Alternative ORFs and small ORFs: shedding light on the dark proteome

MW Orr, Y Mao, G Storz, SB Qian - Nucleic acids research, 2020 - academic.oup.com
Traditional annotation of protein-encoding genes relied on assumptions, such as one open
reading frame (ORF) encodes one protein and minimal lengths for translated proteins. With …

Transposable elements as essential elements in the control of gene expression

A Gebrie - Mobile DNA, 2023 - Springer
Interspersed repetitions called transposable elements (TEs), commonly referred to as mobile
elements, make up a significant portion of the genomes of higher animals. TEs contribute in …

Function and evolution of upstream ORFs in eukaryotes

H Zhang, Y Wang, J Lu - Trends in biochemical sciences, 2019 - cell.com
There is growing interest in the role of translational regulation in cellular homeostasis during
organismal development. Translation initiation is the rate-limiting step in mRNA translation …

Principles, mechanisms, and biological implications of translation termination–reinitiation

ME Sherlock, LB Galvis, Q Vicens, JS Kieft… - RNA, 2023 - rnajournal.cshlp.org
The gene expression pathway from DNA sequence to functional protein is not as
straightforward as simple depictions of the central dogma might suggest. Each step is highly …

Determinants of genome-wide distribution and evolution of uORFs in eukaryotes

H Zhang, Y Wang, X Wu, X Tang, C Wu, J Lu - Nature Communications, 2021 - nature.com
Upstream open reading frames (uORFs) play widespread regulatory functions in modulating
mRNA translation in eukaryotes, but the principles underlying the genomic distribution and …

A novel active transposon creates allelic variation through altered translation rate to influence protein abundance

G Chen, R Wang, Y Jiang, X Dong, J Xu… - Nucleic acids …, 2023 - academic.oup.com
Protein translation is tightly and precisely controlled by multiple mechanisms including
upstream open reading frames (uORFs), but the origins of uORFs and their role in maize are …

[PDF][PDF] Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae

DE Torres, BPHJ Thomma… - Genome Biology and …, 2021 - academic.oup.com
Transposable elements (TEs) are a major source of genetic and regulatory variation in their
host genome and are consequently thought to play important roles in evolution. Many fungal …

Translational regulation by upstream open reading frames and human diseases

J Silva, R Fernandes, L Romão - The mRNA Metabolism in Human …, 2019 - Springer
Short upstream open reading frames (uORFs) are cis-acting elements located within the 5′-
leader sequence of transcripts and are defined by an initiation codon in-frame with a …

Roles of transposable elements in the different layers of gene expression regulation

D Drongitis, F Aniello, L Fucci, A Donizetti - International Journal of …, 2019 - mdpi.com
The biology of transposable elements (TEs) is a fascinating and complex field of
investigation. TEs represent a substantial fraction of many eukaryotic genomes and can …

Transposable elements, contributors in the evolution of organisms (from an arms race to a source of raw materials)

F Pourrajab, S Hekmatimoghaddam - Heliyon, 2021 - cell.com
There is a concept proposing that the primitive lineages of prokaryotes, eukaryotes, and
viruses emerged from the primordial pool of primitive genetic elements. In this genetic pool …