scholarly journals De novo Identification of Essential Protein Domains from CRISPR/Cas9 Tiling-sgRNA Knockout Screens

2019 ◽  
Author(s):  
Wei He ◽  
Liang Zhang ◽  
Oscar D. Villarreal ◽  
Rongjie Fu ◽  
Ella Bedford ◽  
...  
Keyword(s):  
Drug Targets ◽  
De Novo ◽  
Protein Domains ◽  
Computational Method ◽  
Protein Domain ◽  
Post Translational Modification ◽  
Essential Protein ◽  
N Terminus ◽  
Sgrna Design

AbstractHigh-throughput CRISPR/Cas9 knockout screens using a tiling-sgRNA design permit in situ evaluation of protein domain function. To facilitate de novo identification of essential protein domains from such screens, we developed ProTiler, a computational method for the robust mapping of CRISPR knockout hyper-sensitive (CKHS) regions, which refers to the protein regions that are associated with strong sgRNA dropout effect in the screens. We used ProTiler to analyze a published CRISPR tiling screen dataset, and identified 175 CKHS regions in 83 proteins. Of these CKHS regions, more than 80% overlapped with annotated Pfam domains, including all of the 15 known drug targets in the dataset. ProTiler also revealed unannotated essential domains, including the N-terminus of the SWI/SNF subunit SMARCB1, which we validated experimentally. Surprisingly, the CKHS regions were negatively correlated with phosphorylation and acetylation sites, suggesting that protein domains and post-translational modification sites have distinct sensitivities to CRISPR/Cas9 mediated amino acids loss.

scholarly journals De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Wei He ◽  
Liang Zhang ◽  
Oscar D. Villarreal ◽  
Rongjie Fu ◽  
Ella Bedford ◽  
...  
Keyword(s):  
Drug Targets ◽  
De Novo ◽  
Protein Domains ◽  
Computational Method ◽  
Protein Domain ◽  
Post Translational Modification ◽  
Essential Protein ◽  
N Terminus ◽  
Sgrna Design

Abstract High-throughput CRISPR-Cas9 knockout screens using a tiling-sgRNA design permit in situ evaluation of protein domain function. Here, to facilitate de novo identification of essential protein domains from such screens, we propose ProTiler, a computational method for the robust mapping of CRISPR knockout hyper-sensitive (CKHS) regions, which refer to the protein regions associated with a strong sgRNA dropout effect in the screens. Applied to a published CRISPR tiling screen dataset, ProTiler identifies 175 CKHS regions in 83 proteins. Of these CKHS regions, more than 80% overlap with annotated Pfam domains, including all of the 15 known drug targets in the dataset. ProTiler also reveals unannotated essential domains, including the N-terminus of the SWI/SNF subunit SMARCB1, which is validated experimentally. Surprisingly, the CKHS regions are negatively correlated with phosphorylation and acetylation sites, suggesting that protein domains and post-translational modification sites have distinct sensitivities to CRISPR-Cas9 mediated amino acids loss.

scholarly journals Identification of Essential Protein Domains From High-density Transposon Insertion Sequencing

2021 ◽  
Author(s):  
A.S.M. Zisanur Rahman ◽  
Lukas Timmerman ◽  
Flyn Gallardo ◽  
Silvia T. Cardona
Keyword(s):  
Unknown Function ◽  
Plant Pathogens ◽  
Bacterial Species ◽  
Protein Domains ◽  
Essential Genes ◽  
High Density ◽  
Protein Domain ◽  
Burkholderia Cenocepacia ◽  
Data Set ◽  
Essential Protein

Abstract A first clue to gene function can be obtained by examining whether a gene is required for life in certain standard conditions, that is, whether a gene is essential. In bacteria, essential genes are usually identified by high-density transposon mutagenesis followed by sequencing of insertion sites (Tn-seq). These studies assign the term “essential” to whole genes rather than the protein domain sequences that confer the essential functions. However, genes can code for multiple protein domains that evolve their functions independently. Therefore, when essential genes code for more than one protein domain, only one of them could be essential. In this study, we defined this subset of genes as “essential domain-containing” (EDC) genes. Using a Tn-seq data set built-in Burkholderia cenocepacia K56-2, we developed an in silico pipeline to identify EDC genes and the essential protein domains they encode. We found forty candidate EDC genes and demonstrated growth defect phenotypes using CRISPR interference (CRISPRi). This analysis included two knockdowns of genes encoding the protein domains of unknown function DUF2213 and DUF4148. These essential domains are conserved in more than two hundred bacterial species, including human and plant pathogens. Together, our study suggests that essentiality should be assigned to individual protein domains rather than genes, contributing to a first functional characterization of protein domains of unknown function.

