TT-seq in mESCs with and without TIP60
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1065265 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27559337_1.fastq.gz | Fastqsanger.gz | |||
| SRR27559337_2.fastq.gz | Fastqsanger.gz | |||
| SRR27559338_1.fastq.gz | Fastqsanger.gz | |||
| SRR27559338_2.fastq.gz | Fastqsanger.gz | |||
| SRR27559339_1.fastq.gz | Fastqsanger.gz |
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Project description:RNA-seq in mESCs with and without TIP60
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Project description:Transcript buffering entails the reciprocal modulation of mRNA synthesis and degradation rates, ensuring a constant RNA concentration amidst changes in cellular conditions. While an increasing body of research supports a global, non-sequence-specific linkage between mRNA synthesis and degradation, the underlying mechanisms remain elusive. To explore this, we investigated alterations in RNA metabolism following the acute depletion of TIP60/KAT5, the transcriptional coactivator and acetyltransferase subunit of the NuA4 complex, in mouse embryonic stem cells. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling, we show that TIP60 activates transcription of numerous genes, with substantially fewer genes undergoing transcriptional repression. Surprisingly, specific RNA species' transcription changes triggered by TIP60 depletion were counterbalanced by compensatory adjustments in RNA export and/or stability within the nucleus and in RNA stability within the cytoplasm. These discoveries imply that transcript buffering operates on a gene-specific level and suggest that cells continually monitor RNA molecule counts in nuclear and cytoplasmic compartments to maintain cellular homeostasis.
2024-01-30 | GSE253311 | GEO
Project description:Transcript buffering entails the reciprocal modulation of mRNA synthesis and degradation rates, ensuring a constant RNA concentration amidst changes in cellular conditions. While an increasing body of research supports a global, non-sequence-specific linkage between mRNA synthesis and degradation, the underlying mechanisms remain elusive. To explore this, we investigated alterations in RNA metabolism following the acute depletion of TIP60/KAT5, the transcriptional coactivator and acetyltransferase subunit of the NuA4 complex, in mouse embryonic stem cells. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling, we show that TIP60 activates transcription of numerous genes, with substantially fewer genes undergoing transcriptional repression. Surprisingly, specific RNA species' transcription changes triggered by TIP60 depletion were counterbalanced by compensatory adjustments in RNA export and/or stability within the nucleus and in RNA stability within the cytoplasm. These discoveries imply that transcript buffering operates on a gene-specific level and suggest that cells continually monitor RNA molecule counts in nuclear and cytoplasmic compartments to maintain cellular homeostasis.
2024-01-30 | GSE253312 | GEO
Project description:Transcript buffering entails the reciprocal modulation of mRNA synthesis and degradation rates, ensuring a constant RNA concentration amidst changes in cellular conditions. While an increasing body of research supports a global, non-sequence-specific linkage between mRNA synthesis and degradation, the underlying mechanisms remain elusive. To explore this, we investigated alterations in RNA metabolism following the acute depletion of TIP60/KAT5, the transcriptional coactivator and acetyltransferase subunit of the NuA4 complex, in mouse embryonic stem cells. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling, we show that TIP60 activates transcription of numerous genes, with substantially fewer genes undergoing transcriptional repression. Surprisingly, specific RNA species' transcription changes triggered by TIP60 depletion were counterbalanced by compensatory adjustments in RNA export and/or stability within the nucleus and in RNA stability within the cytoplasm. These discoveries imply that transcript buffering operates on a gene-specific level and suggest that cells continually monitor RNA molecule counts in nuclear and cytoplasmic compartments to maintain cellular homeostasis.
