Similar Datasets
Project description:Although PGC 1α is well-established as a transcriptional coactivator for the metabolic adaptation of mammalian cells to diverse physiological stresses, its molecular dynamics at the start and during gene transcription are incompletely understood. Previously, we defined a CBP80-binding motif (CBM) within PGC 1α that binds CBP80 at the 5′-cap of nascent transcripts deriving from PGC 1α-responsive genes. Binding verifies proper 5′-cap assembly, after which gene transcription is somehow promoted. Here, using protein immunoprecipitations, size-exclusion chromatography, PRO-seq, RNA-seq, native RIP-seq, RIP-seq footprinting and CUT&RUN, we report that PGC 1α, serving as a DNA−RNA conduit between promoter-bound ERRα and nascent transcript-bound CBP80, overcomes promoter-proximal pausing of RNAPII by competing against the premature transcription termination complex Integrator and also by recruiting P-TEFb. Using mice homozygous for five amino-acid changes in PGC 1α that destroy CBM function, we demonstrate that efficient differentiation of primary myoblasts to myofibers and effective regeneration of skeletal muscle after injury requires PGC 1α binding to CBP80.
2023-01-19 | GSE197275 | GEO
Project description:Although PGC 1α is well-established as a transcriptional coactivator for the metabolic adaptation of mammalian cells to diverse physiological stresses, its molecular dynamics at the start and during gene transcription are incompletely understood. Previously, we defined a CBP80-binding motif (CBM) within PGC 1α that binds CBP80 at the 5′-cap of nascent transcripts deriving from PGC 1α-responsive genes. Binding verifies proper 5′-cap assembly, after which gene transcription is somehow promoted. Here, using protein immunoprecipitations, size-exclusion chromatography, PRO-seq, RNA-seq, native RIP-seq, RIP-seq footprinting and CUT&RUN, we report that PGC 1α, serving as a DNA−RNA conduit between promoter-bound ERRα and nascent transcript-bound CBP80, overcomes promoter-proximal pausing of RNAPII by competing against the premature transcription termination complex Integrator and also by recruiting P-TEFb. Using mice homozygous for five amino-acid changes in PGC 1α that destroy CBM function, we demonstrate that efficient differentiation of primary myoblasts to myofibers and effective regeneration of skeletal muscle after injury requires PGC 1α binding to CBP80.
2023-01-19 | GSE197311 | GEO
Project description:Although PGC 1α is well-established as a transcriptional coactivator for the metabolic adaptation of mammalian cells to diverse physiological stresses, its molecular dynamics at the start and during gene transcription are incompletely understood. Previously, we defined a CBP80-binding motif (CBM) within PGC 1α that binds CBP80 at the 5′-cap of nascent transcripts deriving from PGC 1α-responsive genes. Binding verifies proper 5′-cap assembly, after which gene transcription is somehow promoted. Here, using protein immunoprecipitations, size-exclusion chromatography, PRO-seq, RNA-seq, native RIP-seq, RIP-seq footprinting and CUT&RUN, we report that PGC 1α, serving as a DNA−RNA conduit between promoter-bound ERRα and nascent transcript-bound CBP80, overcomes promoter-proximal pausing of RNAPII by competing against the premature transcription termination complex Integrator and also by recruiting P-TEFb. Using mice homozygous for five amino-acid changes in PGC 1α that destroy CBM function, we demonstrate that efficient differentiation of primary myoblasts to myofibers and effective regeneration of skeletal muscle after injury requires PGC 1α binding to CBP80.
2023-01-19 | GSE197303 | GEO
Project description:Although PGC 1α is well-established as a transcriptional coactivator for the metabolic adaptation of mammalian cells to diverse physiological stresses, its molecular dynamics at the start and during gene transcription are incompletely understood. Previously, we defined a CBP80-binding motif (CBM) within PGC 1α that binds CBP80 at the 5′-cap of nascent transcripts deriving from PGC 1α-responsive genes. Binding verifies proper 5′-cap assembly, after which gene transcription is somehow promoted. Here, using protein immunoprecipitations, size-exclusion chromatography, PRO-seq, RNA-seq, native RIP-seq, RIP-seq footprinting and CUT&RUN, we report that PGC 1α, serving as a DNA−RNA conduit between promoter-bound ERRα and nascent transcript-bound CBP80, overcomes promoter-proximal pausing of RNAPII by competing against the premature transcription termination complex Integrator and also by recruiting P-TEFb. Using mice homozygous for five amino-acid changes in PGC 1α that destroy CBM function, we demonstrate that efficient differentiation of primary myoblasts to myofibers and effective regeneration of skeletal muscle after injury requires PGC 1α binding to CBP80.