scholarly journals Author Correction: De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Wei He ◽  
Liang Zhang ◽  
Oscar D. Villarreal ◽  
Rongjie Fu ◽  
Ella Bedford ◽  
...  
Keyword(s):  
De Novo ◽  
Protein Domains ◽  
Essential Protein

A novel network-based computational method to predict protein phosphorylation on tyrosine sites

2015 ◽  
Vol 13 (06) ◽  
pp. 1542005 ◽  
Author(s):  
Binghua Wang ◽  
Minghui Wang ◽  
Yujie Jiang ◽  
Dongdong Sun ◽  
Xiaoyi Xu
Keyword(s):  
Tyrosine Phosphorylation ◽  
Computational Methods ◽  
Computational Method ◽  
Superior Performance ◽  
Sequence Information ◽  
Bayesian Decision ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Local Sequence

Phosphorylation plays a great role in regulating a variety of cellular processes and the identification of tyrosine phosphorylation sites is fundamental for understanding the post-translational modification (PTM) regulation processes. Although a lot of computational methods have been developed, most of them only concern local sequence information and few studies focus on the tyrosine sites with in situ PTM information, which refers to different types of PTM occurring on the same modification site. In this study, by constructing the site-modification network that efficiently incorporates in situ PTM information, we introduce a novel network-based computational method, site-modification network-based inference (SMNBI) to predict tyrosine phosphorylation. In order to verify the effectiveness of the proposed method, we compare it with other network-based computational methods. The results clearly show the superior performance of SMNBI. Besides, we extensively compare SMNBI with other sequence-based methods including SVM and Bayesian decision theory. The evaluation demonstrates the power of site-modification network in predicting tyrosine phosphorylation. The proposed method is freely available at http://bioinformatics.ustc.edu.cn/smnbi/ .

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Jacobsen syndrome and neonatal bleeding: report on two unrelated patients

2021 ◽  
Vol 47 (1) ◽  
Author(s):  
Gregorio Serra ◽  
Luigi Memo ◽  
Vincenzo Antona ◽  
Giovanni Corsello ◽  
Valentina Favero ◽  
...  
Keyword(s):  
Developmental Delay ◽  
De Novo ◽  
Comparative Genomic ◽  
Fish Analysis ◽  
Variable Degree ◽  
Jacobsen Syndrome ◽  
Contiguous Gene ◽  
Clinical Consequences ◽  
11Q Deletion

Abstract Introduction In 1973, Petrea Jacobsen described the first patient showing dysmorphic features, developmental delay and congenital heart disease (atrial and ventricular septal defect) associated to a 11q deletion, inherited from the father. Since then, more than 200 patients have been reported, and the chromosomal critical region responsible for this contiguous gene disorder has been identified. Patients’ presentation We report on two unrelated newborns observed in Italy affected by Jacobsen syndrome (JBS, also known as 11q23 deletion). Both patients presented prenatal and postnatal bleeding, growth and developmental delay, craniofacial dysmorphisms, multiple congenital anomalies, and pancytopenia of variable degree. Array comparative genomic hybridization (aCGH) identified a terminal deletion at 11q24.1-q25 of 12.5 Mb and 11 Mb, in Patient 1 and 2, respectively. Fluorescent in situ hybridization (FISH) analysis of the parents documented a de novo origin of the deletion for Patient 1; parents of Patient 2 refused further genetic investigations. Conclusions Present newborns show the full phenotype of JBS including thrombocytopenia, according to their wide 11q deletion size. Bleeding was particularly severe in one of them, leading to a cerebral hemorrhage. Our report highlights the relevance of early diagnosis, genetic counselling and careful management and follow-up of JBS patients, which may avoid severe clinical consequences and lower the mortality risk. It may provide further insights and a better characterization of JBS, suggesting new elements of the genotype-phenotype correlations.

scholarly journals 4E Interacting Protein as a Potential Novel Drug Target for Nucleoside Analogues in Trypanosoma Brucei

2021 ◽  
Vol 9 (4) ◽  
pp. 826
Author(s):  
Dorien Mabille ◽  
Camila Cardoso Santos ◽  
Rik Hendrickx ◽  
Mathieu Claes ◽  
Peter Takac ◽  
...  
Keyword(s):  
Mode Of Action ◽  
Drug Target ◽  
Drug Targets ◽  
De Novo ◽  
Treatment Options ◽  
Adenosine Kinase ◽  
Nucleoside Analogues ◽  
Purine Salvage ◽  
Interacting Protein ◽  
Novel Drug

