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Are Proposed Early Genetic Codes Capable of Encoding Viable Proteins?

Annamária Franciska Ángyán, Csaba Ortutay, Zoltán Gáspári
2014 Journal of Molecular Evolution  
All of the investigated early genetic codes give rise to proteins with enhanced disorder and diminished aggregation propensities.  ...  In this paper we investigate structural preferences of hypothetical proteins translated from random DNA segments using the standard genetic code and three of its proposed evolutionarily predecessor models  ...  András Perczel for helpful discussions. Conflicts of interest The authors declare that they have no conflict of interest.  ... 
doi:10.1007/s00239-014-9622-3 pmid:24826911 fatcat:nup44yhvwfaotfm7hdvw5mx2aa

Why is the average collateral effect of synonymous mutations so similar across alternative reading frames? [article]

Stefan Wichmann, Zachary Ardern
2022 bioRxiv   pre-print
One facet of molecular biology where code structure is particularly important is the origin and evolution of overlapping genes.  ...  We have previously reported that the structure of the standard genetic code ensures that synonymous mutations in a protein coding gene will lead to a remarkably similar average "collateral" mutation effect  ...  Is there a functional reason for the maintenance of overlapping genes in genomes, or the use of alternative frame sequences in protein coding more generally?  ... 
doi:10.1101/2022.03.22.485379 fatcat:p5l2lx7duvcr7h5rrs5nerf3qq

The Hidden Codes That Shape Protein Evolution

R. J. Weatheritt, M. M. Babu
2013 Science  
Acknowledgments: We thank the UK Medical Research Council for support. 10 .1126/science.1248425  ...  How widespread is the phenomenon of "regulatory" codes that overlap the genetic code, and how do they constrain the evolution of protein sequences?  ...  The investigation of overlapping codes opens new vistas on the functional interpretation of variation in coding regions and makes it clear that the story of the genetic code has not yet run its course.  ... 
doi:10.1126/science.1248425 pmid:24337281 pmcid:PMC4167339 fatcat:xbp4qfz7kbh7fjrjzesqrpudaq

Computational design of genes encoding completely overlapping protein domains: Influence of genetic code and taxonomic rank [article]

Stefan Wichmann, Siegfried Scherer, Zachary Ardern
2020 bioRxiv   pre-print
Overlapping genes (OLGs) with long protein-coding overlapping sequences are often excluded by genome annotation programs, with the exception of virus genomes.  ...  There is a tendency indicating that the structure of the standard genetic code could be optimized in its ability to create OLGs while conserving mutational robustness.  ...  Influence of the genetic code and code optimality .  ... 
doi:10.1101/2020.09.25.312959 fatcat:yji6vno2sffutjtuwt2z6qrtju

Two Proteins for the Price of One: The Design of Maximally Compressed Coding Sequences [chapter]

Bei Wang, Dimitris Papamichail, Steffen Mueller, Steven Skiena
2006 Lecture Notes in Computer Science  
We also investigate the impact of alternate coding matrices on overlapping sequence design.  ...  We show that the coding sequence of naturally occurring pairs of overlapping genes approach maximum compression.  ...  Acknowledgments We thank Eckard Wimmer for his interest and support. We also thank Chen Zhao, Huei-Chi Chen, and Rahul Sinha for discussions and contributions to this research.  ... 
doi:10.1007/11753681_31 fatcat:ohwz3mjjzfclnjvtvuunaihkoq

Two proteins for the price of one: the design of maximally compressed coding sequences

Bei Wang, Dimitris Papamichail, Steffen Mueller, Steven Skiena
2006 Natural Computing  
We also investigate the impact of alternate coding matrices on overlapping sequence design.  ...  We show that the coding sequence of naturally occurring pairs of overlapping genes approach maximum compression.  ...  Acknowledgments We thank Eckard Wimmer for his interest and support. We also thank Chen Zhao, Huei-Chi Chen, and Rahul Sinha for discussions and contributions to this research.  ... 
doi:10.1007/s11047-006-9031-7 fatcat:mfgwfz66qfclrn7bfdlbxnne4q

Genetics of RA susceptibility, what comes next?

J. Ding, S. Eyre, J. Worthington
2015 RMD Open  
In common with findings in other autoimmune diseases the lead signals for the majority of these loci do not map to known gene sequences.  ...  This is leading to rapid development in our knowledge as to the function of non-coding regions of the genome.  ...  It is also possible for non-coding SNPs to affect the function of non-coding RNA transcripts, such as those of eRNA of lncRNA, by altering their sequence or expression pattern.  ... 
doi:10.1136/rmdopen-2014-000028 pmid:26509058 pmcid:PMC4612696 fatcat:ebaxcrz5svaf3gzrynwhrzjwjy

A practical guide for the functional annotation of genetic variations using SNPnexus

A. Z. Dayem Ullah, N. R. Lemoine, C. Chelala
2013 Briefings in Bioinformatics  
Broader functional annotation of known as well as putative genetic variations is a valuable mean for prioritizing targets in disease studies and large-scale genotyping projects.  ...  the transcriptome/proteome levels with in-depth analysis of potential deleterious effects, inferring physical and cytogenetic mapping, reporting related HapMap data, finding overlaps with potential regulatory  ...  make sense of the generated data and reduce candidate genes/variants to an optimal number for subsequent investigations.  ... 
doi:10.1093/bib/bbt004 pmid:23395730 fatcat:atc3vyqaxndelotkti7tk7e7aq