2023-01-19 | GSE197279 | GEO
Project description:Although intron losses have been widely reported, it is not clear whether they are neutral and therefore random or driven by positive selection. Intron transcription and splicing are time-consuming and can delay the expression of its host gene. For genes that must be activated quickly to respond to physiological or stress signals, intron delay may be deleterious. Promoter proximally paused (PPP) genes are a group of rapidly expressed genes. To respond quickly to activation signals, they generally initiate transcription competently but stall after synthesizing a short RNA. In this study, performed in Drosophila melanogaster, the PPP genes were found to have a significantly higher rate of intron loss than control genes. However, further analysis did not find more significant shrinkage of intron size in PPP genes. Referring to previous studies on the rates of transcription and splicing and to the time saved by deletion of the introns from mouse gene Hes7, it is here suggested that transcription delay is comparable to splicing delay only when the intron is 28.5 kb or larger, which is greater in size than 95% of vertebrate introns, 99.5% of Drosophila introns, and all the annotated introns of Saccharomyces cerevisiae and Arabidopsis thaliana. Delays in intron splicing are probably a selective force, promoting intron loss from quickly expressed genes. In other genes, it may have been an exaptation during the emergency of developmental clocks.
| S-EPMC4197015 | biostudies-literature
Project description:The association of DSIF and NELF with initiated RNA Polymerase II (Pol II) is the general mechanism for inducing promoter-proximal pausing of Pol II. However, it remains largely unclear how the paused Pol II is released in response to stimulation. Here, we show that the release of the paused Pol II is cooperatively regulated by multiple P-TEFbs which are recruited by bromodomain-containing protein Brd4 and super elongation complex (SEC) via different recruitment mechanisms. Upon stimulation, Brd4 recruits P-TEFb to Spt5/DSIF via a recruitment pathway consisting of Med1, Med23 and Tat-SF1, whereas SEC recruits P-TEFb to NELF-A and NELF-E via Paf1c and Med26, respectively. P-TEFb-mediated phosphorylation of Spt5, NELF-A and NELF-E results in the dissociation of NELF from Pol II, thereby transiting transcription from pausing to elongation. Additionally, we demonstrate that P-TEFb-mediated Ser2 phosphorylation of Pol II is dispensable for pause release. Therefore, our studies reveal a co-regulatory mechanism of Brd4 and SEC in modulating the transcriptional pause release by recruiting multiple P-TEFbs via a Mediator- and Paf1c-coordinated recruitment network.
| S-EPMC5001612 | biostudies-literature
Project description:Piwi-interacting RNAs (piRNAs) play key roles in germline development and genome defence in metazoans. In C. elegans, piRNAs are transcribed from > 15,000 discrete genomic loci by RNA polymerase II (Pol II), resulting in 28 nt short-capped piRNA precursors. Here, we investigate transcription termination at piRNA loci. We show that the Integrator complex, which terminates snRNA transcription, is recruited to piRNA loci. Moreover, we demonstrate that the catalytic activity of Integrator cleaves nascent capped piRNA precursors associated with promoter-proximal Pol II, resulting in termination of transcription. Loss of Integrator activity, however, does not result in transcriptional readthrough at the majority of piRNA loci. Taken together, our results draw new parallels between snRNA and piRNA biogenesis in nematodes and provide evidence of a role for the Integrator complex as a terminator of promoter-proximal RNA polymerase II during piRNA biogenesis.
