Aviad Zick, Yuval Dor, Nir Friedman

Genomic DNA is packed by histone proteins that carry a multitude of post-translational modifications that reflect cellular transcriptional state. Cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells, and as such it retains the histones markings present in the cells of origin. Here, we pioneer chromatin immunoprecipitation followed by sequencing of cell-free nucleosomes (cfChIP-seq) carrying active chromatin marks. Our results show that cfChIP-seq provides multidimensional epigenetic information that recapitulates the epigenetic and transcriptional landscape in the cells of origin. We applied cfChIP-seq to 268 samples including samples from patients with heart and liver pathologies, and 135 samples from 56 metastatic CRC patients. We show that cfChIP-seq can detect pathology-related transcriptional changes at the site of the disease, beyond the information on tissue of origin. In CRC patients we detect clinically-relevant, and patient-specific information, including transcriptionally active HER2 amplifications. cfChIP-seq provides genome-wide information and requires low sequencing depth. Altogether, we establish cell-free chromatin immunoprecipitation as an exciting modality with potential for diagnosis and interrogation of physiological and pathological processes using a simple blood test. One Sentence Summary ChIP-seq of plasma-circulating nucleosomes (cfChIP-seq) from a simple blood test provides detailed information about gene expression programs in human organs, and cancer. ### Competing Interest Statement A patent application for cfChIP-seq has been submitted by the Hebrew University of Jerusalem.

83: IL-11 is a therapeutic target in idiopathic pulmonary fibrosis
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Posted 02 Jun 2018

IL-11 is a therapeutic target in idiopathic pulmonary fibrosis
2,860 downloads bioRxiv molecular biology

Benjamin Ng, Jinrui Dong, Sivakumar Viswanathan, Giuseppe D’Agostino, Anissa A. Widjaja, Wei-Wen Lim, Nicole SJ. Ko, Jessie Tan, Sonia P. Chothani, Benjamin Huang, Chen Xie, Ann-Marie Chacko, Nuno Guimarães-Camboa, Sylvia M Evans, Adam J. Byrne, Toby M Maher, Jiurong Liang, Paul W. Noble, Sebastian Schafer, Stuart A. Cook

Idiopathic pulmonary fibrosis (IPF) remains a progressive disease despite best medical management. We previously identified IL-11 as a critical factor for cardiovascular fibrosis and examine here its role in pulmonary fibrosis. IL-11 is consistently upregulated in IPF genomic datasets, which we confirmed by histology. Pulmonary fibroblasts stimulated with IL-11 transform into invasive myofibroblasts whereas fibroblasts from Il11ra deleted mice did not respond to pro-fibrotic stimuli. In the mouse, injection of recombinant Il-11 or fibroblast-specific expression of Il-11 caused pulmonary fibrosis. We then generated a neutralising IL-11 binding antibody that blocks lung fibroblast activation across species. In a mouse model of IPF, anti-IL-11 therapy attenuated lung fibrosis and specifically blocked ERK activation. These data prioritise IL-11 as an accessible drug target in IPF.

84: Integrated design, execution, and analysis of arrayed and pooled CRISPR genome editing experiments
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Posted 07 Apr 2017

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome editing experiments
2,846 downloads bioRxiv molecular biology

Matthew C. Canver, Maximilian Haeussler, Daniel E Bauer, Stuart H. Orkin, Neville E Sanjana, Ophir Shalem, Guo-Cheng Yuan, Feng Zhang, Jean-Paul Concordet, Luca Pinello

CRISPR genome editing experiments offer enormous potential for the evaluation of genomic loci using arrayed single guide RNAs (sgRNAs) or pooled sgRNA libraries. Numerous computational tools are available to help design sgRNAs with optimal on-target efficiency and minimal off-target potential. In addition, computational tools have been developed to analyze deep sequencing data resulting from genome editing experiments. However, these tools are typically developed in isolation and oftentimes not readily translatable into laboratory-based experiments. Here we present a protocol that describes in detail both the computational and benchtop implementation of an arrayed and/or pooled CRISPR genome editing experiment. This protocol provides instructions for sgRNA design with CRISPOR, experimental implementation, and analysis of the resulting high-throughput sequencing data with CRISPResso. This protocol allows for design and execution of arrayed and pooled CRISPR experiments in 4-5 weeks by non-experts as well as computational data analysis in 1-2 days that can be performed by both computational and non-computational biologists alike.

