High-throughput siRNA screening reveals functional interactions and redundancies of human processive exoribonucleases

ABSTRACTProcessive exoribonucleases, the executors of RNA decay, participate in multiple physical and functional interactions. Unlike physical ones, functional relationships have not been investigated in human cells. Here we have screened cells deficient in DIS3, XRN2, EXOSC10, DIS3L, and DIS3L2 with a custom siRNA library and determined their functional interactions with diverse pathways of RNA metabolism. We uncover a complex network of positive interactions that buffer alterations in RNA degradation. We reveal important reciprocal actions between RNA decay and transcription and explore alleviating interactions between RNA splicing and DIS3 mediated degradation. We also use a large scale library of genes associated with RNA metabolism to determine genetic interactions of nuclear DIS3 and cytoplasmic DIS3L, revealing their unique functions in RNA degradation and uncovering cooperation between the cytoplasmic degradation and nuclear processing of RNA. Finally, genome-wide siRNA screening of DIS3 reveals processes such as microtubule organization and regulation of telomerase activity that are also functionally associated with nuclear exosome-mediated RNA degradation.

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Terminal nucleotidyl transferases (TENTs) in mammalian RNA metabolism

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2018.0162 ◽

2018 ◽

Vol 373 (1762) ◽

pp. 20180162 ◽

Cited By ~ 23

Author(s):

Zbigniew Warkocki ◽

Vladyslava Liudkovska ◽

Olga Gewartowska ◽

Seweryn Mroczek ◽

Andrzej Dziembowski

Keyword(s):

Current Knowledge ◽

Rna Metabolism ◽

Rna Degradation ◽

Mechanisms Of Action ◽

Mammalian Genome ◽

Rna Decay ◽

Theme Issue ◽

Almost All

In eukaryotes, almost all RNA species are processed at their 3′ ends and most mRNAs are polyadenylated in the nucleus by canonical poly(A) polymerases. In recent years, several terminal nucleotidyl transferases (TENTs) including non-canonical poly(A) polymerases (ncPAPs) and terminal uridyl transferases (TUTases) have been discovered. In contrast to canonical polymerases, TENTs' functions are more diverse; some, especially TUTases, induce RNA decay while others, such as cytoplasmic ncPAPs, activate translationally dormant deadenylated mRNAs. The mammalian genome encodes 11 different TENTs. This review summarizes the current knowledge about the functions and mechanisms of action of these enzymes. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.

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Methodical approach to determining permissible time limits of intermittent carbon monoxide exposure in rescuers

Medico-Biological and Socio-Psychological Problems of Safety in Emergency Situations ◽

10.25016/2541-7487-2021-0-1-82-88 ◽

2021 ◽

pp. 82-88

Author(s):

D. V. Myasnikov ◽

P. V. Avitisov ◽

A. V. Zolotukhin ◽

M. F. Barinov

Keyword(s):

Carbon Monoxide ◽

Large Scale ◽

Operation Time ◽

Theoretical Data ◽

Combustion Products ◽

Research Area ◽

Time Limits ◽

Emergency Rescue ◽

Functional Relationships ◽

Methodical Approach

Relevance. Current operation time limits under hazardous chemical conditions (“emergency regulations”) have been developed mainly for a limited number of emergency situations occurring in spacecraft, submarines or other specific objects. At the same time, many emergencies accompanied by large-scale releases of toxic combustion products from various materials and compounds into the environment are not limited to these facilities. Therefore, risks associated with toxic effects of chemicals should be predicted, since permissible time limits with adequate performance of personnel under certain chemical exposures are used for individual protection (time-based protection).Intention: On the basis of physiological aspects, the peculiarities of the work performed by rescuers and the requirements for organizing and conducting emergency rescue operations, to propose a methodical approach to determining the permissible time for rescuers in conditions of intermittent carbon monoxide release.Methodology. The scientific works and results of experiments in the research area were analyzed. Systematization and generalization of empirical and theoretical data, traditional analysis of documents and publications were used with the least squares approximation.Results and Discussion. Specific effects of various carbon monoxide concentrations are shown for different exposure times. Critical concentrations and exposure times are revealed, functional relationships between permissible time of operation and carbon monoxide concentrations are determined. Carboxyhemoglobin formation and effects were taken into account.Conclusion. The data given in the article are an important basis for organizing and conducting emergency rescue operations at increased concentrations of carbon monoxide.

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ASCOT identifies key regulators of neuronal subtype-specific splicing

Nature Communications ◽

10.1038/s41467-019-14020-5 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 2

Author(s):

Jonathan P. Ling ◽

Christopher Wilks ◽

Rone Charles ◽

Patrick J. Leavey ◽

Devlina Ghosh ◽

...

