scholarly journals Whole-genome screening identifies proteins localized to distinct nuclear bodies

2013 ◽  
Vol 203 (1) ◽  
pp. 149-164 ◽  
Author(s):  
Ka-wing Fong ◽  
Yujing Li ◽  
Wenqi Wang ◽  
Wenbin Ma ◽  
Kunpeng Li ◽  
...  
Keyword(s):  
Posttranscriptional Regulation ◽  
Nuclear Bodies ◽  
Cajal Bodies ◽  
Nuclear Speckles ◽  
Genome Wide ◽  
A Genome ◽  
Human Proteins ◽  
Genome Screening ◽  
Interchromatin Space ◽  
Polycomb Bodies

The nucleus is a unique organelle that contains essential genetic materials in chromosome territories. The interchromatin space is composed of nuclear subcompartments, which are defined by several distinctive nuclear bodies believed to be factories of DNA or RNA processing and sites of transcriptional and/or posttranscriptional regulation. In this paper, we performed a genome-wide microscopy-based screening for proteins that form nuclear foci and characterized their localizations using markers of known nuclear bodies. In total, we identified 325 proteins localized to distinct nuclear bodies, including nucleoli (148), promyelocytic leukemia nuclear bodies (38), nuclear speckles (27), paraspeckles (24), Cajal bodies (17), Sam68 nuclear bodies (5), Polycomb bodies (2), and uncharacterized nuclear bodies (64). Functional validation revealed several proteins potentially involved in the assembly of Cajal bodies and paraspeckles. Together, these data establish the first atlas of human proteins in different nuclear bodies and provide key information for research on nuclear bodies.

scholarly journals Genome-Wide Analysis of Histidine Repeats Reveals Their Role in the Localization of Human Proteins to the Nuclear Speckles Compartment

PLoS Genetics ◽  
2009 ◽  
Vol 5 (3) ◽  
pp. e1000397 ◽  
Author(s):  
Eulàlia Salichs ◽  
Alice Ledda ◽  
Loris Mularoni ◽  
M. Mar Albà ◽  
Susana de la Luna
Keyword(s):  
Nuclear Speckles ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Human Proteins

scholarly journals StabilitySort: assessment of protein stability changes on a genome-wide scale to prioritise potentially pathogenic genetic variation

2021 ◽  
Author(s):  
Aaron Chuah ◽  
Sean Li ◽  
Andrea Do ◽  
Matt A Field ◽  
T. Daniel Andrews
Keyword(s):  
Genetic Variation ◽  
Protein Stability ◽  
Missense Mutations ◽  
Link Type ◽  
Genome Wide ◽  
Pathogenic Variation ◽  
A Genome ◽  
Human Proteins ◽  
Wide Scale ◽  
The Stability

AbstractSummaryMissense mutations that change protein stability are strongly associated with human inherited genetic disease. With the recent availability of predicted structures for all human proteins generated using the AlphaFold2 prediction model, genome-wide assessment of the stability effects of genetic variation can, for the first time, be easily performed. This facilitates the interrogation of personal genetic variation for potentially pathogenic effects through the application of stability metrics. Here, we present a novel algorithm to prioritise variants predicted to strongly destabilise essential proteins, available as both a standalone software package and a web-based tool. We demonstrate the utility of this tool by showing that at values of the Stability Sort Z-score above 1.6, pathogenic, protein-destabilising variants from ClinVar are detected at a 58% enrichment, over and above the destabilising (but presumably non-pathogenic) variation already present in the HapMap NA12878 genome.Availability and ImplementationStabilitySort is available as both a web service (http://130.56.244.113/StabilitySort/) and can be deployed as a standalone system (https://gitlab.com/baaron/StabilitySort)[email protected]

scholarly journals Network controllability enrichment analysis reveals that SARS-CoV-2 infection tends to target indispensable nodes of a directed human protein-protein interaction network

2021 ◽  
Author(s):  
Ho-Joon Lee
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
A Genome ◽  
Human Proteins ◽  
Protein Protein Interaction Network ◽  
Network Controllability

The COVID-19 disease has been a global threat caused by the new coronavirus species, SARS-CoV-2, since early 2020 with an urgent need for therapeutic interventions. In order to provide insight into human proteins targeted by SARS-CoV-2, here we study a directed human protein-protein interaction network (dhPPIN) based on our previous work on network controllability of virus targets. We previously showed that human proteins targeted by viruses tend to be those whose removal in a dhPPIN requires more control of the network dynamics, which were classified as indispensable nodes. In this study we introduce a more comprehensive rank-based enrichment analysis of our previous dhPPIN for SARS-CoV-2 infection and show that SARS-CoV-2 also tends to target indispensable nodes in the dhPPIN using multiple proteomics datasets, supporting validity and generality of controllability analysis of viral infection in humans. Also, we find differential controllability among SARS-CoV-2, SARS-CoV-1, and MERS-CoV from a comparative proteomics study. Moreover, we show functional significance of indispensable nodes by analyzing heterogeneous datasets from a genome-wide CRISPR screening study, a time-course phosphoproteomics study, and a genome-wide association study. Specifically, we identify SARS-CoV-2 ORF3A as most frequently interacting with indispensable proteins in the dhPPIN, which are enriched in TGF-beta signaling and tend to be sources nodes and interact with each other. Finally, we built an integrated network model of ORF3A-interacting indispensable proteins with multiple functional supports to provide hypotheses for experimental validation as well as therapeutic opportunities. Therefore, a sub-network of indispensable proteins targeted by SARS-CoV-2 could serve as a prioritized network of drug targets and a basis for further functional and mechanistic studies from a network controllability perspective.

