scholarly journals Promoter architecture determines co-translational regulation of mRNA

2017 ◽  
Author(s):  
Lorena Espinar ◽  
Miquel Àngel Schikora Tamarit ◽  
Júlia Domingo ◽  
Lucas B. Carey
Keyword(s):  
Gene Expression ◽  
Translational Regulation ◽  
Open Reading Frames ◽  
Mrna Levels ◽  
Rna Seq ◽  
Linear Interaction ◽  
Information Encoding ◽  
Inducible Promoters ◽  
Promoter Architecture ◽  
Inducible Genes

AbstractInformation that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of co-translational regulation on mRNA levels is determined by promoter architecture. Using a novel computational-genetic screen of 6402 RNA-seq experiments we identify the RNA helicase Dbp2 as the mechanism by which co-translational regulation is reduced specifically for inducible promoters. Finally, we find that for constitutive genes, but not inducible genes, most of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus the ORF sequence is a major regulator of gene expression, and a non-linear interaction between promoters and ORFs determines mRNA levels.

Temporal and genotypic variation of wound-induced gene expression in bark of Populus tremuloides and P. grandidentata

1998 ◽  
Vol 28 (11) ◽  
pp. 1611-1620 ◽  
Author(s):  
Karen A Thamarus ◽  
Glenn R Furnier
Keyword(s):  
Gene Expression ◽  
Plant Species ◽  
Populus Tremuloides ◽  
Phenylalanine Ammonia Lyase ◽  
Genotypic Variation ◽  
Mrna Levels ◽  
Dot Blot ◽  
Total Rna ◽  
Bark Tissue ◽  
Inducible Genes

In two related experiments, total RNA was extracted from wounded and unwounded bark of young aspen ramets for Northern and dot blot analyses. Wound-inducible genes isolated from other plant species were hybridized to blots, and mRNA levels were estimated. Analyses of variance (ANOVA) were used to examine the significance of experimental factors (wounding, time after wounding, and genotype) affecting variation in mRNA levels. The first experiment examined the timing (0.5-96 h after wounding) of expression of wound-inducible genes in bark tissue of a single Populus tremuloides Michx. genotype. Wounding and variation among RNA samples significantly (p < 0.05) affected mRNA levels of two chitinases (win6, win8) and phenylalanine ammonia-lyase (PAL). The second experiment examined interclonal variation of wound-induced win6 and PAL expression in aspen bark. Ramets of four P. tremuloides and one Populus grandidentata Michx. genotypes were wounded and bark was collected 4, 8, or 12 h later. Genotype, wounding, and time after wounding all significantly affected win6 and PAL mRNA levels, with levels increasing as a result of wounding.

scholarly journals uORFs: Important Cis-Regulatory Elements in Plants

2020 ◽  
Vol 21 (17) ◽  
pp. 6238
Author(s):  
Ting Zhang ◽  
Anqi Wu ◽  
Yaping Yue ◽  
Yu Zhao
Keyword(s):  
Gene Expression ◽  
Translation Initiation ◽  
Translational Control ◽  
Translational Regulation ◽  
Regulatory Elements ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Post Translational Modification ◽  
Cis Acting ◽  
Eukaryotic Mrnas

Gene expression is regulated at many levels, including mRNA transcription, translation, and post-translational modification. Compared with transcriptional regulation, mRNA translational control is a more critical step in gene expression and allows for more rapid changes of encoded protein concentrations in cells. Translation is highly regulated by complex interactions between cis-acting elements and trans-acting factors. Initiation is not only the first phase of translation, but also the core of translational regulation, because it limits the rate of protein synthesis. As potent cis-regulatory elements in eukaryotic mRNAs, upstream open reading frames (uORFs) generally inhibit the translation initiation of downstream major ORFs (mORFs) through ribosome stalling. During the past few years, with the development of RNA-seq and ribosome profiling, functional uORFs have been identified and characterized in many organisms. Here, we review uORF identification, uORF classification, and uORF-mediated translation initiation. More importantly, we summarize the translational regulation of uORFs in plant metabolic pathways, morphogenesis, disease resistance, and nutrient absorption, which open up an avenue for precisely modulating the plant growth and development, as well as environmental adaption. Additionally, we also discuss prospective applications of uORFs in plant breeding.

scholarly journals Cloning of Gonadotropin-Releasing Hormone I Complementary DNAs in Songbirds Facilitates Dissection of Mechanisms Mediating Seasonal Changes in Reproduction