2024-01-30 | GSE253310 | GEO
Project description:TT-seq and RNA-seq in TX1072 XXΔXic and XO mESCs during differentiation
| PRJNA704378 | ENA
Project description:Background Tip60 (KAT5) is the histone acetyltransferase (HAT) of the mammalian Tip60/NuA4 complex. While Tip60 is important for early mouse development and mouse embryonic stem cell (mESC) pluripotency, the function of Tip60 as reflected in a genome-wide context is not yet well understood. Results Gel filtration of nuclear mESCs extracts indicate incorporation of Tip60 into large molecular complexes and exclude the existence of large quantities of âfreeâ Tip60 within the nuclei of ESCs. Thus, monitoring of Tip60 binding to the genome should reflect the behaviour of Tip60-containing complexes. The genome-wide mapping of Tip60 binding in mESCs by chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) shows that the Tip60 complex is present at promoter regions of predominantly active genes that are bound by RNA polymerase II (Pol II) and contain the H3K4me3 histone mark. The coactivator HAT complexes, Tip60- and Mof (KAT8)-containing (NSL and MSL), show a global overlap at promoters, whereas distinct binding profiles at enhancers suggest different regulatory functions of each essential HAT complex. Interestingly, Tip60 enrichment peaks at about 200 bp downstream of the transcription start sites suggesting a function for the Tip60 complexes in addition to histone acetylation. The comparison of genome-wide binding profiles of Tip60 and c-Myc, a somatic cell reprogramming factor that binds predominantly to active genes in mESCs, demonstrate that Tip60 and c-Myc co-bind at 50â60 % of their binding sites. We also show that the Tip60 complex binds to a subset of bivalent developmental genes and defines a set of mESC-specific enhancer as well as super-enhancer regions. Conclusions Our study suggests that the Tip60 complex functions as a global transcriptional co-activator at most active Pol II promoters, co-regulates the ESC-specific c-Myc network, important for ESC self-renewal and cell metabolism and acts at a subset of active distal regulatory elements, or super enhancers, in mESCs. Genome- wide binding of Tip60 co-activator complexes
2015-11-06 | E-GEOD-69671 | biostudies-arrayexpress
Project description:Background Tip60 (KAT5) is the histone acetyltransferase (HAT) of the mammalian Tip60/NuA4 complex. While Tip60 is important for early mouse development and mouse embryonic stem cell (mESC) pluripotency, the function of Tip60 as reflected in a genome-wide context is not yet well understood. Results Gel filtration of nuclear mESCs extracts indicate incorporation of Tip60 into large molecular complexes and exclude the existence of large quantities of “free” Tip60 within the nuclei of ESCs. Thus, monitoring of Tip60 binding to the genome should reflect the behaviour of Tip60-containing complexes. The genome-wide mapping of Tip60 binding in mESCs by chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) shows that the Tip60 complex is present at promoter regions of predominantly active genes that are bound by RNA polymerase II (Pol II) and contain the H3K4me3 histone mark. The coactivator HAT complexes, Tip60- and Mof (KAT8)-containing (NSL and MSL), show a global overlap at promoters, whereas distinct binding profiles at enhancers suggest different regulatory functions of each essential HAT complex. Interestingly, Tip60 enrichment peaks at about 200 bp downstream of the transcription start sites suggesting a function for the Tip60 complexes in addition to histone acetylation. The comparison of genome-wide binding profiles of Tip60 and c-Myc, a somatic cell reprogramming factor that binds predominantly to active genes in mESCs, demonstrate that Tip60 and c-Myc co-bind at 50–60 % of their binding sites. We also show that the Tip60 complex binds to a subset of bivalent developmental genes and defines a set of mESC-specific enhancer as well as super-enhancer regions. Conclusions Our study suggests that the Tip60 complex functions as a global transcriptional co-activator at most active Pol II promoters, co-regulates the ESC-specific c-Myc network, important for ESC self-renewal and cell metabolism and acts at a subset of active distal regulatory elements, or super enhancers, in mESCs.
2015-11-06 | GSE69671 | GEO
Project description:The Tip60 (also known as Kat5) lysine acetyltransferase functions broadly as a transcriptional co-activator that acetylates histones. In contrast, Tip60 functions in embryonic stem cells (ESCs) both to silence genes that promote differentiation and to activate genes required for proliferation. The mechanism by which Tip60 functions as a repressor is unknown. Here we show that the class II histone deacetylase Hdac6 co-purifies with Tip60-p400 complex from ESCs and is necessary for complete silencing of most differentiation genes targeted by Tip60. In contrast to differentiated cells, where Hdac6 is mainly cytoplasmic and does not interact with Tip60, Hdac6 is largely nuclear in ESCs and neural stem cells (NSCs) and interacts with Tip60-p400 in both cell types. Hdac6 is enriched at promoters bound by Tip60-p400 in ESCs, but while Tip60 binds on both sides of transcription start sites (TSSs), Hdac6 binding overlaps with only the downstream Tip60 peak. Surprisingly, Hdac6 does not deacetylate histones at these sites, but rather is required for Tip60 binding. These data suggest that nuclear exclusion of Hdac6 during differentiation plays a major role in modulation of Tip60-p400 function. We determined the genome-wide localization of Tip60 and Hdac6 in mouse ES cells, and examined genomic binding profiles of Tip60 and Hdac6 upon indicated knockdown by ChIP-seq. We examined genomic binding profiles of p400 upon indicated knockdown by ChIP-seq.
2013-11-20 | E-GEOD-42209 | biostudies-arrayexpress
Project description:A large portion of the genome is transcribed but many of the resulting RNAs live only transiently and can generally not be mapped. Here we develop transient transcriptome sequencing (TT-Seq), a protocol that maps transcriptionally active regions in a nearly uniform manner and allows for unbiased monitoring of cellular RNA synthesis activity. Application of TT-Seq to human K562 cells recovers stable mRNAs and long intergenic non-coding RNAs, and additionally maps over 10,000 transient RNAs including enhancer RNAs, antisense RNAs, promoter-associated upstream antisense and convergent RNAs. TT-Seq also provides RNA half-lives, and reveals that transient RNAs are short and lack U1 motifs and secondary structure. TT-Seq further uncovers transcription termination sites and reveals a universal DNA motif for RNA polymerase II release.
2016-06-03 | GSE75792 | GEO