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

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hong Zhang ◽  
Yirong Wang ◽  
Xinkai Wu ◽  
Xiaolu Tang ◽  
Changcheng Wu ◽  
...  
Keyword(s):  
Driving Forces ◽  
Mrna Translation ◽  
Purifying Selection ◽  
Wide Distribution ◽  
Open Reading Frames ◽  
Translation Regulation ◽  
Effective Population ◽  
Upstream Open Reading Frames ◽  
Functional Peptides ◽  
Regulatory Functions

AbstractUpstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood. Here, we analyze ~17 million putative canonical uORFs in 478 eukaryotic species that span most of the extant taxa of eukaryotes. We demonstrate how positive and purifying selection, coupled with differences in effective population size (Ne), has shaped the contents of uORFs in eukaryotes. Besides, gene expression level is important in influencing uORF occurrences across genes in a species. Our analyses suggest that most uORFs might play regulatory roles rather than encode functional peptides. We also show that the Kozak sequence context of uORFs has evolved across eukaryotic clades, and that noncanonical uORFs tend to have weaker suppressive effects than canonical uORFs in translation regulation. This study provides insights into the driving forces underlying uORF evolution in eukaryotes.

scholarly journals Impacts of uORF codon identity and position on translation regulation

2019 ◽  
Vol 47 (17) ◽  
pp. 9358-9367 ◽  
Author(s):  
Yizhu Lin ◽  
Gemma E May ◽  
Hunter Kready ◽  
Lauren Nazzaro ◽  
Mao Mao ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Open Reading Frames ◽  
Translation Regulation ◽  
Coding Region ◽  
Wide Range ◽  
Range Of Functions ◽  
Functional Peptides ◽  
Regulatory Functions ◽  
The Impact ◽  
Reading Frames

Abstract Translation regulation plays an important role in eukaryotic gene expression. Upstream open reading frames (uORFs) are potent regulatory elements located in 5′ mRNA transcript leaders. Translation of uORFs usually inhibit the translation of downstream main open reading frames, but some enhance expression. While a minority of uORFs encode conserved functional peptides, the coding regions of most uORFs are not conserved. Thus, the importance of uORF coding sequences on their regulatory functions remains largely unknown. We investigated the impact of an uORF coding region on gene regulation by assaying the functions of thousands of variants in the yeast YAP1 uORF. Varying uORF codons resulted in a wide range of functions, including repressing and enhancing expression of the downstream ORF. The presence of rare codons resulted in the most inhibitory YAP1 uORF variants. Inhibitory functions of such uORFs were abrogated by overexpression of complementary tRNA. Finally, regression analysis of our results indicated that both codon identity and position impact uORF function. Our results support a model in which a uORF coding sequence impacts its regulatory functions by altering the speed of uORF translation.

scholarly journals Autonomous functionality of an upstream open reading frame in polycistronic mammalian mRNAs

2018 ◽  
Author(s):  
Shohei Kitano ◽  
Gabriel Pratt ◽  
Keizo Takao ◽  
Yasunori Aizawa
Keyword(s):  
Brain Regions ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Upstream Open Reading Frame ◽  
Translation Regulation ◽  
Reading Frame ◽  
Eukaryotic Translation ◽  
Upstream Open Reading Frames ◽  
Human And Mouse ◽  
Reading Frames

SUMMARYUpstream open reading frames (uORFs) are established as cis-acting elements for eukaryotic translation of annotated ORFs (anORFs) located on the same mRNAs. Here, we identified a mammalian uORF with functions that are independent from anORF translation regulation. Bioinformatics screening using ribosome profiling data of human and mouse brains yielded 308 neurologically vital genes from which anORF and uORFs are polycistronically translated in both species. Among them, Arhgef9 contains a uORF named SPICA, which is highly conserved among vertebrates and stably translated only in specific brain regions of mice. Disruption of SPICA translation by ATG-to-TAG substitutions did not perturb translation or function of its anORF product, collybistin. SPICA-null mice displayed abnormal maternal reproductive performance and enhanced anxiety-like behavior, characteristic of ARHGEF9-associated neurological disorders. This study demonstrates that mammalian uORFs can be independent genetic units, revising the prevailing dogma of the monocistronic gene in mammals, and even eukaryotes.

scholarly journals RNA G-quadruplexes mark repressive upstream open reading frames in human mRNAs

2017 ◽  
Author(s):  
Pierre Murat ◽  
Giovanni Marsico ◽  
Barbara Herdy ◽  
Avazeh Ghanbarian ◽  
Guillem Portella ◽  
...  
Keyword(s):  
Secondary Structures ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Translation Regulation ◽  
Physical Interaction ◽  
Protein Coding ◽  
Upstream Open Reading Frames ◽  
Nucleotide Resolution ◽  
Reading Frames

