scholarly journals Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

2015 ◽  
Author(s):  
Jenny Chen ◽  
Alexander A. Shishkin ◽  
Xiaopeng Zhu ◽  
Sabah Kadri ◽  
Itay Maza ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
De Novo ◽  
Functional Characterization ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Evolutionary Analysis ◽  
Sequencing Data ◽  
Manual Curation ◽  
First Time

BACKGROUND: Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across multitudes of species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: 1) identifying truly noncoding genes from de novo reconstructed transcriptomes, and 2) prioritizing hundreds of resulting putative lncRNAs from each sample for downstream experimental interrogation. RESULTS: We present slncky, a computational lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-Sequencing data and further prioritizes lncRNAs by characterizing selective constraint as a proxy for function. Our filtering pipeline is comparable to manual curation efforts and more sensitive than previously published approaches. Further, we develop, for the first time, a sensitive alignment pipeline for aligning lncRNA loci and propose new evolutionary metrics relevant for both sequence and transcript evolution. Our analysis reveals that selection acts in several distinct patterns, and uncovers two notable classes of lncRNAs: one showing strong purifying selection at RNA sequence and another where constraint is restricted to the regulation but not the sequence of the transcript. CONCLUSION: Our novel comparative methods for lncRNAs reveals 233 constrained lncRNAs out of tens of thousands of currently annotated transcripts, which we believe should be prioritized for further interrogation. To aid in their analysis we provide the slncky Evolution Browser as a resource for experimentalists.

scholarly journals Pathogenicity and selective constraint on variation near splice sites

2018 ◽  
Author(s):  
Jenny Lord ◽  
Giuseppe Gallone ◽  
Patrick J. Short ◽  
Jeremy F. McRae ◽  
Holly Ironfield ◽  
...  
Keyword(s):  
Splice Site ◽  
Developmental Disorders ◽  
De Novo ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Splice Sites ◽  
Sequencing Data ◽  
Pathogenic Variants ◽  
Unbiased Manner ◽  
Functional Relevance

AbstractMutations which perturb normal pre-mRNA splicing are significant contributors to human disease. We used exome sequencing data from 7,833 probands with developmental disorders (DD) and their unaffected parents, as well as >60,000 aggregated exomes from the Exome Aggregation Consortium, to investigate selection around the splice site, and quantify the contribution of splicing mutations to DDs. Patterns of purifying selection, a deficit of variants in highly constrained genes in healthy subjects and excess de novo mutations in patients highlighted particular positions within and around the consensus splice site of greater functional relevance. Using mutational burden analyses in this large cohort of proband-parent trios, we could estimate in an unbiased manner the relative contributions of mutations at canonical dinucleotides (73%) and flanking non-canonical positions (27%), and calculated the positive predictive value of pathogenicity for different classes of mutations. We identified 18 patients with likely diagnostic de novo mutations in dominant DD-associated genes at non-canonical positions in splice sites. We estimate 35-40% of pathogenic variants in non-canonical splice site positions are missing from public databases.

scholarly journals Identification and Functional Characterization of the CVOMT and EOMT Genes Promoters from Ocimum Basilicum L

2021 ◽  
Author(s):  
Fatemeh Khakdan ◽  
Zahra Shirazi ◽  
Mojtaba Ranjbar
Keyword(s):  
Water Deficit ◽  
Transcriptional Control ◽  
Functional Characterization ◽  
Pcr Analysis ◽  
Water Deficit Stress ◽  
Specific Expression ◽  
Stress Dependent ◽  
First Time ◽  
Dependent Mechanism

Abstract Methyl chavicol and methyl eugenol are important phenylpropanoid compounds previously purified from basil. These compounds are significantly enhanced by the water deficit stress-dependent mechanism. Here, for the first time, pObCVOMT and pObEOMT promoters were extracted by the genome walking method. They were then cloned into the upstream of the β-glucuronidase (GUS) reporter gene to identify the pattern of GUS water deficit stress-specific expression. Histochemical GUS assays showed in transgenic tobacco lines bearing the GUS gene driven by pObCVOMT and pObEOMT promoters, GUS was strongly expressed under water deficit stress. qRT-PCR analysis of pObCVOMT and pObEOMT transgenic plants confirmed the histochemical assays, indicating that the GUS expression is also significantly induced and up-regulated by increasing density of water deficit stress. This indicates these promoters are able to drive inducible expression. The cis-acting elements analysis showed that the pObCVOMT and pObEOMT promoters contained dehydration or water deficit-related transcriptional control elements.

scholarly journals Functional characterization of motif sequences under purifying selection

2013 ◽  
Vol 41 (4) ◽  
pp. 2105-2120 ◽  
Author(s):  
D.-H. Chen ◽  
A. Y.-F. Chang ◽  
B.-Y. Liao ◽  
C.-H. Yeang
Keyword(s):  
Functional Characterization ◽  
Purifying Selection

Circular RNA profiling reveals abundant and diverse circRNAs of SARS-CoV-2, SARS-CoV and MERS-CoV origin

