Silc1 long noncoding RNA is required for efficient memory formation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA894586 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22055034_1.fastq.gz | Fastqsanger.gz | |||
| SRR22055034_2.fastq.gz | Fastqsanger.gz | |||
| SRR22055035_1.fastq.gz | Fastqsanger.gz | |||
| SRR22055035_2.fastq.gz | Fastqsanger.gz | |||
| SRR22055036_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 102 |
Similar Datasets
Project description:A rich repertoire of long noncoding RNAs (lncRNAs) is expressed in the mammalian nervous system, but their significance and functions remain largely unknown. Co-expression analysis, referred to as guilt-by-association, is often used as a proxy for prediction of lncRNA function, but the validity of the assumptions of this approach remains unclear. Here, we study the functions in the central nervous system of Silc1, a lncRNA we previously shown to be important for neuroregeneration in the peripheral nervous system. Silc1 is located in a gene desert ~200 Kb away from its cis-regulated target gene, Sox11. Silc1 is broadly expressed in the adult brain, and surprisingly, in the hippocampus Silc1 and Sox11 are anti-correlated in their expression domains. Despite this, upon exposure to novel environment, Silc1 transcription or its RNA product are important for proper induction of Sox11 mRNA and protein throughout CA1-3, and for proper expression of key Sox11 target genes. Furthermore, an intact Silc1 is required for efficient spatial learning (but notably not for memory retrieval). Silc1 levels decline during aging and in models of Alzheimer’s disease. Overall, we uncover a novel pathway, acting in mature neurons, which need Silc1 to activate Sox11, a transcription factor mostly studied exclusively in the context of immature neurons, and in turn to induce a neuronal growth-associted transcriptional program required for efficient memory formation.
2023-07-29 | GSE216643 | GEO
Project description:Kat2a regulates hippocampal memory formation
| PRJNA231958 | ENA
Project description:Epigenetic changes are crucial for the generation of immunological memory. Failure to generate or maintain these changes will result in poor memory responses. Similarly, augmenting or stabilizing the correct epigenetic states offers a potential method of enhancing immune memory. Yet the transcription factors that regulate these processes are poorly defined, as are the target genes they control and they chromatin-modifying complexes they recruit. Using model pathogens and three different mouse models, we find that the widely expressed transcription factor Oct1 and its cofactor OCA-B are selectively required for the in vivo generation of functional CD4 memory. In vitro, both proteins are required to maintain a poised state at the Il2 target locus in resting but previously stimulated CD4 T cells, and to generate robust Il2 expression upon restimulation. Gene expression profiling indicates that OCA-B is also required for the robust re-expression of multiple other targets including Ifng and Il17a. ChIPseq identify multiple differentially expressed direct targets. We identify an underlying mechanism involving OCA-B recruitment of the histone lysine demethylase Jmjd1a to targets such as Il2 and Ifng. The findings pinpoint Oct1 and OCA-B as unanticipated mediators of CD4 T cell memory. Examination of transcription factor occupancy in CD4 T cells upon rest and restimulation.
2015-09-17 | E-GEOD-65918 | biostudies-arrayexpress
Project description:Epigenetic changes are crucial for the generation of immunological memory1-4. Failure to generate or maintain these changes will result in poor memory responses. Similarly, augmenting or stabilizing the correct epigenetic states offers a potential method of enhancing immune memory. Yet the transcription factors that regulate these processes are poorly defined, as are the chromatin modifying complexes they recruit and the chromatin modifications they control. Using pathogen infection models and three different mouse models, including a new conditional allele, we find that the widely expressed transcription factor Oct15, and its cofactor OCA-B6,7, are selectively required the in vivo generation of functional CD4 memory. In vitro, both proteins are also required to maintain a poised state at the Il2 target locus in resting but previously stimulated CD4 T cells, and to generate robust Il2 expression upon restimulation. OCA-B is also required for the robust re-expression of other known targets including Il17a, and Ifng. We identify an underlying mechanism involving OCA-B recruitment of the histone lysine demethylase Jmjd1a8 to targets such as Il2 and Ifng. The findings pinpoint Oct1 and OCA-B as unanticipated mediators of CD4 T cell memory. Examination of 4 different conditions in 2 genotypes
2015-09-17 | E-GEOD-62202 | biostudies-arrayexpress
Project description:This project examined the role of linear polyubiquitination in the amygdala during fear memory formation in male and female rats.