Keyword(s):

Rna Splicing ◽

Large Scale ◽

Splice Variants ◽

Next Generation Sequencing Data ◽

Data Sets ◽

Cell Type ◽

Sequencing Data ◽

Large Scale Analysis ◽

Cell Type Specific ◽

Public Archives

AbstractPublic archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by scientists. Here, we present ASCOT, a resource that uses annotation-free methods to rapidly analyze and visualize splice variants across tens of thousands of bulk and single-cell data sets in the public archive. To demonstrate the utility of ASCOT, we identify novel cell type-specific alternative exons across the nervous system and leverage ENCODE and GTEx data sets to study the unique splicing of photoreceptors. We find that PTBP1 knockdown and MSI1 and PCBP2 overexpression are sufficient to activate many photoreceptor-specific exons in HepG2 liver cancer cells. This work demonstrates how large-scale analysis of public RNA-Seq data sets can yield key insights into cell type-specific control of RNA splicing and underscores the importance of considering both annotated and unannotated splicing events.

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A protein interaction map for cell polarity development

The Journal of Cell Biology ◽

10.1083/jcb.200104057 ◽

2001 ◽

Vol 154 (3) ◽

pp. 549-576 ◽

Cited By ~ 226

Author(s):

Becky L. Drees ◽

Bryan Sundin ◽

Elizabeth Brazeau ◽

Juliane P. Caviston ◽

Guang-Chao Chen ◽

...

Keyword(s):

Cell Polarity ◽

Protein Interactions ◽

Large Scale ◽

Interaction Network ◽

Open Reading Frames ◽

Actin Assembly ◽

Protein Protein Interactions ◽

Microtubule Organization ◽

Two Hybrid ◽

Secretory Apparatus

Many genes required for cell polarity development in budding yeast have been identified and arranged into a functional hierarchy. Core elements of the hierarchy are widely conserved, underlying cell polarity development in diverse eukaryotes. To enumerate more fully the protein–protein interactions that mediate cell polarity development, and to uncover novel mechanisms that coordinate the numerous events involved, we carried out a large-scale two-hybrid experiment. 68 Gal4 DNA binding domain fusions of yeast proteins associated with the actin cytoskeleton, septins, the secretory apparatus, and Rho-type GTPases were used to screen an array of yeast transformants that express ∼90% of the predicted Saccharomyces cerevisiae open reading frames as Gal4 activation domain fusions. 191 protein–protein interactions were detected, of which 128 had not been described previously. 44 interactions implicated 20 previously uncharacterized proteins in cell polarity development. Further insights into possible roles of 13 of these proteins were revealed by their multiple two-hybrid interactions and by subcellular localization. Included in the interaction network were associations of Cdc42 and Rho1 pathways with proteins involved in exocytosis, septin organization, actin assembly, microtubule organization, autophagy, cytokinesis, and cell wall synthesis. Other interactions suggested direct connections between Rho1- and Cdc42-regulated pathways; the secretory apparatus and regulators of polarity establishment; actin assembly and the morphogenesis checkpoint; and the exocytic and endocytic machinery. In total, a network of interactions that provide an integrated response of signaling proteins, the cytoskeleton, and organelles to the spatial cues that direct polarity development was revealed.

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Detection and Degradation of Nonsense-mediated mRNA Decay Substrates Involve Two Distinct Upf1-bound Complexes

10.1101/266833 ◽

2018 ◽

Author(s):

Marine Dehecq ◽

Laurence Decourty ◽

Abdelkader Namane ◽

Caroline Proux ◽

Joanne Kanaan ◽

...

Keyword(s):

Large Scale ◽

Mrna Decay ◽

Affinity Purification ◽

Rna Degradation ◽

Degradation Pathway ◽

Telomere Maintenance ◽

Mrna Decapping ◽

Nonsense Mediated Mrna Decay ◽

Decapping Enzyme

AbstractNonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway involved in many cellular pathways and crucial for telomere maintenance and embryo development. Core NMD factors Upf1, Upf2 and Upf3 are conserved from yeast to mammals, but a universal NMD model is lacking. We used affinity purification coupled with mass spectrometry and an improved data analysis protocol to obtain the first large-scale quantitative characterization of yeast NMD complexes in yeast (112 experiments). Unexpectedly, we identified two distinct complexes associated with Upf1: Detector (Upf1/2/3) and Effector. Effector contained the mRNA decapping enzyme, together with Nmd4 and Ebs1, two proteins that globally affected NMD and were critical for RNA degradation mediated by the Upf1 C-terminal helicase region. The fact that Nmd4 association to RNA was dependent on Detector components and the similarity between Nmd4/Ebs1 and mammalian Smg5-7 proteins suggest that in all eukaryotes NMD operates through successive Upf1-bound Detector and Effector complexes.

