Whole-Genome Cartography of Estrogen Receptorα Binding Sites

The productions of antibiotics are usually regulated by cluster-situated regulators (CSRs), which can directly regulate the genes within the corresponding biosynthetic gene cluster (BGC). However, few studies have looked into the regulation of CSRs on the targets outside the BGC. Here, we screened the targets of LmbU in the whole genome of S. lincolnensis, and found 14 candidate targets, among of which, 8 targets can bind to LmbU by EMSAs. Reporter assays in vivo revealed that LmbU repressed transcription of SLINC_RS02575 and SLINC_RS05540, while activated transcription of SLINC_RS42780. In addition, disruptions of SLINC_RS02575, SLINC_RS05540 and SLINC_RS42780 promoted the production of lincomycin, and qRT-PCR showed that SLINC_RS02575, SLINC_RS05540 and SLINC_RS42780 inhibited transcription of the lmb genes, indicating that all the three regulators can negatively regulate lincomycin biosynthesis. What's more, the homologues of LmbU and its targets SLINC_RS02575, SLINC_RS05540 and SLINC_RS42780 are widely found in actinomycetes, while the distributions of DNA-binding sites (DBS) of LmbU are diverse, indicating the regulatory mechanisms of LmbU homologues in various strains are different and complicated.

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Whole Genome Sequence Analysis and Homology Modelling of a 3C Like Peptidase and a Non-Structural Protein 3 of the SARS-CoV-2 Shows Protein Ligand Interaction with an Aza-Peptide and a Noncovalent Lead Inhibitor with Possible Antiviral Properties

10.26434/chemrxiv.11846943.v7 ◽

2020 ◽

Author(s):

Arun Shanker ◽

Divya Bhanu ◽

Anjani Alluri

Keyword(s):

Amino Acids ◽

Binding Sites ◽

Tertiary Structure ◽

Vaccine Development ◽

Homology Modelling ◽

Whole Genome Sequence ◽

Whole Genome ◽

Structural Protein ◽

Ligand Interaction ◽

Percent Identity

The family of viruses belonging to Coronaviridae mainly consist of virulent pathogens that have a zoonotic property, Severe Acute Respiratory Syndrome (SARS-CoV) and Middle East Respiratory Syndrome (MERS-CoV) of this family have emerged before and now the SARS-CoV-2 has emerged in China. Characterization of spike glycoproteins, polyproteins and other viral proteins from viruses are important for vaccine development. Homology modelling of these proteins with known templates offers the opportunity to discover ligand binding sites and explore the possible antiviral properties of these protein ligand complexes. Any information emerging from these protein models can be used for vaccine development. In this study we did a complete bioinformatic analysis, sequence alignment, comparison of multiple sequences and homology modelling of the <a>SARS-CoV-2 </a>whole genome sequences, the spike protein and the polyproteins for homology with known proteins, we also analysed receptor binding sites in these models for possible binding with ligands that exhibit antiviral properties. Our results showed that the tertiary structure of the polyprotein isolate SARS-CoV-2_HKU-SZ-001_2020 had 98.94 percent identity with SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors. <a>Our results indicate that a part of the viral genome </a><a>(residues 3268 -3573 in Frame 2 with 306 amino acids) of the SARS-CoV-2 virus isolate Wuhan-Hu-1 (Genbank Accession Number MN908947.3) </a>when modelled with template 2a5i of the PDB database had 96 percent identity with a 3C like peptidase of SARS-CoV which has ability to bind with Aza-Peptide Epoxide (APE) which is known for irreversible inhibition of SARS-CoV main peptidase. The part of the genome (residues 1568-1882 in Frame 2 with 315 amino acids) when modelled with template 3e9s of the PDB database had 82 percent identity with a papain-like protease/deubiquitinase which when complexed with ligand GRL0617 acts as inhibitor which can block SARS-CoV replication. The regions studied was conserved in more than 90 genomes of SARS-CoV-2. It is possible that these viral inhibiters can be used for vaccine development for the SARS-CoV-2.