2021-06-28 | PXD025483 | Pride
Project description:1. Evaluate the diagnostic value of long noncoding RNA (CCAT1) expression by RT-PCR in peripheral blood in colorectal cancer patients versus normal healthy control personal.
2. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in diagnosis of colorectal cancer patients & its relation to tumor staging.
3. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in precancerous colorectal diseases.
4. Compare long noncoding RNA (CCAT1) expression with traditional marker; carcinoembryonic antigen (CEA) and Carbohydrate antigen 19-9 (CA19-9) in diagnosis of colorectal cancer.
| 2330122 | ecrin-mdr-crc
Project description:Mitophagy, a central guarding process to maintain mitochondrial quality, is commonly impaired in human diseases, but its impacts in adaptive immunity remains unclear. Here, we found that Parkinson’s patients have reduced CD8+ memory T cell abundance and failed to form memory T cells upon COVID-19 vaccination. We further unveiled that regulators of mitophagy, including Parkin and NIX, were upregulated in response to IL-15 for supporting memory T cell formation. Our results indicate that the mitophagy machinery orchestrate survival and metabolic dynamics required for memory T cell formation.
2025-05-20 | GSE223004 | GEO
Project description:Dynamics of hippocampal protein expression during long-term spatial memory formation
2015-12-01 | PXD002176 | Pride
Project description:The hippocampal formation is a brain structure essential for higher-order cognitive functions. It has exquisite differences in anatomical organization and cellular composition, and hippocampal sub-regions have different properties and functional roles. Areas CA1 and CA3 in particular, are key sub-regions for learning and memory formation that fulfill complementary but specific functions. The molecular basis for such specific properties and the link to learning and memory remain unknown. Here using a SWATH-MS proteomic approach and bioinformatic tools, we identify a selective proteomic signature in area CA1 and CA3, and reveal their specific dynamics during memory formation. We show that 30% of all quantifiable proteins are differentially expressed in area CA1 and CA3 at baseline, and that each proteome responds differently during the formation of memory for object or object location. Using clustering and cross-correlational analyses, we outline specific temporal proteomic profiles and an increased correlation between both forms of memory within area CA1, but not within area CA3. These results provide new insight into a proteomic basis for hippocampal sub-region molecular and functional specificity.
2018-03-28 | PXD006382 | Pride
Project description:Epigenetic factors are well established players in memory formation. Specifically, DNA methylation is necessary for the formation of long-term memory in multiple brain regions including the hippocampus. Despite the demonstrated role for DNA methyltransferases (Dnmts) in memory formation whether individual Dnmts play unique or redundant functions in long-term memory formation is not well established. Furthermore, the downstream processes controlled by the Dnmts during the consolidation of memory are not investigated. In this study, we investigated the requirement for Dnmt3a1, the predominant Dnmt in the adult brain, in hippocampal long-term memory formation. Furthermore, we identified an activity-regulated Dnmt3a1-dependent genomic program. Our data showed that Dnmt3a1, similarly to its isoform Dnmt3a2, plays a critical role in memory formation. Furthermore, we uncovered Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 during the formation of memory. Intriguingly, we found that Nrp1 expression is selectively regulated and a specific downstream effector of Dnmt3a1, but not Dnmt3a2. Taken together, our study uncovered a Dnmt3a isoform specific mechanism in memory formation and further highlighted the complex and highly regulated functions of distinct epigenetic regulators in brain function.
2024-05-06 | GSE232630 | GEO