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Series GSE232194 Query DataSets for GSE232194
Status Public on Sep 28, 2023
Title Olfactory receptor mRNAs act as selfish non-coding RNAs that enforce transcriptional singularity (Non-coding OR Hi-C & RNA-seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary To investigate roles for olfactory receptor coding sequence mRNA in trans olfactory receptor gene silencing, and OR-gene enhancer recruitment.
Olfactory receptor (OR) choice provides an extreme example of allelic competition for transcriptional dominance, as every olfactory neuron stably transcribes one out of more than ~2,000 OR alleles1,2. OR gene choice is mediated by a multi-chromosomal enhancer hub that activates transcription at a single OR3,4, followed by ORtranslation dependent feedback that stabilizes this choice5,6. However, with more than one OR enhancer hub in each nucleus7, the mechanism by which only one OR allele is chosen for transcription remains enigmatic. Here, using single cell genomics, we show that only one of the OR enhancer hubs formed in each neuron retains euchromatic features and sustains transcriptional competence. Further, we provide evidence that OR transcription recruits enhancers and reinforces enhancer hub activity locally, while OR RNA inhibits transcription in competing hubs over distance, promoting OR protein-independent transition to singularity. While OR RNA synthesis is sufficient to break the symmetry between equipotent enhancer hubs, OR translation stabilizes transcription at the prevailing hub, revealing dual non-coding and coding mechanisms implemented by OR RNAs for transcriptional prevalence. We propose that coding mRNAs can function as “selfish” non-coding RNAs that influence nuclear architecture, enhance their own transcription, and inhibit their competitors, with generalizable implications in probabilistic cell fate decisions.
 
Overall design CRISPR and transgene creation were used to generate inducible noncoding olfactory receptor genes to test the role of olfactory receptor RNA in olfactory receptor gene silencing and enhancer hub formation, which were assessed by performing RNA-seq and Hi-C.
Web link https://pubmed.ncbi.nlm.nih.gov/38123679/
 
Contributor(s) Pourmorady A, Lomvardas S
Citation(s) 38123679
Submission date May 10, 2023
Last update date Dec 28, 2023
Contact name Ariel Pourmorady
E-mail(s) adp2164@columbia.edu, arielpourmorady@gmail.com
Organization name Columbia University
Department Neurobiology and Behavior
Lab Lomvardas Lab
Street address 3227 Broadway
City New York
State/province NY
ZIP/Postal code 10027
Country USA
 
Platforms (3)
GPL21626 NextSeq 550 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL30172 NextSeq 2000 (Mus musculus)
Samples (41)
GSM7317664 OMPtTAtetOM71(nc)tg, control HiC, r1
GSM7317665 OMPtTAtetOM71(nc)tg, control HiC, r2
GSM7317666 gg8tTAtetOP2(nc), control HiC, r1
This SubSeries is part of SuperSeries:
GSE230380 Olfactory receptor mRNAs act as selfish non-coding RNAs that enforce transcriptional singularity
Relations
BioProject PRJNA971200

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE232194_HiC.Atf5-TR-WT.iRFP.mm10.mapq_30.1000.mcool 1.2 Gb (ftp)(http) MCOOL
GSE232194_OMPtTA.tetOP2.NormalFood.ImmediateFix.Liquid.HiC.AP60.AP94.merge.mm10.mapq_30.1000.mcool 1.5 Gb (ftp)(http) MCOOL
GSE232194_OMPtTAtetOM71KO.AP145.AP146.mm10.mapq_30.1000.mcool 806.4 Mb (ftp)(http) MCOOL
GSE232194_OMPtTAtetOP2KO.AP187.AP188_230921.mm10.mapq_30.1000.mcool 1.3 Gb (ftp)(http) MCOOL
GSE232194_gg8tTAtetOP2KO.GFPPos.AP147.AP149.mm10.mapq_30.1000.mcool 770.5 Mb (ftp)(http) MCOOL
GSE232194_rlog_rna_dev.txt.gz 2.3 Mb (ftp)(http) TXT
GSE232194_rlog_rna_mutants.txt.gz 3.2 Mb (ftp)(http) TXT
GSE232194_rna.OMPM71nc_v_OMPGFPOMPtTA_rlog_rna.txt.gz 377.7 Kb (ftp)(http) TXT
GSE232194_rna.OMPM71nc_v_OMPGFP_rlog_rna.txt.gz 389.5 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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