The RNA binding proteins TIA1 and TIAL1 protect germinal centre responses from apoptosis [iCLIP]
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ABSTRACT:
PROVIDER: PRJNA986857 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25010689.fastq.gz | Fastqsanger.gz | |||
| SRR25010690.fastq.gz | Fastqsanger.gz |
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Project description:Germinal centres (GC) are essential for the establishment of long-lasting antibody responses. In there, GC B cells rely on post-transcriptional RNA mechanisms for translating activation-associated transcriptional programs into functional changes in the cell proteome. However, we still lack knowledge about which are the critical proteins driving these key mechanisms. Here we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses. TIA1 and TIAL1- deficient GC B cells fail to undergo antigen-mediated positive selection, expansion and differentiation into B cell clones producing high-affinity antibodies. Mechanistically, TIA1 and TIAL1 control the transcriptional identity of dark and light zone GC B cells and enable timely expression of the pro-survival molecule MCL1. Altogether, we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.
2023-08-29 | GSE235655 | GEO
Project description:Germinal centres (GC) are essential for the establishment of long-lasting antibody responses. In there, GC B cells rely on post-transcriptional RNA mechanisms for translating activation-associated transcriptional programs into functional changes in the cell proteome. However, we still lack knowledge about which are the critical proteins driving these key mechanisms. Here we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses. TIA1 and TIAL1- deficient GC B cells fail to undergo antigen- mediated positive selection, expansion and differentiation into B cell clones producing high-affinity antibodies. Mechanistically, TIA1 and TIAL1 control the transcriptional identity of dark and light zone GC B cells and enable timely expression of the pro-survival molecule MCL1. Altogether, we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.
2023-08-29 | GSE235358 | GEO
Project description:The RNA binding proteins TIA1 and TIAL1 protect germinal centre responses from apoptosis
| PRJNA985742 | ENA
Project description:iCLIP and iCLAP for TIA1 and TIAL1 proteins
| PRJEB2628 | ENA
Project description:Individual nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) and individual nucleotide resolution UV-crosslinking and affinity purification (iCLAP) were used to identify the global RNA binding sites for TIA1 and TIAL1 proteins. HeLa cells were UV crosslinked before lysing and digested with DNase and low concentration of RNase I. The protein-RNA complex were either immunoprecipitated with specific antibodies against either TIA1 or TIAL1 proteins and ligated to 3 prime adapter before separated by SDS-PAGE. For iCLAP, the His/Strep tagged proteins were overexpressed in HeLa cells, and the protein-RNA complexes were purified via Strep and His tag affinity purification. The proteins were digested by proteinase K and the RNA was reverse transcribed and self-circularised. The cDNA library was prepared by PCR with solexa primers compatible for high-throughput sequencing. This method allowed specific identify of crosslinked nucleotides, and genome-wide targets for TIA1 and TIAL1 not identified before. This method also allowed comparison between the 2 homologous proteins, whose binding sites and functions could be redundent. iCLAP provided an independent way to validate the binding sites identified by iCLIP, since no antibody was used in the iCLAP method.
2011-07-28 | E-MTAB-432 | biostudies-arrayexpress
Project description:B-cell lymphopoiesis requires dynamic modulation of the B-cell transcriptome at the post-transcriptional level, although the implication of RNA-binding proteins (RBPs) remain largely unknown. Here we show that the RBPs TIA1 and TIAL1 are essential in B cells and, if deleted, there is a developmental block at the pro-B cell stage. TIA1 and TIAL1 have redundant functions. They act together as global splicing regulators for the expression of mRNAs including those involved in DNA damage repair in pro-B cells. Mechanistically, TIA1 and TIAL1 bind to 5’splice sites for exon definition, splicing and expression of DNA damage sensors like Chek2 and Rif1. In their absence, pro-B cells show exacerbated DNA damage, altered P53 expression and increased cell death. Altogether, our study uncovers the importance of tight regulation of mRNA splicing by TIA1 and TIAL1 for the expression of integrative transcriptional programs for DNA damage sensing and repair during B-cell development.
2022-12-20 | GSE188556 | GEO
Project description:B-cell lymphopoiesis requires dynamic modulation of the B-cell transcriptome at the post-transcriptional level, although the implication of RNA binding proteins (RBPs) remain largely unknown. Here we show that the RBPs TIA1 and TIAL1 are essential in B cells and, if deleted, there is a developmental block at the pro-B cell stage. TIA1 and TIAL1 have redundant functions. They act together as global splicing regulators for the expression of mRNAs including those involved in DNA damage repair in pro-B cells. Mechanistically, TIA1 and TIAL1 bind to 5’splice sites for exon definition, splicing and expression of DNA damage sensors like Chek2 and Rif1. In their absence, pro-B cells show exacerbated DNA damage, altered P53 expression and increased cell death. Altogether, our study uncovers the importance of tight regulation of mRNA splicing by TIA1 and TIAL1 for the expression of integrative transcriptional programs for DNA damage sensing and repair during B-cell development.
2022-12-20 | GSE186701 | GEO
Project description:The purpose of this experiment was to characterize the network of proteins that interact with TIA1, and to investigate whether tau exerts control over TIA1 protein interactions, TIA1 was immunoprecipitated from cortical brain tissue of 10 month-old WT (C57BL/6J), tau-/- and TIA1-/- mice. The specificity of the TIA1 IP was verified by immunoblotting with anti-TIA1 antibody (Fig. 3A), and the resulting TIA1 proteome was examined by mass spectrometry.
2018-10-26 | PXD003922 | Pride
Project description:Germinal centers (GCs) are essential for the establishment of long-lasting antibody responses. GC B cells rely on post-transcriptional RNA mechanisms to translate activation-associated transcriptional programs into functional changes in the cell proteome. However, the critical proteins driving these key mechanisms are still unknown. Here, we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses. TIA1- and TIAL1-deficient GC B cells fail to undergo antigen-mediated positive selection, expansion and differentiation into B-cell clones producing high-affinity antibodies. Mechanistically, TIA1 and TIAL1 control the transcriptional identity of dark- and light-zone GC B cells and enable timely expression of the prosurvival molecule MCL1. Thus, we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.
| S-EPMC10469172 | biostudies-literature
Project description:Background: Neuronal development is a tightly controlled process involving multi-layered regulatory mechanisms. While transcriptional pathways regulating neurodevelopment are well characterized, post-transcriptional programs are still poorly understood. TIA1 is an RNA-binding protein that can regulate splicing, stability, or translation of target mRNAs, and has been shown to play critical roles in neurodevelopment. However, the identity of mRNAs regulated by TIA1 during neurodevelopment is still unknown. Methods and Results: To identify the mRNAs targeted by TIA1 during the first stages of human neurodevelopment, we performed RNA immunoprecipitation-sequencing (RIP-seq) on human embryonic stem cells (hESCs) and derived neural progenitor cells (NPCs), and cortical neurons. While there was no change in TIA1 protein levels, the number of TIA1 targeted mRNAs decreased from pluripotent cells to neurons. We identified 2400, 845, and 330 TIA1 mRNA targets in hESCs, NPC, and neurons, respectively. The vast majority of mRNA targets in hESC were genes associated with neurodevelopment and included autism spectrum disorder-risk genes that were not bound in neurons. Additionally, we found that most TIA1 mRNA targets have reduced ribosomal engagement levels. Conclusion: Our results reveal TIA1 mRNA targets in hESCs and during human neurodevelopment, indicate that translation repression is a key process targeted by TIA1 binding and implicate TIA1 function in neuronal differentiation.
2021-06-01 | GSE166306 | GEO