Determination of Protein−RNA Interaction Sites in the Cbf5-H/ACA Guide RNA Complex by Mass Spectrometric Protein Footprinting†

Biochemistry ◽  
2008 ◽  
Vol 47 (6) ◽  
pp. 1500-1510 ◽  
Author(s):  
Daniel L. Baker ◽  
Nicholas T. Seyfried ◽  
Hong Li ◽  
Ron Orlando ◽  
Rebecca M. Terns ◽  
...  
Keyword(s):  
Mass Spectrometric ◽  
Protein Footprinting ◽  
Guide Rna ◽  
Interaction Sites ◽  
Rna Interaction ◽  
Rna Complex

scholarly journals SliceIt: A genome-wide resource and visualization tool to design CRISPR/Cas9 screens for editing protein-RNA interaction sites in the human genome

2019 ◽  
Author(s):  
Sasank Vemuri ◽  
Rajneesh Srivastava ◽  
Quoseena Mir ◽  
Seyedsasan Hashemikhabir ◽  
X. Charlie Dong ◽  
...  
Keyword(s):  
Binding Site ◽  
High Throughput ◽  
Binding Sites ◽  
Genome Browser ◽  
Expression Levels ◽  
Guide Rna ◽  
Exon Expression ◽  
Interaction Sites ◽  
Gene Search ◽  
Rna Interaction

AbstractSeveral protein-RNA cross linking protocols have been established in recent years to delineate the molecular interaction of an RNA Binding Protein (RBP) and its target RNAs. However, functional dissection of the role of the RBP binding sites in modulating the post-transcriptional fate of the target RNA remains challenging. CRISPR/Cas9 genome editing system is being commonly employed to perturb both coding and noncoding regions in the genome. With the advancements in genome-scale CRISPR/Cas9 screens, it is now possible to not only perturb specific binding sites but also probe the global impact of protein-RNA interaction sites across cell types. Here, we present SliceIt (http://sliceit.soic.iupui.edu/), a database of in silico sgRNA (single guide RNA) library to facilitate conducting such high throughput screens. SliceIt comprises of ~4.8 million unique sgRNAs with an estimated range of 2–8 sgRNAs designed per RBP binding site, for eCLIP experiments of >100 RBPs in HepG2 and K562 cell lines from the ENCODE project. SliceIt provides a user friendly environment, developed using advanced search engine framework, Elasticsearch. It is available in both table and genome browser views facilitating the easy navigation of RBP binding sites, designed sgRNAs, exon expression levels across 53 human tissues along with prevalence of SNPs and GWAS hits on binding sites. Exon expression profiles enable examination of locus specific changes proximal to the binding sites. Users can also upload custom tracks of various file formats directly onto genome browser, to navigate additional genomic features in the genome and compare with other types of omics profiles. All the binding site-centric information is dynamically accessible via “search by gene”, “search by coordinates” and “search by RBP” options and readily available to download. Validation of the sgRNA library in SliceIt was performed by selecting RBP binding sites in Lipt1 gene and designing sgRNAs. Effect of CRISPR/Cas9 perturbations on the selected binding sites in HepG2 cell line, was confirmed based on altered proximal exon expression levels using qPCR, further supporting the utility of the resource to design experiments for perturbing protein-RNA interaction networks. Thus, SliceIt provides a one-stop repertoire of guide RNA library to perturb RBP binding sites, along with several layers of functional information to design both low and high throughput CRISPR/Cas9 screens, for studying the phenotypes and diseases associated with RBP binding sites.

Tandem Mass Spectrometric Evaluation of Core Structures of Aromatic Compounds after Catalytic Deoxygenation

2017 ◽  
Author(s):  
Xueming Dong
Keyword(s):  
Aromatic Compounds ◽  
Supported Catalyst ◽  
Mass Spectrometric ◽  
Spectrometric Method ◽  
Mass Spectrometric Method ◽  
Aromatic Rings ◽  
Tandem Mass Spectrometric ◽  
Catalytic Deoxygenation ◽  
Oxygen Atoms

Catalytic deoxygenation of coal enhances the stability and combustion performance of coal-derived liquids. However, determination of the selectivity of removal of oxygen atoms incorporated in or residing outside of aromatic rings is challenging. This limits the ability to evaluate the success of catalytic deoxygenation processes. A mass spectrometric method, in-source collision-activated dissociation (ISCAD), combined with high resolution product ion detection, is demonstrated to allow the determination of whether the oxygen atoms in aromatic compounds reside outside of aromatic rings or are part of the aromatic system, because alkyl chains can be removed from aromatic cores via ISCAD. Application of this method for the analysis of a subbituminous coal treated using a supported catalyst revealed that the catalytic treatment reduced the number of oxygen-containing heteroaromatic rings but not the number of oxygen atoms residing outside the aromatic rings.<br>

Tandem Mass Spectrometric Evaluation of Core Structures of Aromatic Compounds after Catalytic Deoxygenation

2017 ◽  
Author(s):  
Xueming Dong
Keyword(s):  
Aromatic Compounds ◽  
Supported Catalyst ◽  
Mass Spectrometric ◽  
Spectrometric Method ◽  
Mass Spectrometric Method ◽  
Aromatic Rings ◽  
Tandem Mass Spectrometric ◽  
Catalytic Deoxygenation ◽  
Oxygen Atoms

Catalytic deoxygenation of coal enhances the stability and combustion performance of coal-derived liquids. However, determination of the selectivity of removal of oxygen atoms incorporated in or residing outside of aromatic rings is challenging. This limits the ability to evaluate the success of catalytic deoxygenation processes. A mass spectrometric method, in-source collision-activated dissociation (ISCAD), combined with high resolution product ion detection, is demonstrated to allow the determination of whether the oxygen atoms in aromatic compounds reside outside of aromatic rings or are part of the aromatic system, because alkyl chains can be removed from aromatic cores via ISCAD. Application of this method for the analysis of a subbituminous coal treated using a supported catalyst revealed that the catalytic treatment reduced the number of oxygen-containing heteroaromatic rings but not the number of oxygen atoms residing outside the aromatic rings.<br>

Authenticity of sugar – Identification of plant source and determination of geographical origin of sucrose

2015 ◽  
pp. 40-43 ◽  
Author(s):  
Andreas G. Degenhardt
Keyword(s):  
Metabolic Pathways ◽  
Isotope Ratio ◽  
Geographical Origin ◽  
Hydrological Cycle ◽  
Isotope Ratios ◽  
Saccharum Officinarum ◽  
Mass Spectrometric ◽  
C3 And C4 Plants ◽  
Plant Source

The isotope ratios of water, organic matter and micronutrients from food are dependent on the circumstances and sites of their origin and production. Analytical methods, based on mass spectrometry, are established for routine determination of isotopes. Differentiation between metabolic pathways of C3 and C4 plants is realizable by determination 13C/12C ratios which can distinguish and identify sucrose from pure beet (Beta vulgaris) and pure cane (Saccharum officinarum). Influenced by the worldwide hydrological cycle the isotope ratios of 2H/1H and 18O/16O vary systematically, the variations give information about geographical origin. The exemplarily determination of authenticity is demonstrated by using mass spectrometric isotope ratio evaluation for identification of plant source and geographical origin with the help of selected sugar samples with known origin.

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