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Integrative Functional Network Interactions Underlie the Association between Physical Activity and Cognition in Neurodegenerative Diseases

10.1101/542936 ◽

2019 ◽

Author(s):

Chia-Hao Shih ◽

Miriam Sklerov ◽

Nina Browner ◽

Eran Dayan

Keyword(s):

Physical Activity ◽

Neurodegenerative Diseases ◽

Cognitive Decline ◽

Cognitive Performance ◽

Large Scale ◽

Healthy Aging ◽

Brain Networks ◽

Neural Substrates ◽

Functional Interactions ◽

False Discovery

Physical activity (PA) has preventive and possibly restorative effects in aging-related cognitive decline, which relate to intrinsic functional interactions (functional connectivity, FC) in large-scale brain networks. Preventive and ameliorative effects of PA on cognitive decline have also been documented in neurodegenerative diseases, such as Parkinson's disease (PD). However, the neural substrates that mediate the association between PA and cognitive performance under such neurological conditions remain unknown. Here we set out to examine if the association between PA and cognitive performance in PD is mediated by FC in large-scale sensorimotor and association brain networks. Data from 51 PD patients were analyzed. Connectome-level analysis based on a whole-brain parcellation showed that self-reported levels of PA were associated with increased FC between, but not within the default mode (DMN) and salience networks (SAL) (p < .05, false discovery rate corrected). Additionally, multiple parallel mediation analysis further demonstrated that FC between left lateral parietal nodes in the DMN and rostral prefrontal nodes in the SAL mediated the association between PA and executive function performance. These findings are in line with previous studies linking FC in large-scale association networks with the effects of PA on cognition in healthy aging. Our results extend these previous results by demonstrating that the association between PA and cognitive performance in neurodegenerative diseases such as PD is mediated by integrative functional interactions in large-scale association networks.

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Cerebral atherosclerosis contributes to Alzheimer’s dementia independently of its hallmark amyloid and tau pathologies

10.1101/793349 ◽

2019 ◽

Cited By ~ 2

Author(s):

Aliza P. Wingo ◽

Wen Fan ◽

Duc M. Duong ◽

Ekaterina S. Gerasimov ◽

Eric B. Dammer ◽

...

Keyword(s):

Human Brain ◽

Rna Splicing ◽

Large Scale ◽

Enrichment Analysis ◽

Neurofilament Light ◽

Synaptic Signaling ◽

Cerebral Atherosclerosis ◽

Dementia Risk ◽

Brain Proteome ◽

Oligodendrocyte Development

AbstractCerebral atherosclerosis is a leading cause of stroke and an important contributor to dementia. However, little is known about its molecular effects on the human brain and how these alterations may contribute to dementia. Here, we investigated these questions using large-scale quantification of over 8300 proteins from 438 post-mortem brains from a discovery and replication cohort. A proteome-wide association study and protein network analysis of cerebral atherosclerosis found 114 proteins and 5 protein co-expression modules associated with cerebral atherosclerosis. Enrichment analysis of these proteins and modules revealed that cerebral atherosclerosis was associated with reductions in synaptic signaling and RNA splicing and increases in oligodendrocyte development and myelination. A subset of these proteins (n=23) and protein modules (n=2) were also associated with Alzheimer’s disease (AD) dementia, implicating a shared mechanism with AD through decreased synaptic signaling and regulation and increased myelination. Notably, neurofilament light (NEFL) and medium (NEFM) chain proteins were among these 23 proteins, and our data suggest they contribute to AD dementia through cerebral atherosclerosis. Together, our findings offer insights into effects of cerebral atherosclerosis on the human brain proteome, and how cerebral atherosclerosis contributes to dementia risk.

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Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell R packages

10.1101/064469 ◽

2016 ◽

Cited By ~ 2

Author(s):

Paul Deveau ◽

Emmanuel Barillot ◽

Valentina Boeva ◽

Andrei Zinovyev ◽

Eric Bonnet

Keyword(s):

Large Scale ◽

Large Body ◽

R Package ◽

Biological Pathways ◽

Biological Data ◽

Cellular Systems ◽

Biological Databases ◽

Data Types ◽

Functional Relationships ◽

Body Of Knowledge

AbstractBiological pathways or modules represent sets of interactions or functional relationships occurring at the molecular level in living cells. A large body of knowledge on pathways is organized in public databases such as the KEGG, Reactome, or in more specialized repositories, such as the Atlas of Cancer Signaling Network (ACSN). All these open biological databases facilitate analyses, improving our understanding of cellular systems. We hereby describe the R packageACSNMineRfor calculation of enrichment or depletion of lists of genes of interest in biological pathways. ACSNMineR integrates ACSN molecular pathways, but can use any molecular pathway encoded as a GMT file, for instance sets of genes available in the Molecular Signatures Database (MSigDB). We also present the R packageRNaviCell, that can be used in conjunction withACSNMineRto visualize different data types on web-based, interactive ACSN maps. We illustrate the functionalities of the two packages with biological data taken from large-scale cancer datasets.