85: Genetic tools weed out misconceptions of strain reliability in Cannabis sativa: Implications for a budding industry
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Posted 28 May 2018

Genetic tools weed out misconceptions of strain reliability in Cannabis sativa: Implications for a budding industry
2,834 downloads bioRxiv molecular biology

Anna L. Schwabe, Mitchell E McGlaughlin

Cannabis sativa is listed as a Schedule I substance by the United States Drug Enforcement Agency and has been federally illegal in the United States since 1937. However, the majority of states in the United States, as well as several countries, now have various levels of legal Cannabis. Products are labeled with identifying strain names but there is no official mechanism to register Cannabis strains, therefore the potential exists for incorrect identification or labeling. This study uses genetic analyses to investigate strain reliability from the consumer point of view. Ten microsatellite regions were used to examine samples from strains obtained from dispensaries in three states. Samples were examined for genetic similarity within strains, and also a possible genetic distinction between Sativa, Indica, or Hybrid types. The analyses revealed genetic inconsistencies within strains. Additionally, although there was strong statistical support dividing the samples into two genetic groups, the groups did not correspond to commonly reported Sativa/Hybrid/Indica types. Genetic differences have the potential to lead to phenotypic differences and unexpected effects, which could be surprising for the recreational user, but have more serious implications for patients relying on strains that alleviate specific medical symptoms.

86: A comprehensive model of DNA fragmentation for the preservation of High Molecular Weight DNA
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Posted 27 Jan 2018

A comprehensive model of DNA fragmentation for the preservation of High Molecular Weight DNA
2,810 downloads bioRxiv molecular biology

Tomas Klingström, Erik Bongcam-Rudloff, Olga Vinnere Pettersson

During DNA extraction the DNA molecule undergoes physical and chemical shearing, causing the DNA to fragment into shorter and shorter pieces. Under common laboratory conditions this fragmentation yields DNA fragments of 5-35 kilobases (kb) in length. This fragment length is more than sufficient for DNA sequencing using short-read technologies which generate reads 50-600 bp in length, but insufficient for long-read sequencing and linked reads where fragment lengths of more than 40 kb may be desirable. This study provides a theoretical framework for quality management to ensure access to high molecular weight DNA in samples. Shearing can be divided into physical and chemical shearing which generate different patterns of fragmentation. Exposure to physical shearing creates a characteristic fragment length where DNA fragments are cut in half by shear stress. This characteristic length can be measured using gel electrophoresis or instruments for DNA fragment analysis. Chemical shearing generates randomly distributed fragment lengths visible as a smear of DNA below the peak fragment length. By measuring the peak of DNA fragment length and the proportion of very short DNA fragments both sources of shearing can be measured using commonly used laboratory techniques, providing a suitable quantification of DNA integrity of DNA for sequencing with long-read technologies.

87: A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
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Posted 22 May 2014

A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
2,805 downloads bioRxiv molecular biology

Henriette O’Geen, Isabelle Marie Henry, Mital S. Bhakta, Joshua F. Meckler, David J. Segal

Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of their target site recognition. Most previous studies have examined predicted off-target binding sites that differ from the perfect target site by one to four mismatches, which represent only a subset of genomic regions. Here, we use ChIP-seq to examine genome-wide CRISPR binding specificity at gRNA-specific and gRNA-independent sites. For two guide RNAs targeting the murine Snurf gene promoter, we observed very high binding specificity at the intended target site while off-target binding was observed at 2- to 6-fold lower intensities. We also identified significant gRNA-independent off-target binding. Interestingly, we found that these regions are highly enriched in the PAM site, a sequence required for target site recognition by CRISPR. To determine the relationship between Cas9 binding and endonuclease activity, we used targeted sequence capture as a high-throughput approach to survey a large number of the potential off-target sites identified by ChIP-seq or computational prediction. A high frequency of indels was observed at both target sites and one off-target site, while no cleavage activity could be detected at other ChIP-bound regions. Our data is consistent with recent finding that most interactions between the CRISPR nuclease complex and genomic PAM sites are transient and do not lead to DNA cleavage. The interactions are stabilized by gRNAs with good matches to the target sequence adjacent to the PAM site, resulting in target cleavage activity.