Detecting conserved coding genomic regions through signal processing of nucleotide substitution patterns

Matteo Ré, Giulio Pavesi
2009 Artificial Intelligence in Medicine  
Because the origins of the signal we investigated in this work is the selective pressure acting on protein coding regions and because this is due to the presence of a near universal genetic code allowing  ...  the use of information encoded in DNA for protein synthesis, we expect the method to be valid for investigations in pairs of species other than human and mouse, as well as the analysis of multiple sequence  ... 
doi:10.1016/j.artmed.2008.07.015 pmid:18809300 fatcat:bwil53semvfdzcgphotdbnv7qy

Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders

David Zhang, Sebastian Guelfi, Sonia Garcia-Ruiz, Beatrice Costa, Regina H. Reynolds, Karishma D'Sa, Wenfei Liu, Thomas Courtin, Amy Peterson, Andrew E. Jaffe, John Hardy, Juan A. Botía (+2 others)
2020 Science Advances  
We explore examples of reannotated disease genes, such as SNCA, for which we experimentally validate a previously unidentified, brain-specific, potentially protein-coding exon.  ...  We anticipate that this resource will facilitate more accurate genetic analysis, with the greatest impact on our understanding of Mendelian and complex neurogenetic disorders.  ...  We also identified a subset of unannotated ERs that have protein coding poten-tial and are highly depleted for genetic variation in humans.  ... 
doi:10.1126/sciadv.aay8299 pmid:32577506 pmcid:PMC7286675 fatcat:wjf4rcgoejendgcdaghunwosdy

Genetic Analysis Workshop 18 single-nucleotide variant prioritization based on protein impact, sequence conservation, and gene annotation

Thomas Nalpathamkalam, Andriy Derkach, Andrew D Paterson, Daniele Merico
2014 BMC Proceedings  
Coding variants were further stratified into protein changing and protein damaging groups based on the effect on protein amino acid sequence.  ...  We defined groups of prioritized variants based on systematic annotation of Genetic Analysis Workshop 18 (GAW18) single-nucleotide variants; we focused on variants detected by whole genome sequencing,  ...  For coding variants, we defined three groups based on expected impact on protein sequence: coding, protein changing, and protein damaging groups.  ... 
doi:10.1186/1753-6561-8-s1-s11 pmid:25519362 pmcid:PMC4143669 fatcat:ejdj3yobezb7pirbxhtebf5q2m

Are Antisense Proteins in Prokaryotes Functional?

Zachary Ardern, Klaus Neuhaus, Siegfried Scherer
2020 Frontiers in Molecular Biosciences  
Many prokaryotic RNAs are transcribed from loci outside of annotated protein coding genes.  ...  There are multiple lines of evidence, however, that many of these newly discovered proteins are of use to the organism. Condition-specific phenotypes have been characterized for a few.  ...  ACKNOWLEDGMENTS Thanks to Christina Ludwig for advice on proteomics references, Christopher Huptas for development of an ORF finder Perl script, and Robin Friedman for providing ribosomal profiling information  ... 
doi:10.3389/fmolb.2020.00187 pmid:32923454 pmcid:PMC7457138 fatcat:zjo6vf7xwncpbcugtkl3ld6cra

Identification of transcribed protein coding sequence remnants within lincRNAs

Sweta Talyan, Miguel A Andrade-Navarro, Enrique M Muro
2018 Nucleic Acids Research  
Long intergenic non-coding RNAs (lincRNAs) are non-coding transcripts >200 nucleotides long that do not overlap protein-coding sequences.  ...  To test this systematically, we developed a novel method that searches for remnants of protein-coding sequences within lincRNA transcripts; the hypothesis is that we can trace back their biogenesis from  ...  We developed an optimized methodology for the alignment of protein-coding sequence remnants within lincRNA genes.  ... 
doi:10.1093/nar/gky608 pmid:29986053 fatcat:4hwbk7cejfbpfbt4wgpwe5nw3a

Small Open Reading Frames: How Important Are They for Molecular Evolution?

Diego Guerra-Almeida, Rodrigo Nunes-da-Fonseca
2020 Frontiers in Genetics  
Before the smORF has been selected for, eventual optimal coding features acquired in the nucleotide sequence could rapidly disappear during genetic drift evolution without fixation.  ...  Before the smORF has been selected for, eventual optimal coding features acquired could rapidly disappear during genetic drift evolution without fixation.  ...  Conflict of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.  ... 
doi:10.3389/fgene.2020.574737 pmid:33193682 pmcid:PMC7606980 fatcat:wjwty52ofbgbtg73aubv4k6agy

Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code

Maria Luisa Chiusano, Fernando Alvarez-Valin, Massimo Di Giulio, Giuseppe D'Onofrio, Gaetano Ammirato, Giovanni Colonna, Giorgio Bernardi
2000 Gene  
required for an optimal structure. q  ...  The nucleotide frequencies in the second codon positions of genes are remarkably different for the coding regions that correspond to different secondary structures in the encoded proteins, namely, helix  ...  Chiusano thanks the European Union for a PhD fellowship. The authors thank Dr O. Clay, Dr R. Ragone and Dr A. Facchiano for useful suggestions for improving the paper.  ... 
doi:10.1016/s0378-1119(00)00521-7 pmid:11164038 fatcat:j2dkj5bhz5a5xgzvi3wyz5dbde
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