Project description:We examined the chromosomal distribution of GFP-tagged Tus (Tus-GFP) in exponentially growing E. coli (KRX) using chromosome immunoprecipitation (ChIP)-Seq. Our ChIP-seq allowed delineation of a refined minimal replication fork trap within E. coli comprising two clusters of three Ter sites

2021-12-01 | GSE163680 | GEO

Simonsiella muelleri strain:DSM 2579

Project description:Simonsiella muelleri DSM 2579 RNA-Seq

| PRJNA795350 | ENA

Differential Gene Expression between ATRA treated and control HL-60 Cells [RNA-seq]

Project description:These RNA-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis. Analysis revealed differential expressed genes in ATRA treated and control HL-60 cells. Changes of gene expression with topological associated domains (TADs) were showd to be correlated with chromatin structure alteration

2018-03-07 | GSE93996 | GEO

Dissecting the binding behavior of the multi-RRM endosomal mRNA transporter Rrm4 [RNA-seq]

Project description:RNA-binding proteins (RBPs) are central players in determining the life cycle of RNA molecules. These proteins are often modular in arrangement, featuring multiple RNA-binding domains, to enhance RNA recognition and functionality. How these multiple RNA-binding domains within individual RBPs work in concert to recognize mRNA targets is still poorly studied. In the model fungus Ustilago maydis, the multi-RRM domain protein Rrm4 plays a key role in mediating the long-distance mRNA transport on the cytoplasmic surface of early endosomes, thereby precisely regulating spatiotemporal gene expression. Rrm4 contains three RNA-recognition motifs (RRMs), organized in an ELAV-like pattern: a tandem RRM domain (RRM1,2) and a separate third RRM domain (RRM3). Utilizing Rrm4 variants with mutations in the RRM domains, we conducted a differential iCLIP analysis to dissect the RNA recognition code of individual RRM domains. Our study reveals that Rrm4 exhibits two binding mode: (i) a one-to-one interaction where the third RRM domain alone binds RNAs by recognizing the shot UAUG motif. (ii) an intricate composite binding mode where all three RRM domains cooperatively bind RNA. Improtantly, our finding demonstrates that it is not the simple one-to-one interaction but rather the complex cooperative binding mode, involving all three RRM domains, is critical for Rrm4 function in maintaining the unipolar growth of the fungal hyphae.

2026-02-18 | GSE288123 | GEO

Role of the SAF-A ATPase and RGG domains in X inactivation, transcription, splicing, and cell proliferation.

Project description:SAF-A/HNRNPU is conserved throughout vertebrates and has emerged as an important factor regulating a multitude of nuclear functions, including lncRNA localization, gene expression, and splicing. SAF-A has several functional domains, including a central ATPase domain and a C-terminal RGG domain. In this study we tested for the role of the ATP binding, ATP hydrolysis and RNA binding in X chromosome inactivation, protein dynamics, gene expression, splicing, and cell proliferation. Here we show that the ATPase and RGG domains are required to maintain XIST RNA localization and XIST-dependent histone modifications on the inactive X chromosome, to execute normal protein dynamics, and to maintain normal cell proliferation. We found that the ATPase and RGG domains are not required to maintain gene expression but play a major role in mRNA splicing. We propose a model whereby RNA binding, ATP binding and ATP hydrolysis promote SAF-A interaction with nascent RNA to promote normal mRNA splicing and XIST localization and function.

2026-02-26 | GSE309811 | GEO

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