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Garcia Sanchez, E.

Publications and source records attributed to Garcia Sanchez, E..

3 recordsLinked to original sources

TBPL2-dependent transcription controls RNA stability and cellular organization in growing oocytes

During oocyte growth, the marked increase in cell size is accompanied by robust RNA polymerase II (Pol II) transcription, generating transcripts that are either translated into proteins or stored as part of the maternal transcriptome. While the RNA decay machinery is known to critically regulate the maternal transcriptome during oocyte maturation, its contribution during the growth phase remains poorly understood. We previously identified an oocyte-specific transcription machinery dependent on the TATA-binding protein paralog TBPL2, which is required for oocyte growth. To investigate how the absence of TBPL2-mediated transcription affects the cellular state of the oocyte, we characterized the phenotypic consequences of the Tbpl2-/- mutation in growing oocytes. Our data reveal that both nuclear and cytoplasmic organizations are profoundly disrupted in the absence of TBPL2-mediated transcription. Given that cytoplasmic organization is closely linked to RNA storage capacity, we examined the expression and localization of proteins involved in mRNA regulation, stability and storage. We observed a marked impairment in the redistribution of these key factors in Tbpl2-/- oocytes. To assess the impact of TBPL2 on RNA storage, we analyzed poly(A) tail length and found a global increase in polyadenylation in mutant oocytes. Gene-specific poly(A) tail analyses revealed differential mRNA changes, with shortened tails for a downregulated transcript and elongated tails for an upregulated one, suggesting stabilization of the latter. Collectively, our findings indicate that TBPL2-mediated transcription is essential for maintaining proper cellular organization in growing oocytes, at least in part by ensuring the functional integrity of the RNA decay machinery.

developmental biology↗

CROCKETA: An automated framework for comprehensive multi-omic analysis of gene expression and clonotype immune repertoire at a single-cell level

CROCKETA (single-Cell Repertoire Organization & Combined Kinetics Exploration for Transcriptomic Analysis) is an automated and adaptable Snakemake pipeline designed to perform fundamental initial stages of single-cell analysis for both transcriptomic and immune repertoire data, with additional steps for detailed assay characterization. CROCKETA stems from the imperative need to devise an optimal methodology for integrating and analyzing single-cell RNA sequencing (scRNA-seq) alongside single-cell T-cell Receptor (scTCR-seq) or B-Cell Receptor (scBCR-seq) data in an automated way by means of state-of-the-art tools. This pipeline encompasses basic steps from primary & secondary scRNA-seq analysis (Quality Control -QC-, sequence alignment, cell-level QC and doublets removal, data preprocessing, cell clustering, cell annotation at both single cell and cluster levels, differential expression analysis, trajectory inference and functional enrichment) along with the incorporation and analysis of immune repertoire data for both B-cells and T-cells, capable of accommodating both human and mouse datasets. The analysis can be conducted from either FastQ-formatted raw data or from expression matrices itself. CROCKETA opens up new horizons of possibilities by providing a reproducible, automated, and efficient solution for processing large volumes of data, addressing a challenge that had yet to be resolved in single-cell analyses.

bioinformatics↗

RNA polymerase II transcription with partially assembled TFIID complexes

The recognition of core promoter sequences by the general transcription factor TFIID is the first step in the process of RNA polymerase II (Pol II) transcription initiation. Metazoan holo-TFIID is composed of the TATA binding protein (TBP) and of 13 TBP associated factors (TAFs). Inducible Taf7 knock out (KO) results in the formation of a Taf7-less TFIID complex, while Taf10 KO leads to serious defects within the TFIID assembly pathway. Either TAF7 or TAF10 depletions correlate with the detected TAF occupancy changes at promoters, and with the distinct phenotype severities observed in mouse embryonic stem cells or mouse embryos. Surprisingly however, under either Taf7 or Taf10 deletion conditions, TBP is still associated to the chromatin, and no major changes are observed in nascent Pol II transcription. Thus, partially assembled TFIID complexes can sustain Pol II transcription initiation, but cannot replace holo-TFIID over several cell divisions and/or development.

molecular biology↗