ABSTRACTRNA secondary structures in the 5’ untranslated regions (UTRs) of mRNAs have been characterised as key determinants of translation initiation. However the role of non-canonical secondary structures, such as RNA G-quadruplexes (rG4s), in modulating translation of human mRNAs and the associated mechanisms remain largely unappreciated. Here we use a ribosome profiling strategy to investigate the translational landscape of human mRNAs with structured 5’ untranslated regions (5’-UTR). We found that inefficiently translated mRNAs, containing rG4-forming sequences in their 5’-UTRs, have an accumulation of ribosome footprints in their 5’-UTRs. We show that rG4-forming sequences are determinants of 5’-UTR translation, suggesting that the folding of rG4 structures thwarts the translation of protein coding sequences (CDS) by stimulating the translation of repressive upstream open reading frames (uORFs). To support our model, we demonstrate that depletion of two rG4s-specialised DEAH-box helicases, DHX36 and DHX9, shifts translation towards rG4-containing uORFs reducing the translation of selected transcripts comprising proto-oncogenes, transcription factors and epigenetic regulators. Transcriptome-wide identification of DHX9 binding sites using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) demonstrate that translation regulation is mediated through direct physical interaction between the helicase and its rG4 substrate. Our findings unveil a previously unknown role for non-canonical structures in governing 5’-UTR translation and suggest that the interaction of helicases with rG4s could be considered as a target for future therapeutic intervention.

Analysis of plant mRNA upstream open reading frames

2005 ◽  
Vol 2 (1) ◽  
pp. 59-66
Author(s):  
Jin Yong-Feng ◽  
Jin Hui-Qing ◽  
Zhou Ping ◽  
Bian Teng-Fei
Keyword(s):  
Plant Species ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Translation Efficiency ◽  
Consensus Sequences ◽  
Codon Context ◽  
Eukaryotic Mrnas ◽  
Upstream Open Reading Frames ◽  
Regulatory Functions ◽  
Reading Frames

AbstractUpstream open reading frames (uORFs) in 5′-untranslated regions (5′-UTRs) of eukaryotic mRNAs play an important role in translation efficiency. Computational analysis of the upstream ATG (uATG) and uORFs of 5′-UTRs of plant mRNAs, adopted from the nucleotide sequence databank, was carried out. Statistical analysis revealed that up to 18% of 5′-UTRs contain uATG, which is much higher than the earlier estimate. Among them, about 50% of the genes have one uATG and nearly 20% of them have two uATGs. About 85% of uORFs are non-overlapping. Thirty per cent of uORF peptides comprise 1–5 aa, and about 80% of uORFs fall in the range of below 20 aa. Sequences flanking the uATG codon differ strikingly from the functional initiation codon and the uATG triplet is more frequently located in a non-optimal context. Consensus sequences of the ATG codon context of mRNA with and without uATG are similar, whereas the ATG codon context of mRNA without uATG is more frequently located in an optimal context than is mRNA with uATG. Most mRNAs with uATGs are possibly related to regulatory functions. In addition, most mRNA uORFs have no similarity between plant species whereas sequences of a few uORFs are highly conserved. For example, mRNA uORFs encoding S-adenosyl-l-methionine decarboxylase (AdoMetDC) share 75–100% homology between plant species, which is much more conserved than AdoMetDC protein.

scholarly journals Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hiro Takahashi ◽  
Shido Miyaki ◽  
Hitoshi Onouchi ◽  
Taichiro Motomura ◽  
Nobuo Idesako ◽  
...  
Keyword(s):  
Regulatory Peptides ◽  
Open Reading Frames ◽  
Dependent Manner ◽  
Wide Range ◽  
Eukaryotic Mrnas ◽  
Taxonomic Range ◽  
Upstream Open Reading Frames ◽  
Functional Peptides ◽  
Reading Frames ◽  
Animal Genomes

Abstract Upstream open reading frames (uORFs) are present in the 5′-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously developed a novel pipeline, ESUCA, to comprehensively identify plant uORFs encoding functional peptides, based on genome-wide identification of uORFs with conserved peptide sequences (CPuORFs). Here, we applied ESUCA to diverse animal genomes, because animal CPuORFs have been identified only by comparing uORF sequences between a limited number of species, and how many previously identified CPuORFs encode regulatory peptides is unclear. By using ESUCA, 1517 (1373 novel and 144 known) CPuORFs were extracted from four evolutionarily divergent animal genomes. We examined the effects of 17 human CPuORFs on mORF translation using transient expression assays. Through these analyses, we identified seven novel regulatory CPuORFs that repressed mORF translation in a sequence-dependent manner, including one conserved only among Eutheria. We discovered a much higher number of animal CPuORFs than previously identified. Since most human CPuORFs identified in this study are conserved across a wide range of Eutheria or a wider taxonomic range, many CPuORFs encoding regulatory peptides are expected to be found in the identified CPuORFs.