scholarly journals Unbiased identification of nanoparticle cell uptake mechanism via a genome-wide CRISPR/Cas9 knockout screen

2020 ◽  
Author(s):  
Eric L. Van Nostrand ◽  
Sarah A. Barnhill ◽  
Alexander A. Shishkin ◽  
David A. Nelles ◽  
Eric Byeon ◽  
...  
Keyword(s):  
Cell Uptake ◽  
Target Cells ◽  
Uptake Mechanism ◽  
Therapeutic Delivery ◽  
Genome Wide ◽  
A Genome ◽  
Technical Reproducibility ◽  
Genome Screening ◽  
Major Bottleneck ◽  
Target Effects

AbstractA major bottleneck in nanocarrier and macromolecule development for therapeutic delivery is our limited understanding of the processes involved in their uptake into target cells. This includes their active interactions with membrane transporters that co-ordinate cellular uptake and processing. Current strategies to elucidate the mechanism of uptake, such as painstaking manipulation of individual effectors with pharmacological inhibitors or specific genetic knockdowns, are limited in scope and biased towards previously studied pathways or the intuition of the investigators. Furthermore, each of these approaches present significant off-target effects, clouding the outcomes. We set out to develop and examine an unbiased whole-genome screening approach using pooled CRISPR/Cas9 libraries for its ability to provide a robust and rapid approach to identify novel effectors of material uptake. Enabling this, we developed a methodology termed fast-library of inserts (FLI)-seq for library preparation and quantitative readout of pooled screens that shows improved technical reproducibility and is easier to perform than existing methods. In this proof-of-concept study we use FLI-seq to identify a solute carrier protein family member, SLC18B1, as a transporter for polymeric micellar nanoparticles, confirming the viability for this approach to yield novel insights into uptake mechanisms.

scholarly journals Mapping the nuclear microenvironment of genes at a genome-wide scale

2021 ◽  
Author(s):  
Asli Yildirim ◽  
Nan Hua ◽  
Lorenzo Boninsegna ◽  
Guido Polles ◽  
Ke Gong ◽  
...  
Keyword(s):  
Single Cells ◽  
Three Dimensional ◽  
Population Based ◽  
Nuclear Bodies ◽  
Cell Models ◽  
Chromatin Compaction ◽  
Functional Potential ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale

The folding and subnuclear compartmentalization of chromosomes relative to nuclear bodies is an integral part of gene function. However, mapping the three-dimensional (3D) organization of all genes, in single cells, on a genome-wide scale remains a major challenge. Here, we demonstrate that data-driven population-based modeling, from ensemble Hi-C data alone, can provide a detailed description of the nuclear microenvironment of genes. We define the microenvironment of a gene by its subnuclear positions with respect to different nuclear bodies, local chromatin compaction, and preferences in chromatin compartmentalization. These structural descriptors are determined in single cell models on a genome-wide scale, thereby revealing the dynamic variability of the subnuclear microenvironment of a gene across a population of cells. We demonstrate that the microenvironment of a gene is directly linked to its functional potential in gene transcription, replication, and subnuclear compartmentalization. Some chromatin regions are distinguished by their strong preferences to a single microenvironment (either transcriptionally active or silenced), due to strong associations to specific nuclear bodies. Other chromatin shows highly variable microenvironments and lacks specific preferences. We demonstrate that our method produces highly predictive genome structures, which accurately reproduce data from TSA-seq, DamID, and DNA-MERFISH imaging. Thus, our method considerably expands the range of Hi-C data analysis.

scholarly journals A Genome-wide Short Hairpin RNA Screening of Jurkat T-cells for Human Proteins Contributing to Productive HIV-1 Replication