Endocrinology ◽  
2009 ◽  
Vol 150 (4) ◽  
pp. 1826-1833 ◽  
Author(s):  
T. J. Stevenson ◽  
K. S. Lynch ◽  
P. Lamba ◽  
G. F. Ball ◽  
D. J. Bernard
Keyword(s):  
Gene Expression ◽  
Seasonal Changes ◽  
Gene Sequence ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Mrna Levels ◽  
European Starlings ◽  
Important Exception ◽  
Reading Frames

Temperate zone animals exhibit seasonal variation in reproductive physiology. In most cases, seasonal changes in reproductive states are regulated by changes in GnRH1 secretion, rather than synthesis, from the preoptic area (POA)/anterior hypothalamus. An important exception occurs in some songbirds that become photorefractory to the stimulatory effects of long days and show profound decreases in brain GnRH1 protein content. Whether this decline reflects changes in gene expression is unknown because of past failures to measure GNRH1 mRNA levels, due in large part to the absence of available GNRH1 gene sequence in this taxon. Here, we report the first cloning of GNRH1 cDNAs in two songbirds: European starlings and zebra finches. Consistent with the size of the prepro-hormone in other avian and non-avian species, the open-reading frames predict proteins of 91 and 92 amino acids, respectively. Whereas the decapeptide in both species is perfectly conserved with chicken GnRH1, the amino acid identity in the signal peptide and GNRH associated peptide subdomains are significantly less well conserved. At the nucleotide level, the starling and zebra finch coding sequences are approximately 88% identical to each other but only approximately 70% identical to chicken GNRH1. In situ hybridization using radiolabeled cRNA probes demonstrated GNRH1 mRNA expression primarily in the POA, consistent with previous studies on the distribution of the GnRH1-immunoreactive cell bodies. Furthermore, we provide evidence for photoperiod-dependent regulation of GNRH1 mRNA in male starlings. Declines in GNRH1 mRNA levels occur in parallel with testicular involution. Thus, photorefractoriness is associated with decreases in GNRH1 gene expression in the medial POA.

scholarly journals Upstream Open Reading Frames (uORFs) in the Apicomplexan Parasites Plasmodium falciparum and Toxoplasma gondii: Small yet Powerful Regulators of Translation

2021 ◽  
Author(s):  
Chhaminder Kaur ◽  
Swati Patankar
Keyword(s):  
Gene Expression ◽  
Plasmodium Falciparum ◽  
Toxoplasma Gondii ◽  
Translational Regulation ◽  
Life Cycles ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Apicomplexan Parasites ◽  
Upstream Open Reading Frames ◽  
Reading Frames

During their complex life cycles, the Apicomplexan parasites, Plasmodium falciparum and Toxoplasma gondii employ several genetic switches to regulate their gene expression. One such switch is mediated at the level of translation through upstream Open Reading Frames (uORFs). As uORFs are found in the upstream regions of a majority of genes in both the parasites, it is essential that their roles in translational regulation be appreciated to a greater extent. This review provides a comprehensive summary of studies that show uORF-mediated gene regulation in these parasites and highlights examples of clinically and physiologically relevant proteins that exhibit uORF-mediated regulation. In addition to these examples, several studies that use bioinformatics, transcriptomics, proteomics, and ribosome profiling also indicate the possibility of widespread translational regulation by uORFs. Further analysis of genome-wide datasets will reveal novel genes involved in key biological pathways such as cell-cycle progression, stress-response, and pathogenicity. The cumulative evidence from studies presented in this review suggests that uORFs will play crucial roles in regulating gene expression during clinical disease caused by these important human pathogens.

scholarly journals Gene Expression and Regulation from the p7 Promoter of Aedes Densonucleosis Virus

1998 ◽  
Vol 72 (5) ◽  
pp. 4364-4370 ◽  
Author(s):  
Michael W. Kimmick ◽  
Boris N. Afanasiev ◽  
Barry J. Beaty ◽  
Jonathan O. Carlson
Keyword(s):  
Gene Expression ◽  
Translational Regulation ◽  
Transcriptional Control ◽  
Regulation Of Gene Expression ◽  
Open Reading Frames ◽  
Gene Expression And Regulation ◽  
Wild Type ◽  
Nonstructural Proteins ◽  
Study Gene Expression ◽  
Reading Frames