88: Neighborhood regulation by lncRNA promoters, transcription, and splicing
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Posted 29 Apr 2016

Neighborhood regulation by lncRNA promoters, transcription, and splicing
2,796 downloads bioRxiv molecular biology

Jesse M. Engreitz, Jenna E. Haines, Glen Munson, Jenny Chen, Elizabeth M. Perez, Michael Kane, Patrick E McDonel, Mitchell Guttman, Eric S Lander

Mammalian genomes are pervasively transcribed to produce thousands of spliced long noncoding RNAs (lncRNAs), whose functions remain poorly understood. Because recent evidence has implicated several specific lncRNA loci in the local regulation of gene expression, we sought to determine whether such local regulation is a property of many lncRNA loci. We used genetic manipulations to dissect 12 genomic loci that produce lncRNAs and found that 5 of these loci influence the expression of a neighboring gene in cis. Surprisingly, however, none of these effects required the specific lncRNA transcripts themselves and instead involved general processes associated with their production, including enhancer-like activity of gene promoters, the process of transcription, and the splicing of the transcript. Interestingly, such effects are not limited to lncRNA loci: we found similar effects on local gene expression at 4 of 6 protein-coding loci. These results demonstrate that 'crosstalk' among neighboring genes is a prevalent phenomenon that can involve multiple mechanisms and cis regulatory signals, including a novel role for RNA splicing. These mechanisms may explain the function and evolution of some genomic loci that produce lncRNAs.

89: Inducible, tunable and multiplex human gene regulation using CRISPR-Cpf1-based transcription factors
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Posted 15 Jun 2017

Inducible, tunable and multiplex human gene regulation using CRISPR-Cpf1-based transcription factors
2,707 downloads bioRxiv molecular biology

Yu Gyoung Tak, Benjamin P. Kleinstiver, James K. Nuñez, Jonathan Y Hsu, Jingyi Gong, Jonathan S. Weissman, J. Keith Joung

Targeted and inducible regulation of mammalian gene expression is a broadly important research capability that may also enable development of novel therapeutics for treating human diseases. Here we demonstrate that a catalytically inactive RNA-guided CRISPR-Cpf1 nuclease fused to transcriptional activation domains can up-regulate endogenous human gene expression. We engineered drug-inducible Cpf1-based activators and show how this system can be used to tune the regulation of endogenous gene transcription in human cells. Leveraging the simpler multiplex capability of the Cpf1 platform, we show that we can induce both synergistic and combinatorial gene expression in human cells. Our work should enable the creation of other Cpf1-based gene regulatory fusion proteins and the development of multiplex gene perturbation library screens for understanding complex cellular phenotypes.

90: Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation
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Posted 12 Sep 2018

Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation
2,698 downloads bioRxiv molecular biology

Phil Oberacker, Peter Stepper, Donna M Bond, Sven Höhn, Jule Focken, Vivien Meyer, Luca Schelle, Victoria J Sugrue, Gert-Jan Jeunen, Tim Moser, Steven R Hore, Ferdinand von Meyenn, Katharina Hipp, Timothy A Hore, Tomasz Piotr Jurkowski

Current molecular biology laboratories rely heavily on the purification and manipulation of nucleic acids. Yet, commonly used centrifuge- and column-based protocols require specialised equipment, often use toxic reagents and are not economically scalable or practical to use in a high-throughput manner. Although it has been known for some time that magnetic beads can provide an elegant answer to these issues, the development of open-source protocols based on beads has been limited. In this article, we provide step-by-step instructions for an easy synthesis of functionalised magnetic beads, and detailed protocols for their use in the high-throughput purification of plasmids, genomic DNA and total RNA from different sources, as well as environmental TNA and PCR amplicons. We also provide a bead-based protocol for bisulfite conversion, and size selection of DNA and RNA fragments. Comparison to other methods highlights the capability, versatility and extreme cost-effectiveness of using magnetic beads. These open source protocols and the associated webpage (https://bomb.bio) can serve as a platform for further protocol customisation and community engagement.

