PRO-cap from K562 (ENCSR756TPG)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE219707 | GEO | 2022/12/04
REPOSITORIES: GEO
Similar Datasets
Project description:CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, both capped and uncapped nascent RNA was selected and PCR amplification was performed before sequencing. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2022-12-04 | GSE219507 | GEO
Project description:CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only uncapped nascent RNA was selected and no PCR amplification was done. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2022-12-04 | GSE219876 | GEO
Project description:CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only uncapped nascent RNA was selected and PCR amplification was performed before sequencing. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2022-12-04 | GSE219473 | GEO
Project description:CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and no PCR amplification was done. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2022-12-04 | GSE219495 | GEO
Project description:CoPRO experiment. A run-on assay was performed on captured nascent RNA with cap state selection. In this experiment, only capped nascent RNA was selected and PCR amplification was performed before sequencing. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
2022-12-04 | GSE219647 | GEO
Project description:CoPRO adapts PRO-cap for paired end sequencing, and includes a total of three different libraries that were enriched for either capped nascent RNAs only, uncapped nascent RNAs only, or both. With paired end sequencing, each read tells us where an RNA polymerase molecule initiated, and then where its active site is located. Comparison of the libraries for different capping states allows us identify the precise location of pausing, and of where nascent RNAs become capped across the tens of thousands of initiation sites that we detect. The paired nature of the data enabled identification of sites of transcription initiation with unprecedented precision: we could use the pattern of pausing and elongation as a sensitive way of calling real initiation sites, and filter out termination by comparing capped and uncapped treatments. Because CoPRO maps nascent RNA, it is not affected by the post-transcriptional stability of the initiation and pausing events detected. Thus, it puts non-coding transcription (such as eRNAs and upstream divergent RNAs) on an equal footing with longer lived RNAs like mRNA and lncRNAs. With our comprehensive maps of transcription initiation, we are able to compare the architecture of initiation sites with other features of the genome. For this purpose, we chose human K562 cells for direct comparison with dozens of publically available genome-wide datasets.
2018-07-02 | GSE116472 | GEO
Project description:The mRNA 5â² cap is normally essential for eukaryotic mRNA translation, stabilization and transport and both the cap and eIF4E are important elements of post-transcriptional gene regulation. To further our understanding of mRNA translation in the human malaria parasite Plasmodium falciparum, we have investigated the parasite translation initiation factor eIF4E and its interaction with 5â² capped mRNA. We have purified P. falciparum eIF4E as a recombinant protein and demonstrated that it has canonical mRNA 5â² cap binding activity. We used this protein to purify P. falciparum full-length 5â² capped mRNAs from total parasite RNA. Microarray analysis comparing total and eIF4E-purified 5â² capped mRNAs shows that a subset of 34 features were more than two-fold under-represented in the purified RNA sample, including 19 features representative of nuclear transcripts. The uncapped nuclear transcripts may represent a class of mRNAs targeted for storage and cap removal. Keywords: total RNA vs purified capped mRNA The microarray data were obtained from four hybridizations using RNA from two independent GST-PfeIF4E purifications from separate malaria cultures.
2010-06-10 | E-GEOD-6356 | biostudies-arrayexpress
Project description:The mRNA 5′ cap is normally essential for eukaryotic mRNA translation, stabilization and transport and both the cap and eIF4E are important elements of post-transcriptional gene regulation. To further our understanding of mRNA translation in the human malaria parasite Plasmodium falciparum, we have investigated the parasite translation initiation factor eIF4E and its interaction with 5′ capped mRNA. We have purified P. falciparum eIF4E as a recombinant protein and demonstrated that it has canonical mRNA 5′ cap binding activity. We used this protein to purify P. falciparum full-length 5′ capped mRNAs from total parasite RNA. Microarray analysis comparing total and eIF4E-purified 5′ capped mRNAs shows that a subset of 34 features were more than two-fold under-represented in the purified RNA sample, including 19 features representative of nuclear transcripts. The uncapped nuclear transcripts may represent a class of mRNAs targeted for storage and cap removal. Keywords: total RNA vs purified capped mRNA
2007-07-07 | GSE6356 | GEO
Project description:As the most common mRNA cap, the m7G cap impacts the fate of an mRNA in eukaryotes. The metabolite and redox agent, nicotinamide adenine diphosphate (NAD+), can be used as an initiating nucleotide in RNA synthesis to result in NAD+-capped RNAs. Such RNAs have been identified in bacteria, yeast, and human cells, but it is not known whether they exist in plant transcriptomes. The functions of the NAD+ cap in RNA metabolism or translation are still poorly understood. Here, through NAD captureSeq, we show that NAD+- capped RNAs are widespread in Arabidopsis thaliana. NAD+-capped RNAs are predominantly messenger RNAs encoded by the nuclear and mitochondrial genomes but not the chloroplast genome. NAD-capped transcripts from the nuclear genome appear to be spliced and polyadenylated. Furthermore, although NAD+-capped transcripts constitute a small proportion of the total transcript pool from any gene, they are enriched in the polysomal fraction and associate with translating ribosomes. Our findings implicate the existence of as yet unknown mechanisms of translation initiation on NAD+-capped mRNAs. More importantly, our findings suggest that cellular metabolic and/or redox states may influence, and maybe regulated by, mRNA NAD capping.
2019-06-03 | GSE127002 | GEO
Project description:All eukaryotic mRNAs contain a 7-methylguanosine (m7G) cap which serves as a platform that recruits proteins to support essential biological functions such as mRNA processing, nuclear export and cap-dependent translation. Although the caping is one of the first steps of transcription and uncapped mRNA is not functional, the fate and turnover of uncapped transcripts have not been studied extensively. Here, we employed fast nuclear depletion of the capping enzymes in yeast Saccharomyces cerevisiae to uncover the turnover of transcripts that failed to be capped. We found that the degradation of non-capped mRNA is mainly performed by Xrn1, the exonuclease which is predominantly localized in the cytoplasm, and the fate of such transcripts is determined principally by the abundance of their synthesis. Nuclear depletion of the capping enzymes increased the levels of poorly expressed mRNAs and non-coding RNAs and did not affect the distribution of RNA Polymerase II on chromatin. Overall, our data indicate that mRNAs that failed to be capped are not directed to any specific quality-control pathway and are stochastically degraded.
2022-09-25 | GSE213942 | GEO