ABSTRACT The nonstructural proteins NS1 and NS2 are thought to be expressed from the p7 promoter of Aedes densonucleosis virus (AeDNV). To study gene expression from the p7 promoter, eight different plasmids were constructed by fusing β-galactosidase or β-glucuronidase into the genome so that the reporter gene was in different open reading frames and under the transcriptional control of the p7 promoter. After transfection into C6/36 Aedes albopictus cells, constructs generated comparable amounts of RNA, but only the NS1 and NS2 fusion constructs produced appreciable levels of active enzyme. NS1 and NS2 fusion constructs contained wild-type AeDNV sequences from the p7 promoter downstream to nucleotide 458. The remaining constructs, with the exception of p7GUS.rf3, lacked some or all of these necessary sequences and inefficiently produced protein. These data suggest that sequences downstream of the p7 promoter play a role in translational regulation of gene expression from the p7 promoter of AeDNV.

scholarly journals Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq

DNA Research ◽  
2019 ◽  
Vol 26 (4) ◽  
pp. 353-363 ◽  
Author(s):  
Xiu Feng ◽  
Yintao Jia ◽  
Ren Zhu ◽  
Kang Chen ◽  
Yifeng Chen
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Tibet Plateau ◽  
Comparative Genomic ◽  
Rna Seq ◽  
Gene Expression Atlas ◽  
Expression Atlas ◽  
Long Read

Abstract The lakes on the Qinghai-Tibet Plateau (QTP) are the largest and highest lake group in the world. Gymnocypris selincuoensis is the only cyprinid fish living in lake Selincuo, the largest lake on QTP. However, its genetic resource is still blank, limiting studies on molecular and genetic analysis. In this study, the transcriptome of G. selincuoensis was first generated by using PacBio Iso-Seq and Illumina RNA-seq. A full-length (FL) transcriptome with 75,435 transcripts was obtained by Iso-Seq with N50 length of 3,870 bp. Among all transcripts, 75,016 were annotated to public databases, 64,710 contain complete open reading frames and 2,811 were long non-coding RNAs. Based on all- vs.-all BLAST, 2,069 alternative splicing events were detected, and 80% of them were validated by reverse transcription polymerase chain reaction (RT-PCR). Tissue gene expression atlas showed that the number of detected expressed transcripts ranged from 37,397 in brain to 19,914 in muscle, with 10,488 transcripts detected in all seven tissues. Comparative genomic analysis with other cyprinid fishes identified 77 orthologous genes with potential positive selection (Ka/Ks > 0.3). A total of 56,696 perfect simple sequence repeats were identified from FL transcripts. Our results provide valuable genetic resources for further studies on adaptive evolution, gene expression and population genetics in G. selincuoensis and other congeneric fishes.

scholarly journals Translation reinitiation at alternative open reading frames regulates gene expression in an integrated stress response

2004 ◽  
Vol 167 (1) ◽  
pp. 27-33 ◽  
Author(s):  
Phoebe D. Lu ◽  
Heather P. Harding ◽  
David Ron
Keyword(s):  
Gene Expression ◽  
Stress Response ◽  
Translational Regulation ◽  
Target Genes ◽  
Open Reading Frames ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Integrated Stress Response ◽  
Eif2α Phosphorylation ◽  
Stressed Cells

Stress-induced eukaryotic translation initiation factor 2 (eIF2) α phosphorylation paradoxically increases translation of the metazoan activating transcription factor 4 (ATF4), activating the integrated stress response (ISR), a pro-survival gene expression program. Previous studies implicated the 5′ end of the ATF4 mRNA, with its two conserved upstream ORFs (uORFs), in this translational regulation. Here, we report on mutation analysis of the ATF4 mRNA which revealed that scanning ribosomes initiate translation efficiently at both uORFs and ribosomes that had translated uORF1 efficiently reinitiate translation at downstream AUGs. In unstressed cells, low levels of eIF2α phosphorylation favor early capacitation of such reinitiating ribosomes directing them to the inhibitory uORF2, which precludes subsequent translation of ATF4 and represses the ISR. In stressed cells high levels of eIF2α phosphorylation delays ribosome capacitation and favors reinitiation at ATF4 over the inhibitory uORF2. These features are common to regulated translation of GCN4 in yeast. The metazoan ISR thus resembles the yeast general control response both in its target genes and its mechanistic details.