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Modelling the Dynamics of a Facility for Understanding Critical Resource Use in Oiled Seabird Rehabilitation

International Oil Spill Conference Proceedings ◽

10.7901/2169-3358-2021.1.688711 ◽

2021 ◽

Vol 2021 (1) ◽

Author(s):

Hugo Nijkamp ◽

Jasper van der Werff-Ten Bosch ◽

Claude Velter

Keyword(s):

Large Scale ◽

Treatment Strategies ◽

Capacity Limits ◽

Functional Relationships ◽

Critical Resource ◽

Set Up ◽

Multiple Species ◽

The Many ◽

The Mathematical Model ◽

Available Resources

Abstract The rehabilitation of oiled birds in a large scale event can be a challenging undertaking, especially because of emergency dynamics which make it difficult to predict when, and how many animals will be arriving at a facility from day to day. Scenarios from past spill events demonstrate that even a small oil spill in a vulnerable area or season can produce hundreds of live oiled birds washing ashore, every day, for many days or weeks in a row. Any facility (permanent or temporary) or a network of facilities near the incident site would have difficulty to admit and process streams of hundreds of birds per day while continuing to try and guarantee mimumum care standards in every stage of the rehabilitation process. Guaranteeing these minimum standards during the whole of the response needs a thorough understanding of the many functional relationships between available resources (people, equipment, consumables, foods etc), the quality and size of the facility set-up, and the maximum number of animals that each department in the facility can treat per time unit, according to these standards. The mathematical model “Birds in Rehab (BiR version 1.0)” was developed between 2012 and 2015 as a simulation tool for facility managers to understand the dynamics of animals of one species (guillemot/murre) flowing through a facility according to realistic decision making of experts on the work floor. Recently, thanks to funds from the Netherlands authorities, the tool was updated (current version: BiR 2.2) in order to be able to simulate multiple species that are admitted to a facility. Different species need different resources, which have been included in the updated model. A new functionality is a calculator, which runs a given scenario in a few seconds, and allow the user to compare the results (survival, release of species) of alternative treatment strategies. This paper will describe the BiR 2.2 model and its applications. One of the useful features is that it provides quantitative overviews of how many animals are in care at any time, and in which phase of treatment they are. This allows a useful assessment of the feasibility of such numbers in relation to available resources, space, and other natural limits of the facility that is simulated. The model can help to explore the capacity limits of a given facility setup and see where bottlenecks may appear. The new version will be used for training and planning purposes, and is guaranteed to assist experts who are interested in deepening their insights in dynamic processes on the work floor of a facility that are impossible to exercise and in reality hard to unravel.

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FIREWORKS: a bottom-up approach to integrative coessentiality network analysis

Life Science Alliance ◽

10.26508/lsa.202000882 ◽

2020 ◽

Vol 4 (2) ◽

pp. e202000882

Author(s):

David R Amici ◽

Jasen M Jackson ◽

Mihai I Truica ◽

Roger S Smith ◽

Sarki A Abdulkadir ◽

...

Keyword(s):

Large Scale ◽

Gene Interaction ◽

Bias Reduction ◽

Functional Relationships ◽

Accessibility Barriers ◽

Common Effect ◽

Human Genes ◽

Case Vignettes ◽

Systematic Biases ◽

Context Specific

Genetic coessentiality analysis, a computational approach which identifies genes sharing a common effect on cell fitness across large-scale screening datasets, has emerged as a powerful tool to identify functional relationships between human genes. However, widespread implementation of coessentiality to study individual genes and pathways is limited by systematic biases in existing coessentiality approaches and accessibility barriers for investigators without computational expertise. We created FIREWORKS, a method and interactive tool for the construction and statistical analysis of coessentiality networks centered around gene(s) provided by the user. FIREWORKS incorporates a novel bias reduction approach to reduce false discoveries, enables restriction of coessentiality analyses to custom subsets of cell lines, and integrates multiomic and drug–gene interaction datasets to investigate and target contextual gene essentiality. We demonstrate the broad utility of FIREWORKS through case vignettes investigating gene function and specialization, indirect therapeutic targeting of “undruggable” proteins, and context-specific rewiring of genetic networks.

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