25 papers · ranked by Valyu relevance
Marc Robinson‐Rechavi
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which allows comparisons which are both large scale and evolutionarily relevant. The…
Rohan Shawn Sunil, Shan Chun Lim, Manoj Itharajula, Marek Mutwil
Elucidating gene function is one of the ultimate goals of plant science. Despite this, only ~15% of all genes in the model plant Arabidopsis thaliana have comprehensively experimentally verified functions. While bioinformatical gene function prediction approaches can guide biologists in their experimental efforts…
Hans Binder, Arsen Arakelyan
The term “gene” was introduced more than a hundred years ago to define a “fundamental physical and functional unit of heredity” [1]. Its use refers back to Mendel’s idea about discrete hereditable units, and it also serves as a reminiscence of Darwin’s pangenesis theory. Watson and Crick’s double helix discovery in…
Jasmine A. Richman, Leah R. Davis, Michael P. Phelps
The genome of many plant and animal species are heavily influenced by ancestral whole genome duplication (WGD) events. These events transform the regulation and function of gene networks, yet the evolutionary forces at work on duplicated genomes are not fully understood. Genes involved in cell surface signaling…
Lerong Li, Momiao Xiong
The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an attractive option to characterize the global changes in transcription. RNA-seq is…
Authors not listed
The reader has undoubtedly noted the conspicuous absence of the word “gene” from the preceding text. The decision to postpone discussion of the term was motivated by the fact that there is no single definition of the term “gene.” For example, the Cambridge Health Institute’s online database entitled “Gene Definitions”…
Claudio Casola, Victor Luria, Nikolaos Vakirlis, Li Zhao + 1 more
The recent Society for Molecular Biology and Evolution Satellite Meeting on De Novo Gene Birth, hosted at Texas A&M University on November 6 to 9, 2023, represented the first-ever opportunity for scientists studying the evolution and biology of de novo genes to gather through a dedicated meeting and discuss about…
Langyu Gu, Chenzheng Li, Xiaobing Mao, Zongfang Wei + 5 more
Genes whose dysfunction do not affect normal survival is a common phenomenon. Are they only meaningless residues during evolution? Here, we identified a fish-specific new gene, which we named lg. Gene knockout resulted in no obvious phenotype in zebrafish, but lg evolves an amino acid mutation that is under positive…
IGVF Consortium
Our genomes influence nearly every aspect of human biology from molecular and cellular functions to phenotypes in health and disease. Human genetics studies have now associated hundreds of thousands of differences in our DNA sequence ("genomic variation") with disease risk and other phenotypes, many of which could…
Yuh Chwen G. Lee, Iuri M. Ventura, Gavin R. Rice, Don-Yuan Chen + 1 more
New genes originated relatively recently and are only present in a subset of species in a phylogeny. Accumulated evidence suggests that new genes, like old genes that are conserved across species, can also take on important functions and be essential for the survival and reproductive success of organisms. While there…
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)…
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…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Evelyn Fox Keller, David Harel, Thomas Zwaka
This paper is a response to the increasing difficulty biologists find in agreeing upon a definition of the gene, and indeed, the increasing disarray in which that concept finds itself. After briefly reviewing these problems, we propose an alternative to both the concept and the word gene-an alternative that, like the…
Reza Rahmanzadeh
First, mutations leading to genetic novelties in a given species during evolution should be guided by the environment surrounding that species. Second, environment and germline are connected with each other via soma-germline messengers e.g., non-coding RNAs (ncRNAs). Third, based on the information that germline…
Michaela Drobek, Nihar R Nayak, Gary Sutkin, Sunil Jaiman
During evolution, gene duplications lead to a naturally increased gene dosage. Duplicated genes can be further retained or eliminated over time by purifying selection pressure. The retention probability is increased by functional diversification and by the acquisition of novel functions. Interestingly, functionally…
Emily L. Rivard, Andrew G. Ludwig, Prajal H. Patel, Anna Grandchamp + 7 more
Comparative genomics has enabled the identification of genes that potentially evolved de novo from non-coding sequences. Many such genes are expressed in male reproductive tissues, but their functions remain poorly understood. To address this, we conducted a functional genetic screen of over 40 putative de novo genes…
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…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Floriane Picolo, Anna Grandchamp, Benoît Piégu, Reiner A. Veitia + 1 more
Gene dosage is important is an important issue both in cell and evolutionary biology. Most genes are present in two copies in eukaryotic cells. The first outstanding exception is monoallelic gene expression (MA) that concerns genes localized on the X chromosome or in regions undergoing parental imprinting in…
J. Peter W. Young
Genes have been in the scientific vocabulary for a hundred years. The term "gene" was proposed by the Danish plant scientist Wilhelm Johannsen in the first decade of the 20th century. For Johannsen, the gene remained an abstract concept, "free of any hypothesis" [1], but others were already pointing to chromosomes as…
Delfi Dorussen, Emilie Knight, James Simmonds, Philippa Borrill
Active transcriptional compensation between gene duplicates (paralogs or homoeologs) has been proposed to facilitate functional redundancy, whereby mutations in multiple gene copies are required before a phenotype is observed. We tested whether transcriptional compensation occurs between homoeologs in response to…
Authors not listed
RNA droplets assembled from co-transcriptionally folded nanostructures have recently emerged as a promising platform for constructing protocells and minimal synthetic cell models. In these systems, a custom-designed DNA template encodes an RNA nanostar, which is produced by transcription and self-assembles into…
Authors not listed
Researching the EEEV virus is challenging due to the virus's high lethality and significant risk. This study employed bioinformatics methods for domain search to investigate the pathogenesis and infection process of the EEEV virus P protein. The results demonstrated that the EEEV virus P protein contains domains that…
Rumiana Tenchov, Janet Sasso, Xinmei Wang, Qiongqiong Angela Zhou
Aging is a dynamic, time-dependent process characterized by a gradual accumulation of cell damage. Continual functional decline in the intrinsic ability of living organisms to accurately regulate homeostasis leads to increased susceptibility and vulnerability to diseases. Anti-aging research has a long history…