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Actin associates with actively elongating genes

ABSTRACT: Actin associates with actively elongating genes

PROVIDER: PRJNA1000942 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25474926.fastq.gz	Fastqsanger.gz
	SRR25474927.fastq.gz	Fastqsanger.gz
	SRR25474928.fastq.gz	Fastqsanger.gz
	SRR25474929.fastq.gz	Fastqsanger.gz
	SRR25474930.fastq.gz	Fastqsanger.gz

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Actin associates with actively elongating genes

Project description:Nuclear actin has been demonstrated to be essential for optimal transcription, but the molecular mechanisms and direct binding partner for actin in the RNA polymerase complex have remained unknown. By using purified proteins in several biochemical assays, we demonstrate a direct and specific interaction between monomeric actin and Cdk9, the kinase subunit of the positive transcription elongation factor b (P-TEFb) required for RNA polymerase II (Pol II) pause-release. This interaction is not dependent on kinase activity of Cdk9 and is not involved with releasing P-TEFb from its inhibitor 7SK snRNP complex. Supporting the specific role for actin in the elongation phase of transcription, chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) reveals that actin interacts with genes only upon their active transcription elongation. This study therefore provides novel insights into the mechanisms by which actin facilitates the transcription process.

2023-09-01 | GSE239771 | GEO

Actin associates with actively elongating genes and binds directly to the Cdk9 subunit of P-TEFb.

Project description:Nuclear actin has been demonstrated to be essential for optimal transcription, but the molecular mechanisms and direct binding partner for actin in the RNA polymerase complex have remained unknown. By using purified proteins in a variety of biochemical assays, we demonstrate a direct and specific interaction between monomeric actin and Cdk9, the kinase subunit of the positive transcription elongation factor b required for RNA polymerase II pause-release. This interaction efficiently prevents actin polymerization, is not dependent on kinase activity of Cdk9, and is not involved with releasing positive transcription elongation factor b from its inhibitor 7SK snRNP complex. Supporting the specific role for actin in the elongation phase of transcription, chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) reveals that actin interacts with genes only upon their active transcription elongation. This study therefore provides novel insights into the mechanisms by which actin facilitates the transcription process.

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The late chromatoid body component TSSK2 associates with translational machinery in elongating spermatids in mice

Project description:Spermatogenesis culminates in a dramatic morphological transformation, including a tight compaction of the chromatin and nuclear re-shaping that largely silences transcription. Due to transcriptional silencing, the production of the sperm-specific proteins needed for the morphological transformation requires active storage and translational regulation of mRNAs transcribed in earlier cell types. The germline-specific ribonucleoprotein (RNP) granule, the chromatoid body (CB), accumulates RNAs and has a role in RNA storage in early haploid cells (round spermatids). In late haploid cells (elongating spermatids), the CB is transformed to so-called late-CB, whose function in RNA regulation has remained elusive. Here we characterized the function of the late-CB by identifying proteins and RNAs interacting with the known late-CB marker, Testis- Specific Serine Kinase 2 (TSSK2). We showed that TSSK2 interacts with eukaryoti5 translation initiation factors and the late-CB associates with active, localized protein synthesis. Furthermore, we revealed an association of TSSK2 with a specific set of mRNAs that are enriched in polysome fractions in elongating spermatids, supporting the role of the late-CB in the temporally regulated translation. These results link the function of the late-CB to the RNA regulation during late spermatogenesis for the first time, providing important novel information about the RNA regulatory processes required for spermatogenesis and male fertility.

2025-10-27 | PXD065042 | Pride

The late chromatoid body component TSSK2 associates with translational machinery in elongating spermatids in mice

Project description:Spermatogenesis culminates in a dramatic morphological transformation, including a tight compaction of the chromatin and nuclear re-shaping that largely silences transcription. Due to transcriptional silencing, the production of the sperm-specific proteins needed for the morphological transformation requires active storage and translational regulation of mRNAs transcribed in earlier cell types. The germline-specific RNP granule, the chromatoid body (CB), accumulates RNAs and has a role in RNA storage in early haploid cells (round spermatids). In late haploid cells (elongating spermatids), the CB is transformed to so-called late-CB, whose function in RNA regulation has remained elusive. Here we characterized the function of the late-CB by identifying proteins and RNAs interacting with the known late-CB marker, Testis-Specific Serine Kinase 2 (TSSK2). We showed that TSSK2 interacts with eukaryotic translation initiation factors and the late-CB associates with active, localized protein synthesis. Furthermore, we revealed an association of TSSK2 with a specific set of mRNAs that are enriched in polysome fractions in elongating spermatids, supporting the role of the late-CB in the temporally regulated translation. These results link the function of the late-CB to the RNA regulation during late spermatogenesis for the first time, providing important novel information about the RNA regulatory processes required for spermatogenesis and male fertility.

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Project description:Actin dynamically shuttles between the nucleus and cytosplasm and regulates a wide range of transcriptional processes within the nucleus We used gene expression profiling of keratinocytes overexpressing wild type actin or actin tagged with a nuclear localisation sequence to identify genes specifically regulated by nuclear actin

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Project description:This study evaluated transcriptomic responses to submergence in elongating and non-elongating leaves of rice near-isogenic lines with and without SUB1A using RNA-Seq. SUB1A is an ERF transcription factor gene and the key regulator of submergence tolerance in rice, restricting underwater elongation and avoiding starvation under the stress. Submergence induces mRNA accumulation of SUB1A similarly in elongating and non-elongating leaves. This study uncovered SUB1A-dependent and independent regulation of adaptive responses to submergence in the two functionally distinct leaves at the global level.

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A functional overlap between actively transcribed genes and insulator elements [RNA-seq]

Project description:A functional overlap between actively transcribed genes and insulator elements [RNA-seq]

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