2020 ◽  
Author(s):  
Shaomin Yang ◽  
Hong Zhou ◽  
Ruth Cruz-Cosme ◽  
Mingde Liu ◽  
Jiayu Xu ◽  
...  
Keyword(s):  
De Novo ◽  
Splice Junction ◽  
Circular Rna ◽  
Circular Rnas ◽  
Sequencing Data ◽  
Rna Profiling ◽  
Systematic Strategy ◽  
Coronavirus Infection ◽  
Abundance And Diversity ◽  
First Time

ABSTRACTCircular RNAs (circRNAs) encoded by DNA genomes have been identified across host and pathogen species as parts of the transcriptome. Accumulating evidences indicate that circRNAs play critical roles in autoimmune diseases and viral pathogenesis. Here we report that RNA viruses of the Betacoronavirus genus of Coronaviridae, SARS-CoV-2, SARS-CoV and MERS-CoV, encode a novel type of circRNAs. Through de novo circRNA analyses of publicly available coronavirus-infection related deep RNA-Sequencing data, we identified 351, 224 and 2,764 circRNAs derived from SARS-CoV-2, SARS-CoV and MERS-CoV, respectively, and characterized two major back-splice events shared by these viruses. Coronavirus-derived circRNAs are more abundant and longer compared to host genome-derived circRNAs. Using a systematic strategy to amplify and identify back-splice junction sequences, we experimentally identified over 100 viral circRNAs from SARS-CoV-2 infected Vero E6 cells. This collection of circRNAs provided the first line of evidence for the abundance and diversity of coronavirus-derived circRNAs and suggested possible mechanisms driving circRNA biogenesis from RNA genomes. Our findings highlight circRNAs as an important component of the coronavirus transcriptome.SummaryWe report for the first time that abundant and diverse circRNAs are generated by SARS-CoV-2, SARS-CoV and MERS-CoV and represent a novel type of circRNAs that differ from circRNAs encoded by DNA genomes.

scholarly journals Contribution of retrotransposition to developmental disorders

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Eugene J. Gardner ◽  
Elena Prigmore ◽  
Giuseppe Gallone ◽  
Petr Danecek ◽  
Kaitlin E. Samocha ◽  
...  
Keyword(s):  
Developmental Disorders ◽  
De Novo ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Protein Coding ◽  
Genome Wide ◽  
De Novo Gene ◽  
The Impact ◽  
Transcribed Sequences

Abstract Mobile genetic Elements (MEs) are segments of DNA which can copy themselves and other transcribed sequences through the process of retrotransposition (RT). In humans several disorders have been attributed to RT, but the role of RT in severe developmental disorders (DD) has not yet been explored. Here we identify RT-derived events in 9738 exome sequenced trios with DD-affected probands. We ascertain 9 de novo MEs, 4 of which are likely causative of the patient’s symptoms (0.04%), as well as 2 de novo gene retroduplications. Beyond identifying likely diagnostic RT events, we estimate genome-wide germline ME mutation rate and selective constraint and demonstrate that coding RT events have signatures of purifying selection equivalent to those of truncating mutations. Overall, our analysis represents a comprehensive interrogation of the impact of retrotransposition on protein coding genes and a framework for future evolutionary and disease studies.

scholarly journals Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Safia Zeghbib ◽  
Róbert Herczeg ◽  
Gábor Kemenesi ◽  
Brigitta Zana ◽  
Kornélia Kurucz ◽  
...  
Keyword(s):  
Geographical Location ◽  
Data Sets ◽  
Evolutionary Analysis ◽  
Evolutionary Patterns ◽  
Host Genus ◽  
Evolution Analysis ◽  
Zoonotic Viruses ◽  
History Of ◽  
First Time

Abstract Bats are reservoirs of numerous zoonotic viruses. The Picornaviridae family comprises important pathogens which may infect both humans and animals. In this study, a bat-related picornavirus was detected from Algerian Minioptreus schreibersii bats for the first time in the country. Molecular analyses revealed the new virus originates to the Mischivirus genus. In the operational use of the acquired sequence and all available data regarding bat picornaviruses, we performed a co-evolutionary analysis of mischiviruses and their hosts, to authentically reveal evolutionary patterns within this genus. Based on this analysis, we enlarged the dataset, and examined the co-evolutionary history of all bat-related picornaviruses including their hosts, to effectively compile all possible species jumping events during their evolution. Furthermore, we explored the phylogeny association with geographical location, host-genus and host-species in both data sets.

scholarly journals Purification and Characterization of the Bacterial UDP-GlcNAc:Undecaprenyl-Phosphate GlcNAc-1-Phosphate Transferase WecA

2008 ◽  
Vol 190 (21) ◽  
pp. 7141-7146 ◽  
Author(s):  
Bayan Al-Dabbagh ◽  
Dominique Mengin-Lecreulx ◽  
Ahmed Bouhss
Keyword(s):  
Cell Envelope ◽  
Functional Characterization ◽  
Integral Membrane Protein ◽  
Minimal Length ◽  
Purification And Characterization ◽  
Effects Of Ph ◽  
Undecaprenyl Phosphate ◽  
First Time ◽  
Lipid Substrate

