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A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies

ABSTRACT: To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data Time-course mRNA profiles of mouse DCs that were stimulated with LPS, and labeled with a short (10 minute) 4sU pulse (0-3 hours, 15 min. intervals, 13 time points).

ORGANISM(S): Mus musculus

SUBMITTER: Michal Rabani

PROVIDER: E-GEOD-56977 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A high resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies

Project description:To monitor the relative regulatory contributions of RNA production, processing and degradation, we sampled RNA from mouse DCs every 15 minutes, for the first 3 hours of their response to LPS (13 samples in total), following a short (10 minute) metabolic labeling pulse with 4sU preceding the sampled time point. We isolated RNA from each of these samples in two ways. First, to comprehensively measure total RNA regardless of its transcription time, we isolated RNA depleted of rRNA. Second, to measure only newly made RNA, we isolated 4sU-labeled RNA, which could only have been transcribed during the 10 minute labeling pulse and is thus enriched for short-lived transcripts, including mRNA precursors and processing intermediates. We deeply sequenced each isolated RNA population to provide the necessary depth to study exons, introns, and splicing junctions across the transcriptome. We showed our approach general utility by also applying it to lincRNAs and early zebrafish development data

2014-12-16 | GSE56977 | GEO

Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [additional RNA]

Project description:Upon recruitment to active enhancers and promoters, RNA polymerase II (Pol_II) generates short non-coding transcripts of unclear function. The mechanisms that control the length and the amount of ncRNAs generated by cis-regulatory elements are largely unknown. Here, we show that the adapter protein WDR82 and its associated complexes actively limit such non-coding transcription. WDR82 targets the SET1/COMPASS H3K4 methyltransferase and the nuclear Protein Phosphatase 1 (PP1) complexes to the initiating Pol_II. WDR82 and PP1 also interact with components of the transcriptional termination and RNA processing machineries. Depletion of WDR82, SET1 or the PP1 subunit required for its nuclear import caused distinct but overlapping transcription termination defects at highly expressed genes, active enhancers and promoters, thus enabling the increased synthesis of unusually long ncRNAs. These data indicate that transcription initiated from cis-regulatory elements is tightly coordinated with termination mechanisms that impose the synthesis of short RNAs. total-mRNAs or 4sU-labeled RNAs from BMDMs, either untreated or treated for with lipopolysaccharide (LPS) for the indicated time. Experiments were carried out in cells containing either a short hairpin targeting either of these: 1) Wdr82; 2) Menin; or a scrambled as a control.

2015-11-09 | E-GEOD-73021 | biostudies-arrayexpress

Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [RNA]

Project description:Upon recruitment to active enhancers and promoters, RNA polymerase II (Pol_II) generates short non-coding transcripts of unclear function. The mechanisms that control the length and the amount of ncRNAs generated by cis-regulatory elements are largely unknown. Here, we show that the adapter protein WDR82 and its associated complexes actively limit such non-coding transcription. WDR82 targets the SET1/COMPASS H3K4 methyltransferase and the nuclear Protein Phosphatase 1 (PP1) complexes to the initiating Pol_II. WDR82 and PP1 also interact with components of the transcriptional termination and RNA processing machineries. Depletion of WDR82, SET1 or the PP1 subunit required for its nuclear import caused distinct but overlapping transcription termination defects at highly expressed genes, active enhancers and promoters, thus enabling the increased synthesis of unusually long ncRNAs. These data indicate that transcription initiated from cis-regulatory elements is tightly coordinated with termination mechanisms that impose the synthesis of short RNAs. polyA-mRNAs or 4sU-labeled RNAs from BMDMs, either untreated or treated for with lipopolysaccharide (LPS) for the indicated time. Experiments were carried out in cells containing either a short hairpin targeting either of these: 1) Wdr82; 2) Set1a+Set1b; 3) Pnuts; or the empty vector (LMP) or a scrambled as a control. When specified, cells were pre-treated with 5,6-Dichloro-1-Î²-D-ribofuranosylbenzimidazole (DRB) in order to prevent RNA polymerase II elongation.

2015-11-09 | E-GEOD-66953 | biostudies-arrayexpress

RNA sequencing of mouse DCs

Project description:RNA-Seq data were targeted for de novo assembly and reconstruction of full-length mouse transcripts. Sequencing of RNA taken from unstimulated DCs.

2011-05-12 | E-GEOD-29209 | biostudies-arrayexpress

Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.