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Cefiderocol Activity against Clinical Pseudomonas aeruginosa Isolates Exhibiting Ceftolozane-Tazobactam Resistance

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab311 ◽

2021 ◽

Author(s):

Patricia J Simner ◽

Stephan Beisken ◽

Yehudit Bergman ◽

Andreas E Posch ◽

Sara E Cosgrove ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Binding Sites ◽

Whole Genome ◽

The Novel ◽

Broth Microdilution ◽

Mechanisms Of Resistance ◽

Fold Reduction ◽

Target Binding

Abstract Objective Mutations in the AmpC-AmpR region are associated with treatment-emergent ceftolozane-tazobactam (TOL-TAZ) and ceftazidime-avibactam (CAZ-AVI) resistance. We sought to determine if these mutations impact susceptibility to the novel cephalosporin-siderophore compound cefiderocol. Methods Thirty-two paired isolates from 16 patients with index P. aeruginosa isolates susceptible to TOL-TAZ and subsequent P. aeruginosa isolates available after TOL-TAZ exposure from January 2019 to December 2020 were included. TOL-TAZ, CAZ-AVI, imipenem-relebactam (IMI-REL), and cefiderocol minimum inhibitory concentrations (MICs) were determined using broth microdilution. Whole genome sequencing of paired isolates was used to identify mechanisms of resistance to cefiderocol that emerged, focusing on putative mechanisms of resistance to cefiderocol or earlier siderophore-antibiotic conjugates based on the previously published literature. Results Analyzing the 16 pairs of P. aeruginosa isolates, ≥4-fold increases in cefiderocol MICs occurred in 4 of 16 isolates. Cefiderocol non-susceptibility criteria was met for only 1 of the 4 isolates, using Clinical and Laboratory Standards Institute criteria. Specific mechanisms identified included the following: AmpC E247K (2 isolates), MexR A66V and L57D (1 isolate each), and AmpD G116D (1 isolate) substitutions. For both isolates with AmpC E247K mutations, ≥4-fold MIC increases occurred for both TOL-TAZ and CAZ-AVI, while a ≥4-fold reduction in IMI-REL MICs was observed. Conclusions Our findings suggest that alterations in the target binding sites of P. aeruginosa derived AmpC β-lactamases have the potential to reduce the activity of three of four novel β-lactams (i.e., ceftolozane-tazobactam, ceftazidime-avibactam, and cefiderocol) and potentially increase susceptibility to imipenem-relebactam. These findings are in need of validation in a larger cohort.

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Finding functional disease-associated non-coding variation using next-generation sequencing

10.1101/060285 ◽

2016 ◽

Author(s):

Paolo Devanna ◽

Xiaowei Sylvia Chen ◽

Joses Ho ◽

Dario Gajewski ◽

Alessandro Gialluisi ◽

...

Keyword(s):

Next Generation Sequencing ◽

Binding Sites ◽

Large Scale ◽

Sequence Data ◽

Whole Genome Sequence ◽

Next Generation Sequencing Data ◽

Whole Genome ◽

Next Generation ◽

Whole Exome ◽

Generation Sequencing

ABSTRACTNext generation sequencing has opened the way for the large scale interrogation of cohorts at the whole exome, or whole genome level. Currently, the field largely focuses on potential disease causing variants that fall within coding sequences and that are predicted to cause protein sequence changes, generally discarding non-coding variants. However non-coding DNA makes up ~98% of the genome and contains a range of sequences essential for controlling the expression of protein coding genes. Thus, potentially causative non-coding variation is currently being overlooked. To address this, we have designed an approach to assess variation in one class of non-coding regulatory DNA; the 3′UTRome. Variants in the 3'UTR region of genes are of particular interest because 3'UTRs are responsible for modulating protein expression levels via their interactions with microRNAs. Furthermore they are amenable to large scale analysis as 3′UTR-microRNA interactions are based on complementary base pairing and as such can be predicted in silico at the genome-wide level. We report a strategy for identifying and functionally testing variants in microRNA binding sites within the 3'UTRome and demonstrate the efficacy of this pipeline in a cohort of language impaired children. Using whole exome sequence data from 43 probands, we extracted variants that lay within 3'UTR microRNA binding sites. We identified a common variant (SNP) in a microRNA binding site and found this SNP to be associated with an endophenotype of language impairment (non-word repetition). We showed that this variant disrupted microRNA regulation in cells and was linked to altered gene expression in the brain, suggesting it may represent a risk factor contributing to SLI. This work demonstrates that biologically relevant variants are currently being under-investigated despite the wealth of next-generation sequencing data available and presents a simple strategy for interrogating non-coding regions of the genome. We propose that this strategy should be routinely applied to whole exome and whole genome sequence data in order to broaden our understanding of how non-coding genetic variation underlies complex phenotypes such as neurodevelopmental disorders.

