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Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

ABSTRACT: Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

PROVIDER: PRJNA339241 | ENA |

REPOSITORIES: ENA

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Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

Project description:We analyzed nascent mtDNA-encoded RNA transcripts from GRO-seq and PRO-seq experiments in a collection of diverse human cell lines and Metazoan organisms. Accurate detection of human mtDNA transcription initiation sites (TIS) in the heavy and light strands revealed a novel transcription pausing site near the light strand TIS, upstream to the transcription-replication transition region, in conserved sequence block III (CSBIII). The transcription pausing index varied quantitatively among the cell lines. In addition to the human cell lines experiments, our experiments and analysis of non-human organisms enabled detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. Whereas mammals (chimpanzee, rhesus macaque, rat, and mouse) showed a human-like mtDNA transcription pattern, the invertebrate pattern (Drosophila and C. elegans) profoundly diverged.

2016-09-30 | GSE85747 | GEO

Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution.

Project description: Not available

| S-EPMC5340964 | biostudies-literature

Relaxed initiation pausing of ribosomes drives oncogenic translation

Project description:Using quantitative profiling of initiating ribosomes, we found that ribosomal pausing at the start codon serves as a “brake” to restrain the translational output. In response to oncogenic RAS signaling, the initiation pausing relaxes and contributes to the increased translational flux. Intriguingly, mRNA m6A modification in the vicinity of start codons influences the behavior of initiating ribosomes. Under oncogenic RAS signaling, the reduced mRNA methylation leads to relaxed initiation pausing, thereby promoting malignant transformation and tumor growth. Restored initiation pausing by inhibiting m6A demethylases suppresses RAS-mediated oncogenic translation and subsequent tumorigenesis. Our findings unveil a new paradigm of translational control that is co-opted by RAS mutant cancer cells to drive malignant phenotypes.

2020-12-29 | GSE159210 | GEO

Initiation Pausing of 80S Ribosome on mRNA Is Governed by 5’UTR and Responsive to mTORC1 Signaling

Project description:This SuperSeries is composed of the following subset Series: GSE25331: Initiation pausing of mRNA translation controlled by mTORC1 signaling (microarray) GSE25626: Initiation pausing of mRNA translation controlled by mTORC1 signaling (RNA-Seq) Refer to individual Series

2011-11-12 | E-GEOD-25627 | biostudies-arrayexpress

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

Project description:Transcription regulation occurs frequently through promoter-associated pausing of RNA polymerase II (Pol II). We developed a Precision nuclear Run-On and sequencing assay (PRO-seq) to map the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution. Pol II accumulates immediately downstream of promoters, at intron-exon junctions that are efficiently used for splicing, and over 3' poly-adenylation sites. Focused analyses of promoters reveal that pausing is not fixed relative to initiation sites nor is it specified directly by the position of a particular core promoter element or the first nucleosome. Core promoter elements function beyond initiation, and when optimally positioned they act collectively to dictate the position and strength of pausing . We test this ‘Complex Interaction’ model with insertional mutagenesis of the Drosophila Hsp70 core promoter. Identification of RNA polymerase active sites in Drosophila S2 cell line using PRO-seq method. Identification of transcription initiation sites in Drosophila S2 cell line using PRO-cap method. Identification of changes in RNA polymerase active sites on transgenic Hsp70 promoters upon disruption of DNA sequence elements in 3 transgenic fly lines using PRO-seq method.

2013-02-01 | E-GEOD-42117 | biostudies-arrayexpress

Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for precise termination of mtDNA replication

Project description:The exact in vivo role for RNase H1 in mammalian mitochondria (mtDNA) has been much debated and we show here that it is essential for processing of RNA primers to provide site-specific initiation of mtDNA replication. Without RNase H1, mtDNA replication is instead initiated at non-canonical sites and becomes impaired. Furthermore, RNase H1 is also needed for replication completion and in its absence linear deleted mtDNA molecules extending between the two origins of mtDNA replication are formed. Finally, we report the first patient with a homozygous pathogenic mutation in the hybrid-binding domain (HBD) of RNase H1 causing impaired mtDNA replication. In contrast to catalytically dead pathological variants of RNase H1, this mutant version has enhanced enzyme activity. This finding shows that the RNase H1 activity must be strictly controlled to allow proper regulation of mtDNA replication.

2022-07-13 | GSE199198 | GEO

Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for precise termination of mtDNA replication

Project description:The exact in vivo role for RNase H1 in mammalian mitochondria has been much debated and we show here that it is essential for site-specific formation of RNA primers to allow initiation of mtDNA replication. Without RNase H1, the RNA:DNA hybrids at the replication origins are not processed and mtDNA replication is instead initiated at non-canonical sites and becomes impaired. Furthermore, RNase H1 is also needed for replication completion and in its absence linear deleted mtDNA molecules extending between the two origins of mtDNA replication are formed. Finally, we report the first patient with a homozygous pathogenic mutation in the hybrid-binding domain (HBD) of RNase H1 causing impaired mtDNA replication. In contrast to catalytically dead pathological variants of RNase H1, this mutant version has enhanced enzyme activity. This finding shows that the RNase H1 activity must be strictly controlled to allow proper regulation of mtDNA replication.

2022-08-16 | GSE199771 | GEO

Relaxed initiation pausing of ribosomes drives oncogenic translation

Project description:Relaxed initiation pausing of ribosomes drives oncogenic translation

| PRJNA667952 | ENA

Initiation Pausing of 80S Ribosome on mRNA Is Governed by 5'UTR and Responsive to mTORC1 Signaling (RNA-Seq)

Project description:Recent studies have revealed that the mRNA translation is punctuated by ribosomal pauses through the body of transcripts. However, little is known about its physiological significance and regulatory aspects. Here we present a multi-dimensional ribosome profiling approach to quantify the dynamics of initiation and elongation of 80S ribosomes across the entire transcriptome in mammalian cells. We show that a subset of transcripts have a significant pausing of 80S ribosome around the start codon, creating a major barrier to the commitment of translation elongation. Intriguingly, genes encoding ribosome proteins themselves exhibit an exceptionally high initiation pausing on their transcripts. Our studies also reveal that the initiation pausing is dependent on the 5M-bM-^@M-^Y untranslated region (5M-bM-^@M-^Y UTR) of mRNAs and subject to the regulation of mammalian target of rapamycin complex 1 (mTORC1). Thus, the initiation pausing of 80S ribosome represents a novel regulatory step in translational control mediated by nutrient signaling pathway. Monitor the translational status of transcriptome in mammalian cells under different conditions

2011-11-12 | E-GEOD-25626 | biostudies-arrayexpress

Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for precise termination of mtDNA replication [RNA-seq]

2022-08-16 | GSE199138 | GEO

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