ABSTRACT To date, the structural and functional characterization of proteins belonging to the polyprenyl-phosphate N-acetylhexosamine-1-phosphate transferase superfamily has been relentlessly held back by problems encountered with their overexpression and purification. In the present work and for the first time, the integral membrane protein WecA that catalyzes the transfer of the GlcNAc-1-phosphate moiety from UDP-GlcNAc onto the carrier lipid undecaprenyl phosphate, yielding undecaprenyl-pyrophosphoryl-GlcNAc, the lipid intermediate involved in the synthesis of various bacterial cell envelope components, was overproduced and purified to near homogeneity in milligram quantities. An enzymatic assay was developed, and the kinetic parameters of WecA as well as the effects of pH, salts, cations, detergents, and temperature on the enzyme activity were determined. A minimal length of 35 carbons was required for the lipid substrate, and tunicamycin was shown to inhibit the enzyme at submicromolar concentrations.

Characterization of the AMP-binding protein gene family in Arabidopsis thaliana: will the real acyl-CoA synthetases please stand up?

2000 ◽  
Vol 28 (6) ◽  
pp. 955-957 ◽  
Author(s):  
J. Shockey ◽  
J. Schnurr ◽  
J. Browse
Keyword(s):  
Protein Gene ◽  
De Novo ◽  
Functional Characterization ◽  
De Novo Synthesis ◽  
Triacylglycerol Composition ◽  
Sequence Comparisons ◽  
Triacylglycerol Metabolism ◽  
Binding Protein Gene

One of the most prominent and important topics in modern agricultural biotechnology is the manipulation of oilseed triacylglycerol composition. Towards this goal, we have sought to identify and characterize acyl-CoA synthetases (ACSs), which play an important role in both de novo synthesis and modification of existing lipids. We have identified and cloned 20 different genes that bear strong sequence homology to known ACSs from other organisms. Through sequence comparisons and functional characterization, we have identified several members of this group that encode ACSs, while the other genes fall into the broader category of genes for AMP-binding proteins (AMPBPs). Distinguishing ACSs from AMPBPs will simplify our efforts to understand the role of ACS in triacylglycerol metabolism.

scholarly journals Can proteomics of snake venoms help drug discovery? A study on the venom of spectacled cobra (Naja naja) from the Western Ghats

2021 ◽  
Author(s):  
Muralidharan Vanuopadath ◽  
Dileepkumar Raveendran ◽  
Bipin Gopalakrishnan Nair ◽  
Sudarslal Sadasivan Nair
Keyword(s):  
Glutathione Peroxidase ◽  
Western Ghats ◽  
De Novo ◽  
Cross Reactivity ◽  
Cobra Venom ◽  
Venom Protein ◽  
Naja Naja ◽  
First Time ◽  
The Western Ghats

AbstractVenom proteome profiling is important to understand the toxicology and treatment of persons poisoned by animal venoms. An in depth understanding of the pharmacological mechanisms induced by venom toxins could help in the discovery of novel drug molecules. In the current study, we aimed to delineate the venom toxins of Indian cobra (Naja naja) from the Western Ghats of India through SDS-PAGE and reversed-phase HPLC followed by Q-TOF LC-MS/MS analysis, incorporating PEAKS and Novor assisted de novo sequencing methodologies. A total of 143 proteins distributed across 17 different enzymatic and non-enzymatic venom protein families were identified. The de novo analysis exclusively yielded 59 peptides representing 28 venom protein families. Among these, glutathione peroxidase and endonuclease were reported for the first time in Indian cobra venom. Immunological cross-reactivity of cobra venom assessed using Indian polyvalent antivenoms suggested that VINS showed better EC50 (2.48 µg/mL) values than that of PSAV (6.04 µg/mL) and Virchow (6.03 µg/mL) antivenoms. Also, immunoaffinity chromatography performed using VINS antivenom indicated that it failed to detect few low molecular mass proteins (<10 kDa) that include three-finger toxins, phospholipase A2s and kunitz-type serine protease inhibitors. Taken together, the present study enabled a large-scale characterization of the venom proteome of Naja naja that offers valuable insights on the possible pharmacological mechanisms and future therapeutic potential of hitherto unexplored snake venom constituents.SignificanceThe present work describes the venom proteome characterization of Naja naja collected from the Western Ghats region in India, incorporating conventional proteomics approaches as well as de novo sequencing methods. Interestingly, we were able to determine proteins belong to glutathione peroxidase and endonuclease family, which was not reported in any of the previous studies on Naja naja venom. Notably, our study has reported the highest number of proteins from cobra venom so far. Also, the current study highlights the importance of developing region-specific antivenoms for improving the specificity and cross-neutralization potential of antivenoms.HighlightsProteomics of cobra venom resulted in the identification of 143 proteins.De novo approaches exclusively yielded 59 peptides representing 28 proteins.Glutathione peroxidase and endonuclease were identified for the first time in Indian cobra venom.Indian polyvalent antivenoms showed varying cross-reactivity towards cobra venom.VINS antivenom failed to detect few low molecular mass proteins (< 10 kDa).

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