CDS Sequences
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ABSTRACT:
PROVIDER: PRJEB36520 | ENA |
REPOSITORIES: ENA
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Project description:Mature messenger RNAs (mRNAs) consist of coding sequence (CDS) and 5’ and 3’ untranslated regions, typically expected to show similar abundance within a given neuron. Examining mRNA from defined neurons we unexpectedly show extremely common unbalanced expression of cognate 3’ UTR and CDS sequences, observing many genes with high UTR relative to CDS, and others with high CDS to UTR. By in situ hybridization 19 of 19 genes examined show a broad range of UTR to CDS expression ratios in different neurons and other tissues. These ratios may be spatially graded or change with developmental age, but are consistent across animals. Further, for two genes examined, a UTR to CDS ratio above a particular threshold in any given neuron correlated with reduced or undetectable protein expression. Our findings raise questions about the role of isolated UTR sequences in regulation of protein expression, and highlight the importance of separately examining UTR and CDS sequences in gene expression analyses.
2016-03-04 | GSE75596 | GEO
Project description:In this study, distinctive biological CDs derived from Codonopsis pilosula were designed and synthesized. In traditional Chinese medicine, Codonopsis pilosula is considered to be a good blood tonic. The synthesized CDs comprise sp2/sp3 carbon atoms and oxygen/nitrogen-based groups and exhibit good biocompatibility and membrane permeability. The in vitro and in vivo experiments were conducted using an erythroid differentiation system and a mouse model, respectively, and showed that the CDs significantly promote the proliferation of erythroid cells. To reveal the detailed mechanisms of CDs in stimulating erythroblast proliferation, we performed RNA sequencing to analyze the gene expression profile change between untreated andmCDs treated erythroblasts.
2024-12-31 | GSE245893 | GEO
Project description:The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common features. First, they contain long and highly structured CDSs, including a region located around nucleotide 70 after the translation initiation site, second, they are directly bound by Dhh1 with a specific binding distribution and third, complementary experimental approaches suggest that they are activated by Dhh1 at the translation initiation step. Our results show that ribosome translocation is not the only unwinding force of CDS and uncover a novel layer of translational control that involves RNA helicases and RNA folding within CDS providing novel opportunities for regulation of membrane and secretome proteins.
2016-11-04 | GSE87888 | GEO
Project description:Sphingomonas sp. CDS-1 Genome sequencing and assembly
| PRJNA387507 | ENA
Project description:Proteogenomics and ribosome profiling concurrently show that genes may code for both a large and one or more small proteins translated from annotated coding sequences (CDSs) and unannotated alternative open reading frames (named alternative ORFs or altORFs), respectively, but the stoichiometry between large and small proteins translated from the same gene is unknown. \textit{MIEF1}, a gene recently identified as a dual-coding gene, harbours a CDS and a newly annotated and actively translated altORF located in the 5’UTR . Here, we use absolute quantification with stable isotope-labeled peptides and parallel reaction monitoring to determine levels of both proteins in two human cells lines and in human colon. We report that the main \textit{MIEF1} translational product is not the canonical 463 amino acid MiD51 protein but the small 70 amino acid alternative MiD51 protein (altMiD51). These results demonstrate the inadequacy of the single CDS concept and provide a strong argument for modernizing functional annotations of genes.
2018-11-21 | PXD008147 | Pride
Project description:Paracentrotus lividus Msx-1 mRNA, complete CDS
| PRJEB21976 | ENA
Project description:We constructed the electroautotrophic bacteria, i.e., Sporomusa ovata together with CdS for artificial photosynthesis that achieved the conversion of carbon dioxide to the acetate. The proteomic analysis in S.ovata-CdS biohybrids and S.ovata-only groups was conducted to propose the working mechanisms including carbon dioxide fixation, electron transfer, energy metabolism and redox oxygen damage repair.
2021-08-18 | PXD027986 |
Project description:BackgroundGenome assemblies rely on the existence of transcript sequence to stitch together contigs, verify assembly of whole genome shotgun reads, and annotate genes. Functional genomics studies also rely on transcript sequence to create expression microarrays or interpret digital tag data produced by methods such as Serial Analysis of Gene Expression (SAGE). Transcript sequence can be predicted based on reconstruction from overlapping expressed sequence tags (EST) that are obtained by single-pass sequencing of random cDNA clones, but these reconstructions are prone to errors caused by alternative splice forms, transcripts from gene families with related sequences, and expressed pseudogenes. These errors confound genome assembly and annotation. The most useful transcript sequences are derived by complete insert sequencing of clones containing the entire length, or at least the full protein coding sequence (CDS) portion, of the source mRNA. While the bovine genome sequencing initiative is nearing completion, there is currently a paucity of bovine full-CDS mRNA and protein sequence data to support bovine genome assembly and functional genomics studies. Consequently, the production of high-quality bovine full-CDS cDNA sequences will enhance the bovine genome assembly and functional studies of bovine genes and gene products. The goal of this investigation was to identify and characterize the full-CDS sequences of bovine transcripts from clones identified in non-full-length enriched cDNA libraries. In contrast to several recent full-length cDNA investigations, these full-CDS cDNAs were selected, sequenced, and annotated without the benefit of the target organism's genomic sequence, by using comparison of bovine EST sequence to existing human mRNA to identify likely full-CDS clones for full-length insert cDNA (FLIC) sequencing.ResultsThe predicted bovine protein lengths, 5' UTR lengths, and Kozak consensus sequences from 954 bovine FLIC sequences (bFLICs; average length 1713 nt, representing 762 distinct loci) are all consistent with previously sequenced mammalian full-length transcripts.ConclusionIn most cases, the bFLICs span the entire CDS of the genes, providing the basis for creating predicted bovine protein sequences to support proteomics and comparative evolutionary research as well as functional genomics and genome annotation. The results demonstrate the utility of the comparative approach in obtaining predicted protein sequences in other species.
| S-EPMC1314900 | biostudies-literature