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Series GSE216643 Query DataSets for GSE216643
Status Public on Jul 29, 2023
Title Silc1 long noncoding RNA is required for efficient memory formation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
 
Overall design RNA-seq and ATAC-Seq from hippocampus following different manipulations and RNA-seq from cultured hippocampus neurons. Single-nucleus RNA sequencing from hippocampus in WT and Silc1-/- hippocampus
 
Contributor(s) Ben-Tov Perry R, Ulitsky I
Citation(s) 37742186
Submission date Oct 26, 2022
Last update date Oct 28, 2023
Contact name Igor Ulitsky
E-mail(s) igor.ulitsky@weizmann.ac.il
Organization name Weizmann Institute of Science
Street address Hertzl St.
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (53)
GSM6685150 ATAC-seq in hippocampus from Silc1-/- mice, replicate 1
GSM6685151 ATAC-seq in hippocampus from Silc1-/- mice, replicate 2
GSM6685152 ATAC-seq in hippocampus from Silc1-/- mice, replicate 3
Relations
BioProject PRJNA894586

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE216643_ATAC_novel.peaks.bed.gz 2.7 Mb (ftp)(http) BED
GSE216643_RAW.tar 5.3 Gb (http)(custom) TAR (of BW, MTX, RESULTS, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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