91: Antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase: pseudouridimycin
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Posted 08 Feb 2017

Antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase: pseudouridimycin
2,682 downloads bioRxiv molecular biology

Sonia I. Maffioli, Yu Zhang, David Degen, Thomas Carzaniga, Giancarlo Del Gatto, Stefania Serina, Paolo Monciardini, Carlo Mazzetti, Paola Guglierame, Gianpaolo Candiani, Alina Iulia Chiriac, Giuseppe Facchetti, Petra Kaltofen, Hans-Georg Sahl, Gianni Dehò, Stefano Donadio, Richard H. Ebright

There is an urgent need for new antibacterial drugs effective against bacterial pathogens resistant to current drugs. Nucleoside-analog inhibitors (NAIs) of viral nucleotide polymerases have had transformative impact in treatment of HIV and HCV. NAIs of bacterial RNA polymerase (RNAP) potentially could have major impact on treatment of bacterial infection, particularly because functional constraints on substitution of RNAP nucleoside triphosphate (NTP) binding sites could limit resistance emergence. Here we report the discovery, from microbial extract screening, of an NAI that inhibits bacterial RNAP and exhibits antibacterial activity against a broad spectrum of drug-sensitive and drug-resistant bacterial pathogens: pseudouridimycin (PUM). PUM is a novel microbial natural product consisting of a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 6'-amino-pseudouridine. PUM potently and selectively inhibits bacterial RNAP in vitro, potently and selectively inhibits bacterial growth in culture, and potently clears infection in a mouse model of Streptococcus pyogenes peritonitis. PUM inhibits RNAP through a binding site on RNAP (the "i+1" NTP binding site) and mechanism (competition with UTP for occupancy of the "i+1" NTP binding site) that differ from those of the RNAP inhibitor and current antibacterial drug rifampin (Rif). PUM exhibits additive antibacterial activity when co-administered with Rif, exhibits no cross-resistance with Rif, and exhibits a spontaneous resistance rate an order-of-magnitude lower than that of Rif. The results provide the first example of a selective NAI of bacterial RNAP, provide an advanced lead compound for antibacterial drug development, and provide structural information and synthetic routes that enable lead optimization for antibacterial drug development.

92: Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9
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Posted 30 Mar 2020

Crystal structure of the SARS-CoV-2 non-structural protein 9, Nsp9
2,680 downloads bioRxiv molecular biology

D. R. Littler, B. S. Gully, R. N. Colson, J Rossjohn

Many of the proteins produced by SARS-CoV-2 have related counterparts across the Severe Acute Respiratory Syndrome (SARS-CoV) family. One such protein is non-structural protein 9 (Nsp9), which is thought to mediate both viral replication and virulence. Current understanding suggests that Nsp9 is involved in viral genomic RNA reproduction. Nsp9 is thought to bind RNA via a fold that is unique to this class of betacoronoaviruses although the molecular basis for this remains ill-defined. We sought to better characterise the SARS-CoV-2 Nsp9 protein and subsequently solved its X-ray crystal structure, in an apo-form and, unexpectedly, in a peptide-bound form with a sequence originating from a rhinoviral 3C protease sequence (LEVL). The structure of the SARS-CoV-2 Nsp9 revealed the high level of structural conservation within the Nsp9 family. The exogenous peptide binding site is close to the dimer interface and impacted on the relative juxtaposition of the monomers within the homodimer. Together we have established a protocol for the production of SARS-CoV-2 Nsp9, determined its structure and identified a peptide-binding site that may warrant further study from the perspective of understanding Nsp9 function.