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Analysis of Whole Genome Sequences and Homology Modelling of a 3C Like Peptidase and a Non-Structural Protein of the Novel Coronavirus COVID-19 Shows Protein Ligand Interaction with an Aza-Peptide and a Noncovalent Lead Inhibitor with Possible Antiviral Properties

10.31219/osf.io/2zuea ◽

2020 ◽

Author(s):

Arun Shanker ◽

Divya Bhanu ◽

Anajani Alluri

Keyword(s):

Binding Sites ◽

Tertiary Structure ◽

Vaccine Development ◽

Homology Modelling ◽

Whole Genome ◽

The Novel ◽

Structural Protein ◽

Genome Sequences ◽

Ligand Interaction ◽

Percent Identity

The family of viruses belonging to Coronaviridae mainly consist of virulent pathogens that have a zoonotic property, Severe Respiratory Syndrome (SARS-CoV) and Middle East Respiratory Syndrome (MERS-CoV) of this family have emerged before and now the Novel COVID-19 has emerged in China. Characterization of spike glycoproteins, polyproteins and other viral proteins from viruses are important for vaccine development. Homology modelling of these proteins with known templates offers the opportunity to discover ligand binding sites and possible antiviral properties of these protein ligand complexes. Any information emerging from these protein models can be used for vaccine development. In this study we did a complete bioinformatic analysis, sequence alignment, comparison of multiple sequences and homology modelling of the Novel COVID-19 whole genome sequences, the spike protein and the polyproteins for homology with known proteins, we also analysed receptor binding sites in these models for possible vaccine development. Our results showed that the tertiary structure of the polyprotein isolate COVID-19 _HKU-SZ-001_2020 had 98.94 percent identity with SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors. Our results indicate that a part of the viral genome (residues 254 to 13480 in Frame 2 with 4409 amino acids) of the Novel COVID-19 virus isolate Wuhan-Hu-1 (Genbank Accession Number MN908947.3) when modelled with template 2a5i of the PDB database had 96 percent identity with a 3C like peptidase of SARS-CoV which has ability to bind with Aza-Peptide Epoxide (APE) which is known for irreversible inhibition of SARS-CoV main peptidase. The part of the genome when modelled with template 3e9s of the PDB database had 82 percent identity with a papain-like protease/deubiquitinase which when complexed with ligand GRL0617 acts as inhibitor which can block SARS-CoV replication. It is possible that these viral inhibiters can be used for vaccine development for the Novel COVID-19.

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Using whole-genome sequencing to implicate the androgen receptor as the predominant driver of DNA breakpoints and fusion events in prostate cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2014.32.4_suppl.67 ◽

2014 ◽

Vol 32 (4_suppl) ◽

pp. 67-67 ◽

Cited By ~ 1

Author(s):

Niall Corcoran ◽

Geoff Macintyre ◽

Matthew Hong ◽

Clare Slogget ◽

Haroon Naeem ◽

...

Keyword(s):

Prostate Cancer ◽

Androgen Receptor ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Receptor Binding ◽

Binding Sites ◽

Whole Genome ◽

Structural Rearrangements ◽

Novel Gene ◽

Close Proximity

67 Background: Structural rearrangements in cancers genomes have the potential to disrupt normal gene function and result in a selective growth advantage, either by inactivating tumour suppressors or creating novel gene fusions with oncogenic gain-of-function. Specific fusion genes identified to date are found in particular tumor types rather than being present in all cancers suggesting there are tissue-specific mechanisms underlying these events. The most well-known fusion event in prostate cancer is TMPRSS2-ERG. Recent studies have suggested that androgen receptor may play a role in the formation of TMPRSS2-ERG fusions, bringing the two loci in close proximity in the nucleus and facilitating DNA strand break and repair along with AR associated enzymes. Methods: To explore this mechanism more comprehensively, we performed whole-genome sequencing of 14 prostate cancers from seven patients as well as paired whole blood controls. Results: Across the cancer genomes we identified approximately 4,500 high confidence DNA breakpoints and found that a large proportion of these breakpoints were in close proximity to curated androgen receptor binding sites. Furthermore, when we examined breakpoints in 11 other cancers from the TCGA and ICGC projects, we identified a similar association with androgen (and estrogen) receptor binding sites specifically in hormone-dependent tumour types, suggesting a role for steroid hormone receptors in the formation of cancer driving structural rearrangements. In addition, in at least one patient, the formation of a novel gene fusion contributed directly to the lethal evolution of his tumour. Conclusions: These data suggest that the androgen receptor drives genome wide breakpoints and novel fusion events in prostate cancer.

