20 papers · ranked by Valyu relevance
Siobhan A Cusack, Peipei Wang, Serena G Lotreck, Bethany M Moore + 5 more
'Fanrui Meng' 'Jeffrey K Conner' 'Patrick J Krysan' 'Melissa D Lehti-Shiu' 'Shin-Han Shiu'] Title: Abstract Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out…
Siobhan A. Cusack, Peipei Wang, Bethany M. Moore, Fanrui Meng + 4 more
Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out (double/higher-order mutant). Previous studies have identified some characteristics common among redundant gene…
Mikhail Spivakov
Transcription factor binding sites (TFBSs) on the DNA are generally accepted as the key nodes of gene control. However, the multitudes of TFBSs identified in genome-wide studies, some of them seemingly unconstrained in evolution, have prompted the view that in many cases TF binding may serve no biological function.…
Huang-Wen Chen, Sunayan Bandyopadhyay, Dennis E Shasha, Kenneth D Birnbaum
'Kenneth D Birnbaum'] Background Gene duplication can lead to genetic redundancy, which masks the function of mutated genes in genetic analyses. Methods to increase sensitivity in identifying genetic redundancy can improve the efficiency of reverse genetics and lend insights into the evolutionary outcomes of gene…
Neda Barghi, Raymond Tobler, Viola Nolte, Ana Marija Jaksic + 6 more
The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic – i.e. result from selection on a large number of genetic loci – but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the…
Silvia Ambrós, Francisca De la Iglesia, Sttefany M. Rosario, Anamarija Butković + 1 more
Genetic redundancy, understood as the functional overlap of different genes, is a double-edge sword. At the one side, it is thought to serve as a robustness mechanism that buffers the deleterious effect of mutations hitting one of the redundant copies, thus resulting in pseudogenization. At the other side, it is…
André G. Mendonça, Renato J. Alves, José B. Pereira-Leal, Yitzhak Pilpel
'Yitzhak Pilpel'] Biological systems evolved to be functionally robust in uncertain environments, but also highly adaptable. Such robustness is partly achieved by genetic redundancy, where the failure of a specific component through mutation or environmental challenge can be compensated by duplicate components capable…
Guillermo Rodrigo, Juan F. Poyatos
Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show instead how such intrinsic noise enhances information transfer in the presence of…
Nen Saito, Shuji Ishihara, Kunihiko Kaneko
Genetic redundancy is ubiquitous and can be found in any organism. However, it has been argued that genetic redundancy reduces total population fitness, and therefore, redundancy is unlikely to evolve. In this letter, we study an evolutionary model with high-dimensional genotype-phenotype mapping (GPM) to investigate…
Rama S. Singh
Genetics and molecular biology research have progressed for over a century; however, no laws of biology resembling those of physics have been identified, despite the expectations of some physicists. It may be that it is not the properties of matter alone but evolved properties of matter in combination with atomic…
Jessica A. Comstock, Merrill E. Asp, Fatmagül Bahar, Isabella Lee + 2 more
Robustness to the impact of mutation can mitigate phenotypes that have the potential to inform gene function. This robustness is often encoded into the genome through gene duplication, among other mechanisms. Duplication is a source of structurally similar genes that can retain some functional overlap as they diverge…
Eline D. Postma, Lucas G.F. Couwenberg, Roderick N. van Roosmalen, Jordi Geelhoed + 2 more
Saccharomyces cerevisiae, whose evolutionary past includes a whole-genome duplication event, is characterised by a mosaic genome configuration with substantial apparent genetic redundancy. This apparent redundancy raises questions about the evolutionary driving force for genomic fixation of ‘minor’ paralogs and…
Anh Tuan Nguyen, Jian Xu, Diu Khue Luu, Qi Zhao + 1 more
Redundancy is a fundamental characteristic of many biological processes such as those in the genetic, visual, muscular and nervous system; yet its function has not been fully understood. The conventional interpretation of redundancy is that it serves as a faulttolerance mechanism, which leads to redundancy's de facto…
Prasad Vaddepalli, Lynette Fulton, Kay Schneitz
Divergence among duplicate genes is one of the important sources of evolutionary innovation. But, the contribution of duplicate divergence to variation in Arabidopsis accessions is sparsely known. Recently, we studied the role of a cell wall localized protein, ZERZAUST (ZET), in Landsberg erecta (Ler) accession. Here…
Rohan Dandage, Mikhail Papkov, Brittany M. Greco, Dmytro Fishman + 9 more
Gene duplication is common across the tree of life, including yeast and humans, and contributes to genomic robustness. In this study, we examined changes in the subcellular localization and abundance of proteins in response to the deletion of their paralogs originating from the whole-genome duplication event, which is…
Dan Graur
Because genomes are products of natural processes rather than "intelligent design," all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called "rubbish DNA." Rubbish DNA consists of "junk DNA," i.e., the fraction of the genome on which selection does not…
Rebekah L. Rogers, Julie M. Cridland, Ling Shao, Tina T. Hu + 2 more
'Peter Andolfatto' 'Kevin Thornton'] Tandem duplications are an essential source of genetic novelty, and their variation in natural populations is expected to influence adaptive walks. Here, we describe evolutionary impacts of recently-derived, segregating tandem duplications in Drosophila yakuba and Drosophila…
J. M. Deutsch
Does regulation in the genome use collective behavior, similar to the way the brain or deep neural networks operate? Here I make the case for why having a genomic network capable of a high level of computation would be strongly selected for, and suggest how it might arise from biochemical processes that succeed in…
Miloje Rakočević
In some previous works (2018a,b; 2019, 2021a,b, 2022) we presented a new type of mirror symmetry, expressed in the set of protein amino acids; such a symmetry, that it simultaneously represents the semiotic essence of the genetic code. In this paper we provide new evidences that the genetic code represents the unity of…
Benjamin King, Max Winokan, Paul Stevenson, Jim Al-Khalili + 2 more
The adenine-thymine tautomer (A-T) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A-T while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A-T as…