93: Transcription Factors Orchestrate Dynamic Interplay Between Genome Topology And Gene Regulation During Cell Reprogramming
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Posted 30 Apr 2017

Transcription Factors Orchestrate Dynamic Interplay Between Genome Topology And Gene Regulation During Cell Reprogramming
2,677 downloads bioRxiv molecular biology

Ralph Stadhouders, Enrique Vidal, François Serra, Bruno Di Stefano, François le Dily, Javier Quilez, Antonio Gomez, Samuel Collombet, Clara Berenguer, Yasmina Cuartero, Jochen Hecht, Guillaume Filion, Miguel Beato, Marc A. Marti-Renom, Thomas Graf

Chromosomal architecture is known to influence gene expression, yet its role in controlling cell fate remains poorly understood. Reprogramming of somatic cells into pluripotent stem cells by the transcription factors (TFs) Oct4, Sox2, Klf4 and Myc offers an opportunity to address this question but is severely limited by the low proportion of responding cells. We recently developed a highly efficient reprogramming protocol that synchronously converts somatic into pluripotent stem cells. Here, we employ this system to integrate time-resolved changes in genome topology with gene expression, TF binding and chromatin state dynamics. This revealed that TFs drive topological genome reorganization at multiple architectural levels, which often precedes changes in gene expression. Removal of locus-specific topological barriers can explain why pluripotency genes are activated sequentially, instead of simultaneously, during reprogramming. Taken together, our study implicates genome topology as an instructive force for implementing transcriptional programs and cell fate in mammals.

94: Efficient Zygotic Genome Editing via RAD51-Enhanced Interhomolog Repair
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Posted 11 Feb 2018

Efficient Zygotic Genome Editing via RAD51-Enhanced Interhomolog Repair
2,660 downloads bioRxiv molecular biology

Jonathan J. Wilde, Tomomi Aida, Martin Wienisch, Qiangge Zhang, Peimin Qi, Guoping Feng

Recent advances in genome editing have greatly improved knock-in (KI) efficiency. Searching for factors to further improve KI efficiency for therapeutic use and generation of non-human primate (NHP) models, we found that the strand exchange protein RAD51 can significantly increase homozygous KI using CRISPR/Cas9 in mouse embryos through an interhomolog repair (IHR) mechanism. IHR is well-described in the context of meiosis, but only occurs at low frequencies in mitotic cells and its existence in zygotes is controversial. Using a variety of approaches, we provide evidence for an endogenous IHR mechanism in zygotes that can be enhanced by RAD51. We show that this process can be harnessed for generating homozygous KI animals from wildtype zygotes based on exogenous donors and for converting heterozygous alleles into homozygous alleles without exogenous templates. Furthermore, we elucidate additional factors that contribute to zygotic IHR and identify a RAD51 mutant capable of insertion-deletion (indel)-free stimulation of IHR. Thus, our study provides conclusive evidence for the existence of zygotic IHR and demonstrates methods to enhance IHR for potential use in gene drives, gene therapy, and biotechnology.

95: The human secretome – the proteins secreted from human cells
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Posted 26 Nov 2018

The human secretome – the proteins secreted from human cells
2,639 downloads bioRxiv molecular biology

Mathias Uhlén, Hanna Tegel, Åsa Sivertsson, Chih-Chung Kuo, Jahir M. Gutierrez, Nathan E Lewis, Björn Forsström, Melanie Dannemeyer, Linn Fagerberg, Magdalena Malm, Helian Vunk, Fredrik Edfors, Andreas Hober, Evelina Sjöstedt, David Kotol, Jan Mulder, Adil Mardinoglu, Jochen M Schwenk, Peter Nilsson, Martin Zwahlen, Jenny Ottosson Takanen, Kalle von Feilitzen, Charlotte Stadler, Cecilia Lindskog, Fredrik Ponten, Jens Nielsen, Bernhard O Palsson, Anna-Luisa Volk, Magnus Lundqvist, Anna Berling, Anne-Sophie Svensson, Sara Kanje, Henric Enstedt, Delaram Afshari, Siri Ekblad, Julia Scheffel, Borbala Katona, Jimmy Vuu, Emil Lindström, LanLan Xu, Roxana Mihai, Lucas Bremer, Malin Westin, Muna Muse, Lorenz M Mayr, Sinead Knight, Sven Göpel, Rick Davies, Paul Varley, Diane Hatton, Ray Fields, Bjørn G Voldborg, Johan Rockberg, Lovisa Holmberg Schiavone, Sophia Hober