scholarly journals Selective 40S footprinting reveals that scanning ribosomes remain cap-tethered in human cells

2019 ◽  
Author(s):  
Jonathan Bohlen ◽  
Kai Fenzl ◽  
Günter Kramer ◽  
Bernd Bukau ◽  
Aurelio A. Teleman
Keyword(s):  
Translation Initiation ◽  
Human Cells ◽  
Open Reading Frames ◽  
Translation Regulation ◽  
List Type ◽  
Translation Efficiency ◽  
Initiation Factors ◽  
Upstream Open Reading Frames

SUMMARYTranslation regulation occurs largely during initiation. Currently, translation initiation can be studied in vitro, but these systems lack features present in vivo and on endogenous mRNAs. Here we develop selective 40S footprinting for visualizing initiating 40S ribosomes on endogenous mRNAs in vivo. It pinpoints where on an mRNA initiation factors join the ribosome to act, and where they leave. We discover that in human cells most scanning ribosomes remain attached to the 5’ cap. Consequently, only one ribosome scans a 5’UTR at a time, and 5’UTR length affects translation efficiency. We discover that eIF3B, eIF4G1 and eIF4E remain on translating 80S ribosomes with a decay half-length of ∼12 codons. Hence ribosomes retain these initiation factors while translating short upstream Open Reading Frames (uORFs), providing an explanation for how ribosomes can re-initiate translation after uORFs in humans. This method will be of use for studying translation initiation mechanisms in vivo.HIGHLIGHTSSelective 40S FPing visualizes regulation of translation initiation on mRNAs in vivoScanning ribosomes are cap-tethered in human cellsOnly one ribosome scans a 5’UTR at a time in human cellsRibosomes retain eIFs during early translation, allowing reinitiation after uORFs

scholarly journals Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes

2019 ◽  
Author(s):  
Hiro Takahashi ◽  
Shido Miyaki ◽  
Hitoshi Onouchi ◽  
Taichiro Motomura ◽  
Nobuo Idesako ◽  
...  
Keyword(s):  
Regulatory Peptides ◽  
Open Reading Frames ◽  
Dependent Manner ◽  
Wide Range ◽  
Eukaryotic Mrnas ◽  
Taxonomic Range ◽  
Upstream Open Reading Frames ◽  
Functional Peptides ◽  
Reading Frames ◽  
Animal Genomes

AbstractUpstream open reading frames (uORFs) are present in the 5’-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously developed a novel pipeline, ESUCA, to comprehensively identify plant uORFs encoding functional peptides, based on genome-wide identification of uORFs with conserved peptide sequences (CPuORFs). Here, we applied ESUCA to diverse animal genomes, because animal CPuORFs have been identified only by comparing uORF sequences between a limited number of species, and how many previously identified CPuORFs encode regulatory peptides is unclear. By using ESUCA, 1,517 (1,373 novel and 144 known) CPuORFs were extracted from four evolutionarily divergent animal genomes. We examined the effects of 17 human CPuORFs on mORF translation using transient expression assays. Through these analyses, we identified seven novel regulatory CPuORFs that repressed mORF translation in a sequence-dependent manner, including one conserved only among Eutheria. We discovered a much higher number of animal CPuORFs than previously identified. Since most human CPuORFs identified in this study are conserved across a wide range of Eutheria or a wider taxonomic range, many CPuORFs encoding regulatory peptides are expected to be found in the identified CPuORFs.

scholarly journals Control of eukaryotic protein synthesis by upstream open reading frames in the 5′-untranslated region of an mRNA

2002 ◽  
Vol 367 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Hedda A. MEIJER ◽  
Adri A.M. THOMAS
Keyword(s):  
Translational Control ◽  
Untranslated Region ◽  
Developmental Stages ◽  
Mrna Translation ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Internal Ribosome Entry ◽  
Control Of Gene Expression ◽  
Reading Frame ◽  
Upstream Open Reading Frames

Control of gene expression is achieved at various levels. Translational control becomes crucial in the absence of transcription, such as occurs in early developmental stages. One of the initiating events in translation is that the 40S subunit of the ribosome binds the mRNA at the 5′-cap structure and scans the 5′-untranslated region (5′-UTR) for AUG initiation codons. AUG codons upstream of the main open reading frame can induce formation of a translation-competent ribosome that may translate and (i) terminate and re-initiate, (ii) terminate and leave the mRNA, resulting in down-regulation of translation of the main open reading frame, or (iii) synthesize an N-terminally extended protein. In the present review we discuss how upstream AUGs can control the expression of the main open reading frame, and a comparison is made with other elements in the 5′-UTR that control mRNA translation, such as hairpins and internal ribosome entry sites. Recent data indicate the flexibility of controlling translation initiation, and how the mode of ribosome entry on the mRNA as well as the elements in the 5′-UTR can accurately regulate the amount of protein synthesized from a specific mRNA.

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