Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA half-life regulation reveals countercyclical regulation of buffered RNAs and RNAs undergoing changes in abundance [trim-Qfilt]

ABSTRACT: RNA half-life regulation reveals countercyclical regulation of buffered RNAs and RNAs undergoing changes in abundance [trim-Qfilt]

PROVIDER: PRJNA1167753 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR30855126_1.fastq.gz	Fastqsanger.gz
	SRR30855126_2.fastq.gz	Fastqsanger.gz
	SRR30855127_1.fastq.gz	Fastqsanger.gz
	SRR30855127_2.fastq.gz	Fastqsanger.gz
	SRR30855128_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 60

Similar Datasets

RNA half-life regulation reveals countercyclical regulation of buffered RNAs and RNAs undergoing changes in abundance [trim-Qfilt]

Project description:mRNA abundances are regulated by the opposing forces of transcription and decay, and yet how decay contributes to mRNA abundance regulation is largely unexplored. We addressed this question using genome-wide data on mRNA rates of abundance change, half-lives, and transcription rates of leaf cells responding to a transdifferentiation stimulusulus. Half-life regulation was common (22% of mRNAs underwent changes in half-life), but RNA abundance regulation by decay alone or by decay that supported transcriptional regulation was rare. Instead, most altered RNA half-lives opposed changes in transcription. Oppositionally regulated mRNAs were characterized by large changes in transcription and decay rates yet changes in mRNA abundances were either modest or undetectable, suggestive of RNA buffering. Oppositionally-regulated and buffered RNAs showed very similar dynamics, suggesting use of a common mechanism. The strongest contributions of RNA decay to RNA abundance regulation was in synergistically regulated transcripts, where rate changes in decay and transcription rates worked together to change RNA abundances.

2024-10-11 | GSE278543 | GEO

RNA half-life regulation reveals countercyclical regulation of buffered RNAs and RNAs undergoing changes in abundance

Project description:RNA half-life regulation reveals countercyclical regulation of buffered RNAs and RNAs undergoing changes in abundance

| PRJNA1167762 | ENA

RNA half-life regulation reveals countercyclical regulation of buffered RNAs and RNAs undergoing changes in abundance

2024-10-11 | GSE278544 | GEO

Explore the effect of m6A reader YTHDF1 on RNAs half-life

Project description:Explore the effect of m6A reader YTHDF1 on RNAs half-life

| PRJNA602480 | ENA

Buffering of transcription rate by mRNA half-life is a conserved feature of Rett syndrome models

Project description:Models of MECP2 dysfunction in Rett syndrome (RTT) assume that transcription rate changes directly correlate with altered steady-state mRNA levels. However, limited evidence suggests that transcription rate changes are buffered by poorly understood compensatory post-transcriptional mechanisms. Here we measure transcription rate and mRNA half-life changes in RTT patient neurons using RATE-seq, and re-interpret nuclear and whole-cell RNAseq from Mecp2 mice. Genes are dysregulated by changing transcription rate only or half-life only and are buffered when both are changed. We utilized classifier models to understand the direction of transcription rate changes based on gene-body DNA sequence, and combined frequencies of three dinucleotides were better predictors than contributions by CA and CG. MicroRNA and RNA-Binding Protein (RBP) motifs were enriched in 3ʹUTRs of genes with half-life changes. Motifs for nuclear localized RBPs were enriched on buffered genes with increased transcription rate. Our findings identify post-transcriptional mechanisms in humans and mice that alter half-life only or buffer transcription rate changes when a transcriptional modulator gene is mutated in a neurodevelopmental disorder.

2023-01-27 | GSE191168 | GEO

Post-transcriptional regulation by the let-7 microRNA and the TRIM-NHL protein LIN41

Project description:Post-transcriptional regulation by the let-7 microRNA and the TRIM-NHL protein LIN41

| PRJNA318055 | ENA

Buffered hypercapnia alters the transcriptional profile in monocytes.

Project description:In monocytes we used RNA-sequencing to investigate the effect of 4hrs of exposure to buffered hypercapnia (10% CO2) compared to normocapnia (5% CO2) with and without the pro-inflammatory stimulus LPS (2.5ug/ml) for the final 2hrs. Buffered hypercapnia causes transcriptional changes associated with altered metabolic function in both the basal and stimulated states.

2023-04-07 | GSE206333 | GEO

Sudden reduction of miRNAs during embryonic development-- cohort, buffered regulation of miRNA in Dorsal Root Ganglion

Project description:Micro RNAs (miRNA) are short, endogenous non-coding RNAs, they function via base pairing with complementary sequences with their targets. With the current advance in modern technologies including Next Generation Sequencing, miRNAs have rapidly emerged as important regulators in various functions in cell proliferation, differentiation, cell death and metabolisms. miRNAs showed specifically important roles in central nerve system development with specific temporal spatial regulation, such as neuronal cell proliferation, neuronal differentiation, cell fate determination, axon outgrowth, dendritogenesis, synaptogenesis, and gliogenesis, neuronal guidance to form neuronal circuits. In this study, we will first focus on how microRNA regulates neuronal specification, proliferation and differentiation by investigating microRNA profiling in Dorsal Root Ganglion (DRG) at different embryonic stages both in chickens and mice. Second, we will investigate how the microRNA expression correlates with important transcription factors and neurotrophic factor receptors during the neuron cell specification, such as Runx3, TrkC. Third, we study the regulated miRNA targets and their impact on neurogenesis and development. Last, we will study how conserved roles of miRNA between mouse and chicken in the neuro-specification. We found dramatic reduction of large amount miRNA during specific embryonic stage. Their target genes overrepresent dentrites, synaps and neurogenesis genes, as well as genes largely involved in transcription. The study shows the importance of miRNA in neuronal development, and they function in cohort, buffered, flexible manner.

2020-03-31 | GSE129264 | GEO

Understanding regulation of KSHV/EBV circular RNAs

Project description:Understanding regulation of KSHV/EBV circular RNAs

| PRJNA694872 | ENA

Regulation of nuclear transcription by mitochondrial RNAs

Project description:Regulation of nuclear transcription by mitochondrial RNAs

| PRJNA873067 | ENA