The proteins secreted by human tissues (the secretome) are important for the basic understanding of human biology, but also for identification of potential targets for future diagnosis and therapy. Here, we present an annotated list of all predicted secreted proteins (n=2,623) with information about cellular origin and spatial distribution in the human body. A high-throughput mammalian cell factory was established to create a resource of recombinant full-length proteins. This resource was used for phenotypic assays involving β-cell dedifferentiation and for development of targeted proteomics assays. A comparison between host cells, including omics analysis, shows that many of the proteins that failed to be generated in CHO cells could be rescued in human HEK 293 cells. In conclusion, the human secretome has been mapped and characterized and a resource has been generated to facilitate further exploration of the human secretome.

96: 5′ Modifications Improve Potency and Efficacy of DNA Donors for Precision Genome Editing
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Posted 22 Jun 2018

5′ Modifications Improve Potency and Efficacy of DNA Donors for Precision Genome Editing
2,624 downloads bioRxiv molecular biology

Krishna S. Ghanta, Gregoriy A. Dokshin, Aamir Mir, Pranathi Meda Krishnamurthy, Hassan Gneid, Alireza Edraki, Jonathan K. Watts, Erik J. Sontheimer, Craig C Mello

Nuclease-directed genome editing is a powerful tool for investigating physiology and has great promise as a therapeutic approach that directly addresses the underlying genetic basis of disease. In its most precise form, genome editing can use cellular homology-directed repair (HDR) pathways to insert information from an exogenously supplied DNA repair template (donor) directly into a targeted genomic location. Unfortunately, particularly for long insertions, toxicity and delivery considerations associated with repair template DNA can limit the number of donor molecules available to the HDR machinery, thus limiting HDR efficacy. Here, we explore modifications to both double-stranded and single-stranded repair template DNAs and describe simple 5′ end modifications that consistently and dramatically increase donor potency and HDR efficacy across cell types and species.

97: Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci
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Posted 29 Apr 2016

Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci
2,615 downloads bioRxiv molecular biology

Paulo P. Amaral, Tommaso Leonardi, Namshik Han, Emmanuelle Viré, Dennis K Gascoigne, Raúl Arias-Carrasco, Magdalena Büscher, Anda Zhang, Stefano Pluchino, Vinicius Maracaja-Coutinho, Helder Takashi Imoto Nakaya, Martin Hemberg, Ramin Shiekhattar, Anton J Enright, Tony Kouzarides

The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider positional conservation across mammalian genomes as an indicator of functional commonality. We identify 665 conserved lncRNA promoters in mouse and human genomes that are preserved in genomic position relative to orthologous coding genes. The identified positionally conserved lncRNA genes are primarily associated with developmental transcription factor loci with which they are co-expressed in a tissue-specific manner. Strikingly, over half of all positionally conserved RNAs in this set are linked to distinct chromatin organization structures, overlapping the binding sites for the CTCF chromatin organizer and located at chromatin loop anchor points and borders of topologically associating domains (TADs). These topological anchor point (tap)RNAs possess conserved sequence domains that are enriched in potential recognition motifs for Zinc Finger proteins. Characterization of these non-coding RNAs and their associated coding genes shows that they are functionally connected: they regulate each other ′s expression and influence the metastatic phenotype of cancer cells in vitro in a similar fashion. Thus, interrogation of positionally conserved lncRNAs identifies a new subset of tapRNAs with shared functional properties. These results provide a large dataset of lncRNAs that conform to the ″extended gene″ model, in which conserved developmental genes are genomically and functionally linked to regulatory lncRNA loci across mammalian evolution.

