Transcription start site positioning is not affected by +1 nucleosome depletion
Ontology highlight
ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
PROVIDER: GSE85046 | GEO | 2018/06/30
REPOSITORIES: GEO
Similar Datasets
Project description:Retrotransposable elements are genomic parasites that are both key drivers of evolution and the ancestors of retroviruses. Although host cells have developed numerous mechanisms to keep these elements in check, there is also evidence from yeast to mammals that stressed cells sometimes activate transposition. Here we show that the fission yeast tf2 retrotransposons are regulated by alternative transcription start site (TSS) usage. Which TSS is used is determined by nucleosome positioning, which is in turn controlled by the Fun30 chromatin remodelers Fft2 and Fft3. By maintaining a high level of nucleosome occupancy at retrotransposon-flanking Long Terminal Repeat (LTR) elements, Fft2 and Fft3 promote the use of a downstream TSS and the production of RNA incapable of reverse transcription and retrotransposition. More generally, we show that Fft2 and Fft3 are involved in repressing the transcriptional response to stress, of which retrotransposon activation is a part. Finally, we show that in stressed cells retrotransposon TSS usage switches, allowing the production of full-length retrotransposon RNA. We propose that allowing retrotransposon transcription from a nonproductive TSS allows for the rapid activation of these elements in times of stress, while preventing their uncontrolled proliferation in the genome.
2016-03-03 | GSE57068 | GEO
Project description:Retrotransposable elements are genomic parasites that are both key drivers of evolution and the ancestors of retroviruses. Although host cells have developed numerous mechanisms to keep these elements in check, there is also evidence from yeast to mammals that stressed cells sometimes activate transposition. Here we show that the fission yeast tf2 retrotransposons are regulated by alternative transcription start site (TSS) usage. Which TSS is used is determined by nucleosome positioning, which is in turn controlled by the Fun30 chromatin remodelers Fft2 and Fft3. By maintaining a high level of nucleosome occupancy at retrotransposon-flanking Long Terminal Repeat (LTR) elements, Fft2 and Fft3 promote the use of a downstream TSS and the production of RNA incapable of reverse transcription and retrotransposition. More generally, we show that Fft2 and Fft3 are involved in repressing the transcriptional response to stress, of which retrotransposon activation is a part. Finally, we show that in stressed cells retrotransposon TSS usage switches, allowing the production of full-length retrotransposon RNA. We propose that allowing retrotransposon transcription from a nonproductive TSS allows for the rapid activation of these elements in times of stress, while preventing their uncontrolled proliferation in the genome.
2016-03-03 | GSE57067 | GEO
Project description:More than half of human protein-coding genes have an alternative transcription start site (TSS). We aimed to investigate the contribution of alternative TSSs to the acute-stress–induced transcriptome response in human tissue (skeletal muscle) using the cap analysis of gene expression approach. TSSs were examined at baseline and during recovery after acute stress (a cycling exercise). We identified 44,680 CAGE TSS clusters (including 3,764 first defined) belonging to 12,268 genes and annotated for the first time 290 TSSs belonging to 163 genes. The transcriptome dynamically changes during the first hours after acute stress; the change in the expression of 10% of genes was associated with the activation of alternative TSSs, indicating differential TSSs usage. The majority of the alternative TSSs do not increase proteome complexity suggesting that the function of thousands of alternative TSSs is associated with the fine regulation of mRNA isoform expression from a gene due to the transcription factor-specific activation of various alternative TSSs. We identified individual muscle promoter regions for each TSS using muscle open chromatin data (ATAC-seq and DNase-seq). Then, using the positional weight matrix approach we predicted time course activation of “classic” transcription factors involved in response of skeletal muscle to contractile activity, as well as diversity of less/un-investigated factors. Transcriptome response induced by acute stress related to activation of the alternative TSSs indicates that differential TSSs usage is an essential mechanism of fine regulation of gene response to stress stimulus. A comprehensive resource of accurate TSSs and individual promoter regions for each TSS in muscle was created. This resource together with the positional weight matrix approach can be used to accurate prediction of TFs in any gene(s) of interest involved in the response to various stimuli, interventions or pathological conditions in human skeletal muscle.
2020-12-31 | GSE164081 | GEO
Project description:Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically incorporates the MINUSCULE (MINU) catalytic subunits and the TRIPLE PHD FINGERS (TPF) signature subunits. Here we report experimental evidence that establishes the functional relevance of TPF proteins for the complex activity. Our results show that depletion of TPF triggers similar pleiotropic phenotypes and molecular defects to those found in minu mutants. Moreover, we report the genomic location of MINU2 and TPF proteins as representative members of the plant BAF-like complex and their impact on nucleosome positioning and transcription. These analyses unravel the binding of the complex to thousands of expressed genes where it modulates the position of the +1 nucleosome. These targets tend to produce 5´-shifted transcripts in the tpf and minu mutants pointing to the participation of the complex in alternative transcriptional start site (TSS) usage. Interestingly, there is a remarkable correlation between +1 nucleosome shift and upstream TSS usage suggesting their functional connection. In summary, this study unravels the function of a plant SWI/SNF complex involved in +1 nucleosome positioning and alternative TSS usage.
