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Are Proposed Early Genetic Codes Capable of Encoding Viable Proteins?
2014
Journal of Molecular Evolution
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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]
2022
bioRxiv
pre-print
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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
2013
Science
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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]
2020
bioRxiv
pre-print
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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]
2006
Lecture Notes in Computer Science
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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
2006
Natural Computing
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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?
2015
RMD Open
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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
2013
Briefings in Bioinformatics
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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
2009
Artificial Intelligence in Medicine
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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
2020
Science Advances
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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
2014
BMC Proceedings
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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?
2020
Frontiers in Molecular Biosciences
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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
2018
Nucleic Acids Research
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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?
2020
Frontiers in Genetics
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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
2000
Gene
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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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