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Identification of the transcription start site of transcribed sequences from the mouse Sry locus by CAGE-seq

ABSTRACT: Identification of the transcription start site of transcribed sequences from the mouse Sry locus by CAGE-seq

PROVIDER: PRJNA635924 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11878477.fastq.gz	Fastqsanger.gz
	SRR11878478.fastq.gz	Fastqsanger.gz
	SRR11878479.fastq.gz	Fastqsanger.gz
	SRR11878480.fastq.gz	Fastqsanger.gz

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Identification of the transcription start site of transcribed sequences from the mouse Sry locus by CAGE-seq

Project description:The mammalian sex-determining gene Sry induces male development. Through analyzing transcriptome of pre-Sertoli cells, we identified a novel sequence transcribed within palindromic sequence surrounding Sry. To examine whether this sequence contains transcription start site, Cap analysis gene expression (CAGE) -seq analysis was performed, in which putative transcriptional start sites can be identified by sequencing the 3’ end of cDNA corresponding to 5’ end of RNA. CAGE seq revealed that Cap site was absent within the novel sequence, whereas Sry transcription start site found to locate in minus strand at chrY:2,663,800-2,663,900. Combining the result from long-read RNA seq, we concluded that this sequence is the second exon of mouse Sry.

2020-10-01 | GSE151473 | GEO

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NET-CAGE Characterizes the Dynamics and Topology of Human Transcribed Cis-regulatory Elements

Project description:Promoters and enhancers are key cis-regulatory elements, but how they operate to generate cell-type-specific transcriptomes is not fully understood. We developed a simple and robust approach to sensitively detect 5’-ends of nascent RNAs (NET-CAGE) in diverse cells and tissues, including unstable transcripts such as enhancer-derived RNAs. We studied RNA synthesis and degradation at the transcription start site (TSS) level, characterizing the impact of differential promoter usage on transcript stability. We quantified transcription from cis-regulatory elements without the influence of RNA turnover, and show that enhancer-promoter pairs are generally activated simultaneously upon stimulation. By integrating NET-CAGE data with chromatin interaction maps, we show that cis-regulatory elements are topologically connected according to their cell-type specificity. We identified new enhancers with high sensitivity, and delineated primary locations of transcription within super-enhancers. Our NET-CAGE dataset derived from human and mouse cells expands the FANTOM5 catalogue of transcribed enhancers, with broad applicability to biomedical research.

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CAGE-seq Profiling of Transcription Start Site Usage in mock-infected and human cytomegalovirus (HCMV) infected human embryonic lung fibroblasts (HELF) cells (human)

Project description:CAGE-seq (Cap Analysis of Gene Expression coupled with deep sequencing) was used to map transcription start site (TSS) usage in human embryonic lung fibroblast (HELF) cells in response to infection with the human cytomegalovirus (HCMV) HAN strain. Total RNA from infected cells at 72 hours post-infection and mock-infected controls was profiled. The analysis detected 224,206 and 292,294 CAGE transcription start sites (CTSSs) in infected and mock samples, respectively, which grouped into 20,532 and 26,407 transcript clusters (TCs). Comparative analysis identified 3,302 consensus clusters with significant shifts in TSS positions, spanning 2,487 protein-coding genes and 134 non-coding RNAs. These findings reveal extensive infection-associated remodeling of promoter choice across the host transcriptome.

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Project description:We used SLIC-CAGE to map transcription start sites (TSSs) of mouse primordial germ cells from embryonic days 9.5-16.5, postnatal oocytes (P6, P14 and MII), and early 2-cell and 4-cell mouse embryos. We use this TSS data to show that the mouse germline development starts with the somatic promoter code with a prominent switch to the maternal code (W-box dependent) occurring during the follicular oogenesis. We also find that the promoters of gonadal germ cells are characterised by a previously unknown divergence from the somatic transcription initiation. This divergence is distinct from the promoter code used later by the developing oocytes and reveals genome-wide promoter remodelling during early female and male germline development.

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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.

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CAGE sequences from three developmental states in the microcrustacean Daphnia pulex.

Project description:We report the application of CAGE (Cap Analysis of Gene Expression) on collections of Daphnia pulex individuals representing three major developmental states. This submission comes from a project of Michael Lynch and was funded by a grant from the National Institutes of Health entitled 'Population Genomics of Daphnia pulex' (Project Number: 1R01GM101672-01A1).

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