scholarly journals A spatiotemporal translatome of mouse tissue development

2020 ◽  
Author(s):  
Hongwei Wang ◽  
Yan Wang ◽  
Jiaqi Yang ◽  
Nan Tang ◽  
Huihui Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Translational Control ◽  
Translational Regulation ◽  
Regulation Of Gene Expression ◽  
Open Reading Frames ◽  
Mouse Tissue ◽  
Specific Gene ◽  
Translational Efficiency ◽  
Tissue Development ◽  
Mouse Tissues

AbstractThe precise regulation of gene expression in mammalian tissues during development results in their functional specification. Although previous transcriptomic and proteomic analyses have provided great biological insights into tissue-specific gene expression and the physiological relevance of these tissues in development, our understanding of translational regulation in developing tissues is lacking. In this study, we performed a spatiotemporally resolved translatome analysis of six mouse tissues at the embryonic and adult stages to quantify the effects of translational regulation and identify new translational components. We quantified the spatial and temporal divergences of gene expression and detected specific changes in gene expression and pathways underlying these divergences. We further showed that dynamic translational control can be achieved by modulating the translational efficiency, which resulted in the enhancement of tissue specificity during development. We also discovered thousands of actively translated upstream open reading frames (ORFs) that exhibited spatiotemporal patterns and demonstrated their regulatory roles in translational regulation. Furthermore, we identified known and novel micropeptides encoded by small ORFs from long noncoding RNAs that are functionally relevant to tissue development. Our data and analyses facilitate a better understanding of the complexity of translational regulation across tissue and developmental spectra and serve as a useful resource of the mouse translatome.

scholarly journals Regulation of gene expression by the APP family in the adult cerebral cortex

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Hye Ji Cha ◽  
Jie Shen ◽  
Jongkyun Kang
Keyword(s):  
Gene Expression ◽  
Cerebral Cortex ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Mrna Levels ◽  
Rna Seq ◽  
Cellular Functions ◽  
Organization Learning ◽  
Transcriptional Changes

AbstractAmyloid precursor protein (APP) is associated with both familial and sporadic forms of Alzheimer’s disease. APP has two homologs, amyloid precursor-like protein 1 and 2 (APLP1 and APLP2), and they have functional redundancy. APP intracellular c-terminal domain (AICD), produced by sequential α- or β- and γ-secretase cleavages, is thought to control gene expression, similarly as the ICD of Notch. To investigate the role of APP family in transcriptional regulation, we examined gene expression changes in the cerebral cortex of APP/APLP1/APLP2 conditional triple knockout (cTKO) mice, in which APP family members are selectively inactivated in excitatory neurons of the postnatal forebrain. Of the 12 previously reported AICD target genes, only Nep and Npas4 mRNA levels were significantly reduced in the cerebral cortex of cTKO mice, compared to littermate controls. We further examined global transcriptional changes by RNA-seq and identified 189 and 274 differentially expressed genes in the neocortex and hippocampus, respectively, of cTKO mice relative to controls. Gene Ontology analysis indicated that these genes are involved in a variety of cellular functions, including extracellular organization, learning and memory, and ion channels. Thus, inactivation of APP family alters transcriptional profiles of the cerebral cortex and affects wide-ranging molecular pathways.

scholarly journals Global Changes in Cellular Gene Expression during Bacteriophage PRD1 Infection

2006 ◽  
Vol 80 (16) ◽  
pp. 8081-8088 ◽  
Author(s):  
Minna M. Poranen ◽  
Janne J. Ravantti ◽  
A. Marika Grahn ◽  
Rashi Gupta ◽  
Petri Auvinen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Gene ◽  
Open Reading Frames ◽  
Global Changes ◽  
Mrna Levels ◽  
Cellular Gene ◽  
Cellular Gene Expression ◽  
Bacteriophage Prd1 ◽  
Genome Level ◽  
Induced Changes

ABSTRACT Virus-induced changes in cellular gene expression and host physiology have been studied extensively. Still, there are only a few analyses covering the entire viral replication cycle and whole-host gene pool expression at the resolution of a single gene. Here we report changes in Escherichia coli gene expression during bacteriophage PRD1 infection using microarray technology. Relative mRNA levels were systematically measured for over 99% of the host open reading frames throughout the infection cycle. Although drastic modifications could be detected in the expression of individual genes, global changes at the whole-genome level were moderate. Notably, the majority of virus-induced changes took place only after the synthesis of virion components, indicating that there is no major reprogramming of the host during early infection. The most highly induced genes encoded chaparones and other stress-inducible proteins.

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