| S-EPMC7917550 | biostudies-literature
Project description:Transcriptional coactivator PGC-1α and its splice variant NT-PGC-1α play crucial roles in regulating cold-induced thermogenesis in brown adipose tissue (BAT). PGC-1α and NT-PGC-1α are highly induced by cold in BAT and subsequently bind to and coactivate many transcription factors to regulate expression of genes involved in mitochondrial biogenesis, fatty acid oxidation, respiration and thermogenesis. To identify the complete repertoire of PGC-1α and NT-PGC-1α target genes in BAT, we analyzed genome-wide DNA-binding and gene expression profiles. We find that PGC-1α-/NT-PGC-1α binding broadly associates with cold-mediated transcriptional activation. In addition to their known target genes in mitochondrial biogenesis and oxidative metabolism, PGC-1α and NT-PGC-1α additionally target a broad spectrum of genes involved in diverse biological pathways including ubiquitin-dependent protein catabolism, ribonucleoprotein complex biosynthesis, phospholipid biosynthesis, angiogenesis, glycogen metabolism, phosphorylation, and autophagy. Our findings expand the number of genes and biological pathways that may be regulated by PGC-1α and NT-PGC-1α and provide further insight into the transcriptional regulatory network in which PGC-1α and NT-PGC-1α coordinate a comprehensive transcriptional response in BAT in response to cold.
| S-EPMC5959870 | biostudies-other
Project description:Brown fat expresses two PGC-1α isoforms (PGC-1α and NT-PGC-1α) and both play a central role in the regulation of cellular energy metabolism and adaptive thermogenesis by interacting with a wide range of transcription factors including PPARγ, PPARα, ERRα, and NRF1. PGC-1α consists of 797 amino acids, whereas alternative splicing of the PGC-1α gene produces a shorter protein called NT-PGC-1α (aa 1-270). We report in this paper that transcriptional activity of PGC-1α and NT-PGC-1α is differently affected by the transcriptional regulator, Twist-1. Twist-1 suppresses PGC-1α but not NT-PGC-1α. The inhibition of PGC-1α activity by Twist-1 is mediated by direct interaction through the C-terminal region of PGC-1α (aa 353-797). Thus, the absence of the corresponding C-terminal domain in NT-PGC-1α allows NT-PGC-1α to be free from Twist-1-mediated inhibition. Overexpression of Twist-1 in brown adipocytes suppresses transcription of a subset of PGC-1α-target genes involved in mitochondrial fatty acid oxidation and uncoupling (CPT1β, UCP1, and ERRα). In contrast, NT-PGC-1α-mediated induction of these genes is unaffected by Twist-1. These findings show that differences in inhibitory protein-protein interactions of PGC-1α and NT-PGC-1α with Twist-1 lead to differential regulation of their function by Twist-1.
| S-EPMC3474972 | biostudies-literature
Project description:Recent evidence suggests that exercise stimulates the degradation of cellular components in skeletal muscle through activation of autophagy, but the time course of the autophagy response during recovery from exercise has not been determined. Furthermore, the regulatory mechanisms behind exercise-induced autophagy remain unclear, although the muscle oxidative phenotype has been linked with basal autophagy levels. Therefore, the aim of this study was to investigate the role of the key regulator of muscle oxidative capacity, PGC-1α, in exercise-induced autophagy at several time points during recovery. Mice with transgenic muscle-specific overexpression (TG) or knockout (MKO) of PGC-1α and their respective littermate controls were subjected to a single 1 h bout of treadmill running and euthanized immediately (0 h), 2, 6, and 10 h after exercise. In the PGC-1α MKO strain, quadriceps protein content of the autophagy marker LC3II was increased from 2 h into recovery in lox/lox control, but not in MKO mice. In the PGC-1α TG strain, quadriceps protein content of LC3II was increased from 2 h after exercise in TG, but not in WT. Although AMPK and ACC phosphorylation was increased immediately following exercise, the observed exercise-induced autophagy response was not associated with phosphorylation of the AMPK-target ULK1. However, lower protein carbonyl content was observed in lox/lox and TG mice after exercise coinciding with the increased LC3 lipidation. In conclusion, the present results suggest a role of skeletal muscle PGC-1α in coordinating several exercise-induced adaptive responses including autophagic removal of damaged cellular components.
| S-EPMC4758928 | biostudies-other