2022-09-20 | PXD035892 | Pride
Project description:The chromosomes of eukaryotes are organized into structurally and functionally discrete domains. This implies the presence of insulator elements that separate adjacent domains, allowing them to maintain different chromatin structures. We show that the Fun30 chromatin remodeler, Fft3, is essential for maintaining a proper chromatin structure at centromeres and subtelomeres. Fft3 is localized to insulator elements and inhibits euchromatin assembly in silent chromatin domains. In its absence, euchromatic histone modifications and histone variants invade centromeres and subtelomeres, causing a mis-regulation of gene expression and severe chromosome segregation defects. Our data strongly suggest that Fft3 controls the identity of chromatin domains by protecting these regions from euchromatin assembly.
2011-04-02 | E-MEXP-3044 | biostudies-arrayexpress
Project description:We addressed the lack of experimentally supported transcript annotations in the Rhesus macaque genome by ab initio identification of the transcription start sites (TSSs). We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)'s ability to mark TSSs and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures in the macaque brain. We then integrated the two types of our newly generated data with genomic sequence features and extended a TSS prediction algorithm to ab initio predict and verify 16,833 of previously electronically annotated transcription start sites at 500 bp resolution and predicted ~10,000 new TSSs. We took advantage of histone H3 lysine 4 trimethylation (H3K4me3)M-bM-^@M-^Ys ability to mark transcription start sites (TSSs) and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures. By integrating the ChIP-seq, RNA-seq and small RNA-seq data (previously uploaded to GEO as GSM450615 by our collaborator) with genomic sequence features and extending and improving a state-of-the-art TSS prediction algorithm, we ab initio predicted and verified previously electronically annotated TSSs at a high resolution, and predicted some novel TSSs.
2010-10-18 | E-GEOD-24538 | biostudies-arrayexpress
Project description:The selection and activity of transcription start sites (TSSs) are central to gene regulation and depend on sequence and chromatin features within a core promoter region. We present, at single-bp resolution, the TSS landscape of Oikopleura dioica, a marine chordate in the sister group to vertebrates and relate dynamics of promoter usage, and their architectures, across its life cycle, to chromatin features. TSS selection grammars include a genome-wide shift during spermatogenesis to promoters with a novel, position-specific, core promoter element, present in >70% of male-specific promoters. Differential promoter usage in spermatogenesis includes the activation of cryptic internal promoters within polycistronic operons, alternative TSS selection within promoters of genes expressed in earlier development and the exclusion of trans-splice sites. In contrast, maternal promoters, which are active in endocycling nurse nuclei in O. dioica, lack position-specific motifs, have dispersed TSS usage, ordered nucleosomes around the TSS and typical histone modifications associated with broad promoters. Furthermore, our results indicate that the cell cycle regulator, E2F1, acts as a master regulator of these maternally expressed genes. Zygotic promoters are also predominantly broad and the vertebrate maternal to zygotic switch in mode of TSS-selection is absent. DNA methylation in gene bodies is an ancient property of eukaryotic genomes and is thought to repress alternative TSSs. We report a strong association between gene body DNA methylation, H3K4me3-depletion and TATA-dependent sharp promoters in O. dioica. Core promoter features may therefore determine the subset of gene bodies that are methylated in this invertebrate genome.
2018-02-05 | GSE78794 | GEO
Project description:We used SLIC-CAGE to map transcriptional start sites (TSSs) of P14 WT and P14 Tbpl2-/- mutant mouse oocytes. Comparison of WT and Tbpl2-/- oocytes demonstrates that Tbpl2 guides transcriptional start site selection in the growing oocyte. This TSS selection is different compared to the canonical somatic type of TSS selection and depends on TATA-like elements as core promoter motifs, recognised by Tbpl2.
2020-11-12 | E-MTAB-8866 | biostudies-arrayexpress
Project description:In eukaryotic cells, local chromatin structure and chromatin organization in the nucleus both influence transcriptional regulation. At the local level, the Fun30 chromatin remodeler Fft3 is essential for maintaining proper chromatin structure at centromeres and subtelomeres in fission yeast. Using genome-wide mapping and live cell imaging, we show that this role is linked to controlling nuclear organization of its targets. In fft3M-NM-^T cells, subtelomeres lose their association with the LEM domain protein Man1 at the nuclear periphery and move to the interior of the nucleus. Furthermore, genes in these domains are upregulated and active chromatin marks increase. Fft3 is also enriched at retrotransposon-derived long terminal repeat (LTR) elements at the borders of subtelomeres and at tRNA genes. In cells lacking Fft3, these sites lose their peripheral positioning and show reduced nucleosome occupancy. We propose that Fft3 has a global role in mediating association between specific chromatin domains and components of the nuclear envelope by maintaining chromatin structure required for anchoring DNA insulators to nuclear pores. For MNase samples, duplicate mutant mononucleosome fractions were compared with duplicate WT mononucleosomes.
2015-03-02 | E-GEOD-58012 | biostudies-arrayexpress
Project description:We develop a method Re-Cappable-seq for determining eukaryotic transcription start sites derived from all RNA polymerases at nucleotide resolution. In particular, this method identifies the Pol-I and Pol-III TSSs, which are missing by CAGE. Applied to human A549 cell line, our method results in the identification of 33,468 and 5,269 high confidence Pol-II and non-Pol-II TSS respectively. Re-Cappable-seq identifies Pol-II TSS with higher specificity than CAGE.
2019-06-14 | GSE132660 | GEO