98: Re-analysis of SARS-CoV-2 infected host cell proteomics time-course data by impact pathway analysis and network analysis. A potential link with inflammatory response.
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Posted 28 Mar 2020

Re-analysis of SARS-CoV-2 infected host cell proteomics time-course data by impact pathway analysis and network analysis. A potential link with inflammatory response.
2,598 downloads bioRxiv molecular biology

Ignacio Ortea, Jens-Ole Bock

The disease known as coronavirus disease 19 (COVID-19), potentially caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has hit the world hard, and has led to an unprecedent health and economic crisis. In order to develop treatment options able to stop or ameliorate SARS-CoV-2 effects, we need to understand the biology of the virus inside cells, but this kind of studies are still scarce. A recent study investigated translatome and proteome host cell changes induced in vitro by SARS-CoV-2. In the present study, we use the publicly available proteomics data from this study to re-analyze the mechanisms altered by the virus infection by impact pathways analysis and network analysis. Proteins linked to inflammatory response, but also proteins related to chromosome segregation during mitosis, were found to be regulated. The up-regulation of the inflammatory-related proteins observed could be linked to the propagation of inflammatory reaction and lung injury that is observed in advanced stages of COVID-19 patients.

99: Comparative performance of four nucleic acid amplification tests for SARS-CoV-2 virus
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Posted 29 Mar 2020

Comparative performance of four nucleic acid amplification tests for SARS-CoV-2 virus
2,575 downloads bioRxiv molecular biology

Yujuan Xiong, Zhen-Zhen Li, Qi-Zhen Zhuang, Yan Chao, Fei Li, Yi-Yuan Ge, Yi Wang, Pei-Feng Ke, Xian-Zhang Huang

Coronavirus disease 2019 (COVID-19) can be screened and diagnosed through the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction. SARS-CoV-2 nucleic acid amplification tests (NAATs) have been rapidly developed and quickly applied to clinical testing during the pandemic. However, studies evaluating the performance of these NAAT assays are limited. We evaluated the performance of four NAATs, which were marked by the Conformité Européenne and widely used in China during the pandemic. Results showed that the analytical sensitivity of the four assays was significantly lower than that claimed by the NAAT manufacturers. The limit of detection (LOD) of Daan, Sansure, and Hybribio NAATs was 3000 copies/mL, whereas the LOD of Bioperfectus NAATs was 4000 copies/mL. The results of the consistency test using 46 samples showed that Daan, Sansure, and Hybribio NAATs could detect the samples with a specificity of 100% (30/30) and a sensitivity of 100% (16 /16), whereas Bioperfectus NAAT detected the samples with a specificity of 100% (30/30) and a sensitivity 81.25% (13/16). The sensitivity of Bioperfectus NAAT was lower than that of the three other NAATs; this finding was consistent with the result that Bioperfectus NAAT had a higher LOD than the three other kinds of NAATs. The four above mentioned reagents presented high specificity; however, for the detection of the samples with low virus concentration, Bioperfectus reagent had the risk of missing detection. Therefore, the LOD should be considered in the selection of SARS-CoV-2 NAATs.

100: CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks
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Posted 29 Mar 2020

CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks
2,574 downloads bioRxiv molecular biology

Ellen D. Zhong, Tristan Bepler, Bonnie Berger, Joseph H. Davis

Cryo-EM single-particle analysis has proven powerful in determining the structures of rigid macromolecules. However, many protein complexes are flexible and can change conformation and composition as a result of functionally-associated dynamics. Such dynamics are poorly captured by current analysis methods. Here, we present cryoDRGN, an algorithm that for the first time leverages the representation power of deep neural networks to efficiently reconstruct highly heterogeneous complexes and continuous trajectories of protein motion. We apply this tool to two synthetic and three publicly available cryo-EM datasets, and we show that cryoDRGN provides an interpretable representation of structural heterogeneity that can be used to identify discrete states as well as continuous conformational changes. This ability enables cryoDRGN to discover previously overlooked structural states and to visualize molecules in motion.

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