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Abstract 202: Enrichment of Transcription Factor Binding Sites in the Promoter Regions of Differentially Expressed Genes in Vascular Smooth Muscle Cells from Abdominal Aortic Aneuryms.

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.33.suppl_1.a202 ◽

2013 ◽

Vol 33 (suppl_1) ◽

Author(s):

Nathan Airhart ◽

John Curci

Keyword(s):

Gene Ontology ◽

Transcription Factor ◽

Binding Sites ◽

Developmental Process ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Whole Genome ◽

Promoter Regions ◽

Factor Binding ◽

Upregulated Genes

Background We have previously shown that VSMC from AAA are unique compared to cells from normal aorta (NAA) and carotid endarterectomy (CEA) with increased production of matrix metalloproteinases and elastin degrading activity. The purpose of this study was to explore the mechanisms behind this phenotype. Methods Tissue for VSMC cultures was obtained from patients undergoing AAA repair and CEA. NAA tissue was obtained from renal transplant patients (NAA). Total RNA was isolated from VSMC and subjected to whole-genome microarray. Enrichment of binding sites for transcription factors (TF) within 5 kD of transcription start sites of upregulated genes were identified using Whole Genome rVista. Enriched gene ontology terms were identified using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Results Gene profiles of 22 AAA, 29 CEA, and 17 NAA cell lines were compared. We identified 120 upregulated genes in AAA-VSMC relative to NAA and CEA-VSMC (FDR<0.05). Analysis of transcription factor binding sites of these genes showed enrichment of TFs including members of the ETS, AP-1, and Rel/Ankyrin families. Gene ontology (GO) revealed enrichment of developmental process and immune system genes. Analysis by cell compartment showed enrichment of extracellular matrix and intermediate filament cytoskeleton genes (Table 1). Conclusion This is the first study to demonstrates enrichment of TF families such as ETS, AP-1 and Rel-Ankyrin in AAA VSMC. This suggests that VSMC in AAA may not just be responding to inflammatory or other local stimuli, but may be directly contributing to the ECM changes that define AAA.

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Reprogramming of DNA methylation at NEUROD2-bound sequences during cortical neuron differentiation

Science Advances ◽

10.1126/sciadv.aax0080 ◽

2019 ◽

Vol 5 (10) ◽

pp. eaax0080 ◽

Cited By ~ 6

Author(s):

Maria A. Hahn ◽

Seung-Gi Jin ◽

Arthur X. Li ◽

Jiancheng Liu ◽

Zhijun Huang ◽

...

Keyword(s):

Dna Methylation ◽

Binding Sites ◽

Bisulfite Sequencing ◽

Dna Demethylation ◽

Whole Genome ◽

Dna Hypomethylation ◽

Embryonic Neurogenesis ◽

Genome Bisulfite Sequencing ◽

Developing Neurons

The characteristics of DNA methylation changes that occur during neurogenesis in vivo remain unknown. We used whole-genome bisulfite sequencing to quantitate DNA cytosine modifications in differentiating neurons and their progenitors isolated from mouse brain at the peak of embryonic neurogenesis. Localized DNA hypomethylation was much more common than hypermethylation and often occurred at putative enhancers within genes that were upregulated in neurons and encoded proteins crucial for neuronal differentiation. The hypomethylated regions strongly overlapped with mapped binding sites of the key neuronal transcription factor NEUROD2. The 5-methylcytosine oxidase ten-eleven translocation 2 (TET2) interacted with NEUROD2, and its reaction product 5-hydroxymethylcytosine accumulated at the demethylated regions. NEUROD2-targeted differentially methylated regions retained higher methylation levels in Neurod2 knockout mice, and inducible expression of NEUROD2 caused TET2-associated demethylation at its in vivo binding sites. The data suggest that the reorganization of DNA methylation in developing neurons involves NEUROD2 and TET2-mediated DNA demethylation.