2019-11-12 | PXD010845 | Pride

Functional coordination and HuR-mediated regulation of mRNA stability during T cell activation

2015-10-28 | GSE71382 | GEO

Functional coordination and HuR-mediated regulation of mRNA stability during T cell activation

Project description:We evaluated changes in mRNA stability and transcription using 4sU metabolic pulse labeling across a four hour time course following activation of Jurkat T cells with PMA and PHA Measurement of total mRNA (T) and 4sU labeled mRNA (IP) in three biological replicates at five time points: prior to activation (U) and the first four hours after activation (1-4)

2015-10-28 | E-GEOD-71382 | biostudies-arrayexpress

Mapping Human Transient Transcriptomes Using Single Nucleotide Resolution 4sU Sequencing (SNU-Seq)

Project description:Genomes are pervasively transcribed leading to stable and unstable transcripts that define functional regions of genomes and contribute to cellular phenotypes. Defining comprehensive nascent transcriptomes is pivotal to understand gene regulation, disease processes, and the impact of extracellular signals on cells. However, currently employed methods are laborious, technically challenging and costly. We developed single-nucleotide resolution 4sU-sequencing (SNU-Seq), involving pulse labelling, biotinylation and direct isolation of nascent transcripts. Artificial poly-(A)-tailing of the 3’ most nucleotide of nascent transcripts ensures oligo-d(T) primer-based library preparation and sequencing using commercial 3’ RNA-Seq kits. We show that SNU-Seq is a cost-effective new method generating even read profiles across transcription units. We used SNU-Seq to identify transcription elongation parameters, to map usage of polyadenylation (PAS) sites and novel enhancers. Remarkably, 4sU labelled nascent RNA accumulates short ~100nt transcripts that map to the 5’ end of genes. We show that isolation of these short nascent RNA and sequencing the 5’ and 3’ ends using size-selected SNU-Seq (ssSNU-Seq) provides highly sensitive annotations of mapped and novel TSSs, promoter-proximal pause/termination sites. Thus, SNU-seq and ssSNU-seq combined yield comprehensive transcriptomics data at low cost with high spatial and temporal resolution.

2022-04-01 | GSE179306 | GEO

Minimal metabolic pathway structure is consistent with associated macromolecular interactions.

Project description:We sequenced mRNA of three dual perturbation experiments of E. coli K12 MG1655 changing both genetic and environmental conditions. Each dual perturbation experiment consists of four RNA-seq samples (WT, WT+nutrient supplementation, transcription factor KO, transcription factor KO+nutrient supplementation). The three conditions are: 1) adenine supplementation/nac KO, 2) L-tryptophan supplementation/cra KO, 3) anaerobic/mntR KO. Determination of whether a transcription factor plays a regulatory role in a particular environmental shift by examining differential expression of mRNA levels.

2014-06-30 | E-GEOD-48324 | biostudies-arrayexpress

Temporal response of DCs to LPS stimulation: 4sU_sequencing

Project description:Regulation of RNA levels is critical for the response to external stimuli and determined through the interplay between RNA production, processing and degradation. Despite the centrality of these processes, most global studies of RNA regulation do not distinguish their separate contributions and relatively little is known about how they are temporally integrated. Here, we combine metabolic labeling of RNA with advanced RNA quantification assays and computational modeling to estimate RNA transcription and degradation during the response of immune dendritic cells (DCs) to pathogens, a critical and tightly regulated step in innate immunity. We find that transcription regulation plays a major role in shaping most temporal changes in RNA levels, but that changes in degradation rate are important for shaping sharp M-bM-^@M-^XpeakedM-bM-^@M-^Y responses. We find that transcription changes precede corresponding RNA changes by a small lag (15-30 min), which is shorter for induced than for repressed genes. Massively parallel sequencing of the entire RNA population M-bM-^@M-^S including non-polyadenylated transcripts M-bM-^@M-^S allows us to estimate RNA processing, and identify specific groups of transcripts, mostly cytokines and transcription factors, undergoing enhanced mRNA maturation. This suggests an additional role for splicing in regulating mRNA maturation. Our method provides a new quantitative approach to study key steps in the integrative process of RNA regulation. Sequencing of 4sU-labeled RNA taken from a 7 samples time-series (one sample every 1 hour) during the response of DCs to LPS stimulation. 4-thiouridine was added 45 minutes prior to sample collection. Data presented here for six timepoints: 0, 1, 3-6 hrs. 2hr timepoint not included.

2011-04-24 | E-GEOD-25432 | biostudies-arrayexpress

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