20 papers · ranked by Valyu relevance
Yusuf Tutar
Pseudogenes are ubiquitous and abundant in genomes. Pseudogenes were once called “genomic fossils” and treated as “junk DNA” several years. Nevertheless, it has been recognized that some pseudogenes play essential roles in gene regulation of their parent genes, and many pseudogenes are transcribed into RNA. Pseudogene…
Michael J. Milligan, Leonard Lipovich
In the more than one decade since the completion of the Human Genome Project, the prevalence of non-protein-coding functional elements in the human genome has emerged as a key revelation in post-genomic biology. Highlighted by the ENCODE (Encyclopedia of DNA Elements) and FANTOM (Functional Annotation of Mammals)…
Sébastien Cabanac, Christophe Dunand, Catherine Mathé
Formerly considered as part of “junk DNA”, pseudogenes are nowadays known for their role in the post-transcriptional regulation of functional genes. In addition, their identification allows a better understanding of gene evolution in the frame of multigenic families. Despite this, there is, to our knowledge, no fully…
Yi Yang, Pengzhi Wang, Samir El Qaidi, Philip R. Hardwidge + 2 more
'Jinlin Huang' 'Guoqiang Zhu'] Abstract Pseudogenes are defined as “non-functional” copies of corresponding parent genes. The cognition of pseudogenes continues to be refreshed through accumulating and updating research findings. Previous studies have predominantly focused on mammals, but pseudogenes have received…
Mitchell J. Syberg-Olsen, Arkadiy I. Garber, Patrick J. Keeling, John P. McCutcheon + 1 more
Prokaryotic genomes are generally gene dense and encode relatively few pseudogenes, or nonfunctional/inactivated remnants of genes. However, in certain contexts, such as recent ecological shifts or extreme population bottlenecks (such as those experienced by symbionts and pathogens), pseudogenes can quickly accumulate…
Jin Xiao, Manoj Kumar Sekhwal, Pingchuan Li, Raja Ragupathy + 4 more
'Sylvie Cloutier' 'Xiue Wang' 'Frank M. You' 'Lam-Son Phan Tran'] Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally…
Yunzhe Jiang, Yucheng T. Yang, Cristina Sisu, Tianxing He + 2 more
Although gene expression in the brain has been extensively investigated and compared to other tissues, the activity of pseudogenes has not been comprehensively surveyed. Here, leveraging large-scale RNA-seq data, we construct consistent pseudogene expression profiles in human and macaque brains and compare them to 29…
Francesca Magrinelli, Katja Lohmann
The term pseudogene (“pseudo-” from Ancient Greek pseudés, “fake, mimic”) was coined by Jacq et al in 1977 to indicate a nearly identical reproduction of the 5S ribosomal RNA gene paired with the gene itself in a unit tandemly repeated in Xenopus laevis. Thenceforth, similar gene multiplications were recognized for…
Ingrid Lafontaine, Bernard Dujon
Background Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only…
Joannie St-Germain, Muhammad Riaz Khan, Viktoriia Bavykina, Rebecka Desmarais + 4 more
The majority of pseudogenes are generated when an RNA transcript is reverse-transcribed and integrated into the genome at a new location. Pseudogenes are often considered as an imperfect and silent copy of a functional gene because of the accumulation of numerous mutations in their sequence. Here we report the presence…
Dustin M. Hanke, Yiqing Wang, Tal Dagan
Evidence for gene non-functionalization due to mutational processes is found in genomes in the form of pseudogenes. Pseudogenes are known to be rare in prokaryote chromosomes, with the exception of lineages that underwent an extreme genome reduction (e.g., obligatory symbionts). Much less is known about the frequency…
Domenico Rau, Chiara Maria Posadinu, Maria Leonarda Murgia, Davide Fois + 1 more
Pseudogenes provide valuable insight into the evolutionary history of genomes which can be challenging to ascertain through the examination of functional loci alone. This study presents the findings of a comprehensive, two-step genome-wide survey for the identification and characterization of pseudogenes in Fusarium…
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…
Iakes Ezkurdia, David Juan, José Manuel Rodrı́guez, Adam Frankish + 5 more
'Mark Diekhans' 'Jennifer Harrow' 'Jesús Vázquez' 'Alfonso Valencia' 'Michael L. Tress'] - 1. Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, CNIC, Melchor Fernández Almagro, 3, rid, 28029, MadSpain - 2. Structural Biology and Bioinformatics Programme, Spanish National Cancer Research Centre…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Valentina Agoni
Many efforts have been done in order to explain the role of junk DNA, but its function remain to be elucidated. In addition the GC-content variations among species still represent an enigma. Both these two mysteries can have a common explanation: we hypothesize that the role of junk DNA is to preserve the mutations…
Aditi Gupta, Thomas LaBar, Miriam Miyagi, Christoph Adami
Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in amoeba. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as point mutation rate, population size, insertions and deletions, and genome editing mechanisms…
Rebekah L. Rogers, Stephanie L. Grizzard, James Titus‐McQuillan, Katherine D. Bockrath + 4 more
'Katherine D. Bockrath' 'Sagar Patel' 'John P. Wares' 'Jeffrey T. Garner' 'Cathy C. Moore'] Freshwater unionid bivalves currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways, and overfishing. These species…
Heng Li, Maximillian G. Marin, Maha Farhat
Results: We developed pangene, a computational tool to identify gene orientation, gene order and gene copy-number changes in a collection of genomes. Pangene aligns a set of input protein sequences to the genomes, resolves redundancies between protein sequences and constructs a gene graph with each genome represented…
Authors not listed
We present a chemical framework in which adaptive organization is achieved by tuning a gated quantum resonator (adaptive genomic resonator) {driven quantum oscillator} across a driven, dissipative reaction manifold (fitness landscape) {Hamiltonian potential surface}. In this view, catalytic elements set gain and phase…