Expression profiles of lncRNAs and mRNAs in fission yeast.
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ABSTRACT:
PROVIDER: PRJNA707002 | ENA |
REPOSITORIES: ENA
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Project description:We explored transcriptional profiles of the fission yeast Schizosaccharomyces pombe. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in wild type cells.
2024-03-04 | GSE168346 | GEO
Project description:We explored transcriptional responses of the fission yeast Schizosaccharomyces pombe to DNA damage. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in response to four DNA damage agents: Camptothecin, Hydroxyurea, Methyl methanesulfonate, Phleomycin.
2024-03-04 | GSE168230 | GEO
Project description:Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long non-coding (aslnc)RNAs by RNA-Seq and/or micro-arrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used Native Elongating Transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site. RNA profiling revealed that the resulting aslncRNAs mainly correspond to cryptic Xrn1/Exo2-sensitive transcripts (XUTs). ChIP-Seq analyses showed that antisense (as)XUTs expression is associated with specific histone modifications patterns. Finally, we showed that asXUTs are controlled by the histone chaperone Spt6 and respond to meiosis induction, in both cases anti-correlating with levels of the paired-sense mRNAs, supporting physiological significance to antisense-mediated gene attenuation. Our work highlights that antisense transcription is much more extended than anticipated and might constitute an additional non-promoter determinant of gene regulation complexity.
2017-11-09 | GSE72381 | GEO
Project description:The fission yeast Schizosaccharomyces pombe
| PRJNA413028 | ENA
Project description:Messenger RNAs (mRNAs) in higher eukaryotes that encode highly expressed proteins important for the assembly of the translational apparatus (e.g. ribosomal proteins) often harbour a pyrimidine-rich motif at the extreme 5’ end known as a 5’ terminal oligopyrimidine (5’TOP) sequence. Members of the La-related protein 1 (LARP1) family control 5’TOP expression through a conserved DM15 motif, but the mechanism is not well understood. 5’TOP motifs have not been described in many lower organisms, but fission yeast (and many other single-celled eukaryotes) harbour a LARP1 homolog that also lacks a DM15 motif. In this work, we show that the fission yeast LARP1 homolog, Slr1p, controls the translation and stability of mRNAs encoding proteins analogous to 5’TOP mRNAs in higher eukaryotes, which we thus refer to as proto-5’TOPs. Our data suggest that the LARP1 DM15 motif and the mRNA 5’TOP motif may be features that were scaffolded over a more fundamental mechanism of LARP1 family member-associated control of gene expression that is still utilized in lower systems.
2023-07-18 | GSE237526 | GEO
Project description:Messenger RNAs (mRNAs) in higher eukaryotes that encode highly expressed proteins important for the assembly of the translational apparatus (e.g. ribosomal proteins) often harbour a pyrimidine-rich motif at the extreme 5’ end known as a 5’ terminal oligopyrimidine (5’TOP) sequence. Members of the La-related protein 1 (LARP1) family control 5’TOP expression through a conserved DM15 motif, but the mechanism is not well understood. 5’TOP motifs have not been described in many lower organisms, but fission yeast (and many other single-celled eukaryotes) harbour a LARP1 homolog that also lacks a DM15 motif. In this work, we show that the fission yeast LARP1 homolog, Slr1p, controls the translation and stability of mRNAs encoding proteins analogous to 5’TOP mRNAs in higher eukaryotes, which we thus refer to as proto-5’TOPs. Our data suggest that the LARP1 DM15 motif and the mRNA 5’TOP motif may be features that were scaffolded over a more fundamental mechanism of LARP1 family member-associated control of gene expression that is still utilized in lower systems.
2023-07-21 | GSE237860 | GEO
Project description:In this study, to identify the target genes of PWRN2, we first constructed lentivirus shRNA vectors to infect the KGN cell lines to gain three KGN/shPWRN2 cell lines with down-regulated PWRN2 expression levels. Then, the expression profiles of mRNAs and lncRNAs in KGN/shPWRN2 cells were determined by microarray. The results revealed thousands of lncRNAs and mRNAs expressed in KGN/shPWRN2. The expression of 176 lncRNAs significantly changed in KGN/shPWRN2 cell lines relative to control NC cell lines. Among these, 118 were up-regulated, whereas 58 were down-regulated. A total of 131 mRNAs significantly changed in expression: 84 were upregulated, and 47 were downregulated (fold change≥2.0, P value<0.05). We further do some bioinformatic analysis for the data. Our results will provide some new information to help us understand the molecular roles of PWRN2.
2018-01-01 | GSE97772 | GEO
Project description:We explored transcriptional responses of the fission yeast to DNA damage. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in wild type cells and cells treated by four DNA damage agents: Camptothecin, Hydroxyurea, Methyl methanesulfonate and Phleomycin.
2024-04-30 | GSE173677 | GEO
Project description:Microarray expression profiles of mRNAs, lncRNAs, and circRNAs in human colorectal cancer
| PRJNA870501 | ENA
Project description:Chemoresistance is a major cause of poor prognosis of breast cancer.More and more mRNAs and lncRNAs are reported to upregulate chemoresistance in breast cancer.To explore the how mRNAs and lncRNAs involved in chemoresistance of breast cancer,we sceened upregulated mRNAs and lncRNA from parental MCF-7 , chemoresistant MCF-7 cells as well as 4 breast cancer tissue sensitive to chemotherapy and 4 resistant to chemotherapy . Total RNA was extracted using Trizol reagent. Agilent Human lncRNA Microarray V6 (4*180K) was used to analyze the global profiling of human lncRNAs and protein-coding transcripts in these samples. The microarray contains 83,835 lncRNAs and 27,233 coding genes.
2020-02-25 | E-MTAB-8787 | biostudies-arrayexpress