2009 ◽  
Vol 284 (29) ◽  
pp. 19463-19473 ◽  
Author(s):  
Man Lung Yeung ◽  
Laurent Houzet ◽  
Venkat S. R. K. Yedavalli ◽  
Kuan-Teh Jeang
Keyword(s):  
T Cells ◽  
Short Hairpin Rna ◽  
Jurkat T Cells ◽  
Hairpin Rna ◽  
Genome Wide ◽  
A Genome ◽  
Human Proteins ◽  
Short Hairpin ◽  
Hiv 1

scholarly journals Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus

2017 ◽  
Author(s):  
Sofia A. Quinodoz ◽  
Noah Ollikainen ◽  
Barbara Tabak ◽  
Ali Palla ◽  
Jan Marten Schmidt ◽  
...  
Keyword(s):  
Genome Organization ◽  
Genomic Dna ◽  
Spatial Association ◽  
Higher Order ◽  
Nuclear Bodies ◽  
Dimensional Structure ◽  
Nuclear Speckles ◽  
3 Dimensional ◽  
Proximity Ligation ◽  
Genome Wide

ABSTRACTEukaryotic genomes are packaged into a 3-dimensional structure in the nucleus of each cell. There are currently two distinct views of genome organization that are derived from different technologies. The first view, derived from genome-wide proximity ligation methods (e.g. Hi-C), suggests that genome organization is largely organized around chromosomes. The second view, derived from in situ imaging, suggests a central role for nuclear bodies. Yet, because microscopy and proximity-ligation methods measure different aspects of genome organization, these two views remain poorly reconciled and our overall understanding of how genomic DNA is organized within the nucleus remains incomplete. Here, we develop Split-Pool Recognition of Interactions by Tag Extension (SPRITE), which moves away from proximity-ligation and enables genome-wide detection of higher-order DNA interactions within the nucleus. Using SPRITE, we recapitulate known genome structures identified by Hi-C and show that the contact frequencies measured by SPRITE strongly correlate with the 3-dimensional distances measured by microscopy. In addition to known structures, SPRITE identifies two major hubs of inter-chromosomal interactions that are spatially arranged around the nucleolus and nuclear speckles, respectively. We find that the majority of genomic regions exhibit preferential spatial association relative to one of these nuclear bodies, with regions that are highly transcribed by RNA Polymerase II organizing around nuclear speckles and transcriptionally inactive and centromere-proximal regions organizing around the nucleolus. Together, our results reconcile the two distinct pictures of nuclear structure and demonstrate that nuclear bodies act as inter-chromosomal hubs that shape the overall 3-dimensional packaging of genomic DNA in the nucleus.

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

2020 ◽  
Author(s):  
Mary V. Arrastia ◽  
Joanna W. Jachowicz ◽  
Noah Ollikainen ◽  
Matthew S. Curtis ◽  
Charlotte Lai ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Organization ◽  
Single Cells ◽  
Genome Structure ◽  
Higher Order ◽  
Nuclear Bodies ◽  
Nuclear Function ◽  
Genome Wide ◽  
A Genome ◽  
Order Structures

ABSTRACTIn 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 many aspects of nuclear function, including DNA replication, transcription, and cell cycle progression. Nuclear structure intrinsically occurs within single cells; however, measuring such a broad spectrum of 3D DNA interactions on a genome-wide scale and at the single cell level has been a great challenge. To address this, we developed single-cell split-pool recognition of interactions by tag extension (scSPRITE), a new method that enables measurements of genome-wide maps of 3D DNA structure in thousands of individual nuclei. scSPRITE maximizes the number of DNA contacts detected per cell enabling high-resolution genome structure maps within each cells and is easy-to-use and cost-effective. scSPRITE accurately detects chromosome territories, active and inactive compartments, topologically associating domains (TADs), and higher-order structures within single cells. In addition, scSPRITE measures cell-to-cell heterogeneity in genome structure at different levels of resolution and shows that TADs are dynamic units of genome organization that can vary between different cells within a population. scSPRITE will improve our understanding of nuclear architecture and its relationship to nuclear function within an individual nucleus from complex cell types and tissues containing a diverse population of cells.

scholarly journals Assessing Computational Steps for CLIP-Seq Data Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Qi Liu ◽  
Xue Zhong ◽  
Blair B. Madison ◽  
Anil K. Rustgi ◽  
Yu Shyr
Keyword(s):  
Binding Sites ◽  
Posttranscriptional Regulation ◽  
Motif Discovery ◽  
Rna Binding ◽  
Pcr Amplification ◽  
Systematic Evaluation ◽  
Genome Wide ◽  
A Genome ◽  
Control Samples

RNA-binding protein (RBP) is a key player in regulating gene expression at the posttranscriptional level. CLIP-Seq, with the ability to provide a genome-wide map of protein-RNA interactions, has been increasingly used to decipher RBP-mediated posttranscriptional regulation. Generating highly reliable binding sites from CLIP-Seq requires not only stringent library preparation but also considerable computational efforts. Here we presented a first systematic evaluation of major computational steps for identifying RBP binding sites from CLIP-Seq data, including preprocessing, the choice of control samples, peak normalization, and motif discovery. We found that avoiding PCR amplification artifacts, normalizing to input RNA or mRNAseq, and defining the background model from control samples can reduce the bias introduced by RNA abundance and improve the quality of detected binding sites. Our findings can serve as a general guideline for CLIP experiments design and the comprehensive analysis of CLIP-Seq data.

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