Results 21 to 30 of about 627,878 (334)

Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs

Nature Communications, 2021
Ribosome can mediate piRNA biogenesis from long non-coding RNAs following translation of the short open reading frames. Here the authors show that 80S ribosome also guides piRNA production from 3’ UTR of protein-coding genes after translation of long ...
Yu H. Sun, Ruoqiao Huiyi Wang, Khai Du, Jiang Zhu, Jihong Zheng, Li Huitong Xie, Amanda A. Pereira, Chao Zhang, Emiliano P. Ricci, Xin Zhiguo Li   +9 more
doaj   +1 more source

Standardized annotation of translated open reading frames. [PDF]

Nat Biotechnol, 2022
Ribosome profiling (Ribo-seq) has extended our understanding of the translational ‘vocabulary’ of the human genome, uncovering thousands of open reading frames (ORFs) within long noncoding RNAs (lncRNAs) and presumed untranslated regions (UTRs) of protein-coding genes.
Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S.   +34 more
europepmc   +8 more sources

Selecting Open Reading Frames From DNA [PDF]

Genome Research, 2003
We describe a method to select DNA encoding functional open reading frames (ORFs) from noncoding DNA within the context of a specific vector. Phage display has been used as an example, but any system requiring DNA encoding protein fragments, for example, the yeast two-hybrid system, could be used.
Zacchi P., Sblattero D., FLORIAN, FIORELLA, MARZARI, ROBERTO, Bradbury A.   +4 more
openaire   +3 more sources

Noise reduction by upstream open reading frames. [PDF]

Nat Plants, 2022
AbstractGene expression is prone to burst production, making it a highly noisy process that requires additional controls. Upstream open reading frames (uORFs) are widely present in the 5′ leader sequences of 30–50% of eukaryotic messenger RNAs1–3. The translation of uORFs can repress the translation efficiency of the downstream main coding sequences ...
Wu HW, Fajiculay E, Wu JF, Yan CS, Hsu CP, Wu SH.   +5 more
europepmc   +3 more sources

Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides

BMC Genomics, 2006
Background Approximately 40% of mammalian mRNA sequences contain AUG trinucleotides upstream of the main coding sequence, with a quarter of these AUGs demarcating open reading frames of 20 or more codons.
Wang Xue-Qing, Crowe Mark L, Rothnagel Joseph A   +2 more
doaj   +1 more source

The mitochondrial genome of Cavia aperea

Mitochondrial DNA. Part B. Resources, 2020
Cavia aperea is a wild guinea pig found throughout South America. The previously published mitochondrial sequence for C. aperea was highly divergent from the C. porcellus sequence and contained stop codons within open reading frames.
Azizia Wahedi, Anja Günther, Alexandra Weyrich, Neal Sondheimer   +3 more
doaj   +1 more source

RiboNT: A Noise-Tolerant Predictor of Open Reading Frames from Ribosome-Protected Footprints

Life, 2021
Ribo-seq, also known as ribosome profiling, refers to the sequencing of ribosome-protected mRNA fragments (RPFs). This technique has greatly advanced our understanding of translation and facilitated the identification of novel open reading frames (ORFs ...
Bo Song, Mengyun Jiang, Lei Gao
doaj   +1 more source

REPARATION : ribosome profiling assisted (re-)annotation of bacterial genomes [PDF]

, 2017
Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes.
Giess, Adam, Jonckheere, Veronique, Menschaert, Gerben, Ndah, Elvis, Valen, Eivind, Van Damme, Petra   +5 more
core   +1 more source

Predicting functional upstream open reading frames in Saccharomyces cerevisiae

BMC Bioinformatics, 2009
Background Some upstream open reading frames (uORFs) regulate gene expression (i.e., they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not yet fully understood. In order to get
Kristiansson Erik, Sarv Janeli, Kemp Graham JL, Bryant Christopher H, Selpi, Sunnerhagen Per   +5 more
doaj   +1 more source

Evolutionary divergence of novel open reading frames in cichlids speciation

Scientific Reports, 2020
Novel open reading frames (nORFs) with coding potential may arise from noncoding DNA. Not much is known about their emergence, functional role, fixation in a population or contribution to adaptive radiation.
Shraddha Puntambekar, Rachel Newhouse, Jaime San Miguel Navas, Ruchi Chauhan, Grégoire Vernaz, Thomas Willis, Matthew T. Wayland, Yagnesh Umrania, Eric A. Miska, Sudhakaran Prabakaran   +9 more
doaj   +1 more source