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Engineering and optimising deaminase fusions for genome editing

Nature Communications ◽

10.1038/ncomms13330 ◽

2016 ◽

Vol 7 (1) ◽

Cited By ~ 38

Author(s):

Luhan Yang ◽

Adrian W. Briggs ◽

Wei Leong Chew ◽

Prashant Mali ◽

Marc Guell ◽

...

Keyword(s):

Genome Editing ◽

Binding Sites ◽

Chromosomal Abnormalities ◽

Whole Genome ◽

Bacterial Cells ◽

Site Specific ◽

Cytidine Deaminases ◽

Genome Modification ◽

Dna Binding Affinity ◽

Cytidine Deamination

Abstract Precise editing is essential for biomedical research and gene therapy. Yet, homology-directed genome modification is limited by the requirements for genomic lesions, homology donors and the endogenous DNA repair machinery. Here we engineered programmable cytidine deaminases and test if we could introduce site-specific cytidine to thymidine transitions in the absence of targeted genomic lesions. Our programmable deaminases effectively convert specific cytidines to thymidines with 13% efficiency in Escherichia coli and 2.5% in human cells. However, off-target deaminations were detected more than 150 bp away from the target site. Moreover, whole genome sequencing revealed that edited bacterial cells did not harbour chromosomal abnormalities but demonstrated elevated global cytidine deamination at deaminase intrinsic binding sites. Therefore programmable deaminases represent a promising genome editing tool in prokaryotes and eukaryotes. Future engineering is required to overcome the processivity and the intrinsic DNA binding affinity of deaminases for safer therapeutic applications.

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Whole Genome Sequence Analysis and Homology Modelling of a 3C Like Peptidase and a Non-Structural Protein 3 of the SARS-CoV-2 Shows Protein Ligand Interaction with an Aza-Peptide and a Noncovalent Lead Inhibitor with Possible Antiviral Properties

10.26434/chemrxiv.11846943.v6 ◽

2020 ◽

Author(s):

Arun Shanker ◽

Divya Bhanu ◽

Anjani Alluri

Keyword(s):

Amino Acids ◽

Binding Sites ◽

Tertiary Structure ◽

Vaccine Development ◽

Homology Modelling ◽

Whole Genome Sequence ◽

Whole Genome ◽

Structural Protein ◽

Ligand Interaction ◽

Percent Identity

The family of viruses belonging to Coronaviridae mainly consist of virulent pathogens that have a zoonotic property, Severe Acute Respiratory Syndrome (SARS-CoV) and Middle East Respiratory Syndrome (MERS-CoV) of this family have emerged before and now the SARS-CoV-2 has emerged in China. Characterization of spike glycoproteins, polyproteins and other viral proteins from viruses are important for vaccine development. Homology modelling of these proteins with known templates offers the opportunity to discover ligand binding sites and explore the possible antiviral properties of these protein ligand complexes. Any information emerging from these protein models can be used for vaccine development. In this study we did a complete bioinformatic analysis, sequence alignment, comparison of multiple sequences and homology modelling of the <a>SARS-CoV-2 </a>whole genome sequences, the spike protein and the polyproteins for homology with known proteins, we also analysed receptor binding sites in these models for possible binding with ligands that exhibit antiviral properties. Our results showed that the tertiary structure of the polyprotein isolate SARS-CoV-2_HKU-SZ-001_2020 had 98.94 percent identity with SARS-Coronavirus NSP12 bound to NSP7 and NSP8 co-factors. <a>Our results indicate that a part of the viral genome </a><a>(residues 3268 -3573 in Frame 2 with 306 amino acids) of the SARS-CoV-2 virus isolate Wuhan-Hu-1 (Genbank Accession Number MN908947.3) </a>when modelled with template 2a5i of the PDB database had 96 percent identity with a 3C like peptidase of SARS-CoV which has ability to bind with Aza-Peptide Epoxide (APE) which is known for irreversible inhibition of SARS-CoV main peptidase. The part of the genome (residues 1568-1882 in Frame 2 with 315 amino acids) when modelled with template 3e9s of the PDB database had 82 percent identity with a papain-like protease/deubiquitinase which when complexed with ligand GRL0617 acts as inhibitor which can block SARS-CoV replication. The regions studied was conserved in more than 90 genomes of SARS-CoV-2. It is possible that these viral inhibiters can be used for vaccine development for the SARS-CoV-2.

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