18 papers · ranked by Valyu relevance
Baikang Pei, Cristina Sisu, Adam Frankish, Cédric Howald + 10 more
'Lukas Habegger' 'Xinmeng Jasmine Mu' 'Rachel Harte' 'Suganthi Balasubramanian' 'Andrea Tanzer' 'Mark Diekhans' 'Alexandre Reymond' 'Tim J Hubbard' 'Jennifer Harrow' 'Mark B Gerstein'] Background Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of…
Cristina Sisu, Paul Muir, Adam Frankish, Ian Fiddes + 8 more
Pseudogenes are ideal markers of genome remodeling. In turn, the mouse is an ideal platform for studying them, particularly with the availability of developmental transcriptional data and the sequencing of 18 strains. Here, we present a comprehensive genome-wide annotation of the pseudogenes in the mouse reference…
Cristina Sisu, Paul Muir, Adam Frankish, Ian Fiddes + 8 more
'David Thybert' 'Duncan T. Odom' 'Paul Flicek' 'Thomas M. Keane' 'Tim Hubbard' 'Jennifer Harrow' 'Mark Gerstein'] Pseudogenes are ideal markers of genome remodelling. In turn, the mouse is an ideal platform for studying them, particularly with the recent availability of strain-sequencing and transcriptional data. Here…
Mengyao Sun, Yanni Ma, Jia Yu
Pseudogenes, as important products of genomic evolution, play unique regulatory roles in species adaptation. This review systematically summarizes the major types, functions, and regulatory mechanisms of metazoans pseudogenes, with a particular focus on their formation during primate evolution and the mechanisms…
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…
Deyou Zheng, Mark B Gerstein
Background Pseudogenes are inheritable genetic elements showing sequence similarity to functional genes but with deleterious mutations. We describe a computational pipeline for identifying them, which in contrast to previous work explicitly uses intron-exon structure in parent genes to classify pseudogenes. We require…
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…
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…
Yunzhe Jiang, Beatrice Borsari, Mark Gerstein
Pseudogenes have long been considered non-functional remnants of genome evolution. However, compared to other noncoding elements, their epigenetic regulation remains poorly understood, largely due to their sequence similarity to parent genes and the lack of systematic functional analyses. Here, we leverage matched…
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…
Ze-Hao Zhang, Bo-Han Li, Yin-Wei Wang, Sheng Hu Qian + 4 more
The functional significance of long non-coding RNAs (lncRNAs) remains a subject of debate, largely due to the complexity and cost associated with their validation experiments. However, emerging evidence suggests that pseudogenes, once viewed as genomic relics, may contribute to the origin of functional lncRNA genes. In…
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…
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…
Chris Marriott, Jobran Chebib
Emergence is a phenomenon taken for granted in science but also still not well understood. We have developed a model of artificial genetic evolution intended to allow for emergence on genetic, population and social levels. We present the details of the current state of our environment, agent, and reproductive models.…
Surya Saha, Scott Cain, Ethalinda K. S. Cannon, Nathan Dunn + 7 more
'Andrew Farmer' 'Zhiliang Hu' 'G. Maslen' 'Sierra Moxon' 'Chris Mungall' 'Rex T. Nelson' 'Monica F. Poelchau'] ((1) Boyce Thompson Institute, Ithaca, NY, (2) Ontario Institute for Cancer Research, Toronto, Canada, (3) USDA, Agricultural Research Service, Corn, Insects, and Crop Genetics Research Unit, (4) Truveta…
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…
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…