Human African trypanosomiasis is a neglected parasitic disease for which the current treatment options are quite limited. Trypanosomes are not able to synthesize purines de novo and thus solely depend on purine salvage from the host environment. This characteristic makes players of the purine salvage pathway putative drug targets. The activity of known nucleoside analogues such as tubercidin and cordycepin led to the development of a series of C7-substituted nucleoside analogues. Here, we use RNA interference (RNAi) libraries to gain insight into the mode-of-action of these novel nucleoside analogues. Whole-genome RNAi screening revealed the involvement of adenosine kinase and 4E interacting protein into the mode-of-action of certain antitrypanosomal nucleoside analogues. Using RNAi lines and gene-deficient parasites, 4E interacting protein was found to be essential for parasite growth and infectivity in the vertebrate host. The essential nature of this gene product and involvement in the activity of certain nucleoside analogues indicates that it represents a potential novel drug target.

scholarly journals Associations between Amplification (1q) and Prior Cancer in a Real-World De Novo Myeloma Cohort

2021 ◽  
Author(s):  
Elizabeth B Lamont ◽  
Andrew J Yee ◽  
Stuart L Goldberg ◽  
David S Siegel ◽  
Andrew D Norden
Keyword(s):  
Real World ◽  
Fluorescent In Situ Hybridization ◽  
De Novo ◽  
Chromosome 1 ◽  
Second Malignancies ◽  
Cancer History ◽  
Screening Strategies ◽  
Cytogenetic Testing

Abstract Genomic biomarkers inform treatment in multiple myeloma (MM) making patient clinical data a potential window into MM biology. We evaluated de novo MM patients for associations between specific MM cytogenetic patterns and prior cancer history. Analyzing a MM real-world dataset (RWD), we identified a cohort of 1,769 patients with fluorescent in-situ hybridization (FISH) cytogenetic testing at diagnosis. Fully 241 patients (0.14) had histories of prior cancer(s). Amplification of the long arm of chromosome 1 [amp(1q)] varied by prior cancer history (0.31 with prior cancer vs 0.24 without; p = .02). No other MM translocations, amplifications, or deletions were associated with prior cancers. Amp(1q) and cancer history remained strongly associated in a logistic regression adjusting for patient demographic and disease attributes. The results merit follow-up regarding carcinogenic treatment effects and screening strategies for second malignancies. Broadly the findings suggest analyses of patient-level phenotypic-genomic RWD may accelerate cancer research through hypothesis generating studies.

scholarly journals Giant Cell Carcinosarcoma of the Parotid Gland With a PLAG 1 Translocation in Association With a Pleomorphic Adenoma With HMGA2 Translocation

2020 ◽  
Vol 154 (6) ◽  
pp. 811-815
Author(s):  
Levon Katsakhyan ◽  
Virginia A LiVolsi ◽  
Ara A Chalian ◽  
Paul J Zhang
Keyword(s):  
Salivary Gland ◽  
In Situ Hybridization ◽  
Parotid Gland ◽  
Giant Cell ◽  
Pleomorphic Adenoma ◽  
De Novo ◽  
Sarcomatous Component ◽  
Gland Tumor ◽  
Parotid Gland Tumor

Abstract Objectives Carcinosarcomas of the salivary gland are rare neoplasms and have been described arising de novo or in association with pleomorphic adenoma (PA). PLAG1 and HMGA2 translocations are known to occur in PAs and carcinomas ex PA but are mutually exclusive. Methods We report a case of a carcinosarcoma in the parotid gland of a 77-year-old man with unusual anaplastic sarcomatoid giant cell morphology. Results Microscopically, a small separate PA was found adjacent to the carcinosarcoma. By conventional notion, the PA and carcinosarcoma would be considered related, as carcinosarcomas are well known to arise from PAs (carcinosarcoma ex PA). However, fluorescence in situ hybridization (FISH) assay demonstrated PLAG1 translocation in the carcinosarcoma and HMGA2 translocation in the separate PA. Conclusions These findings support that the carcinosarcoma likely originated from another PA with a PLAG1 translocation or de novo but not from the coexisting PA harboring a different translocation. To our knowledge, the case is the first to demonstrate PLAG1 translocation by FISH in a sarcomatous component of any parotid gland tumor, which may help better classify these tumors. In addition, multiple PAs are commonly found in the salivary gland, and to our knowledge, our case is the first to demonstrate that the same parotid gland can host PAs and PA-related tumors with different translocations.

In Situ Growth of a Cationic Polymer from the N-Terminus of Glucose Oxidase To Regulate H2O2 Generation for Cancer Starvation and H2O2 Therapy

2019 ◽  
Vol 11 (10) ◽  
pp. 9756-9762 ◽  
Author(s):  
Hanjun Hao ◽  
Mengmeng Sun ◽  
Pengyong Li ◽  
Jiawei Sun ◽  
Xinyu Liu ◽  
...  
Keyword(s):  
Glucose Oxidase ◽  
Cationic Polymer ◽  
In Situ Growth ◽  
N Terminus ◽  
H2o2 Generation
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