GSE158730
NFI transcription factors regulate zonal olfactory receptor expression
Expression of one out of > 1000 olfactory receptor (OR) genes is stochastic, yet organized into anatomic "zones" along the dorsoventral axis of the olfactory epithelium. Here we profile the gene expression, chromatin state and nuclear architecture of olfactory sensory neurons and olfactory progenitors of different zones. We discovered that zonal OR expression is specified by two processes: low-level polygenic transcription of OR genes in olfactory progenitors, as wells as the chromatin structure and nuclear architecture during olfactory differentiation. Specifically, in cells of any zonal segment, polygenic transcription in olfactory progenitors defines the OR repertoire eligible for OR choice as the cells mature, while an increased level of heterochromatin and chromatin compaction represses ectopic more dorsally expressed ORs.  We find that this process is regulated by the NFI family of transcription factors that are expressed in a graded fashion in the olfactory epithelium. Conditional deletion of NFI A, B, and X results in a transformation of the chromatin state and nucellar architecture and an accompanying shift in the preferred OR repertoire. Overall design: Several types of data are included: RNA-seq profiles the expression differences between GBC, INP, iOSN and mOSN cells from zone1 (dorsal most), zone2/3 (dorsomedial) and zone4/5 (ventral most). RNA-seq data also profiles gene expression in the olfactory epithelium upon conditional NFI A, B and X deletion either early (in olfactory progenitors) or late (in mature OSNs). RNA-seq also profiles gene expression changes in mature OSNs and olfactory progenitors from zone5 (the ventral most zone) in NFI A,B,X deletion, NFI A,B deletion, NFIX deletion, and NFI A,B,X heterozygotes. Single-cell RNA-seq in cells from zone1/2 and zones 3/4/5 profiles gene expression in single cells.  Spatial transcriptomics shows the shift in the position of olfactory receptor expression within the olfactory epithelium upon Nfi A,B,X deletion. Native ChIP-seq for H3K9me3 and H3K79me3 profiles deposition of these chromatin marks during differentiation (in GBC, INP, iOSN and mOSN cells), in OSNs from different zones (zone1, zone2/3, zone4/5 and Olfr1507+ expressing zone5 mOSNs), as well as in zone4/5 cells upon NFI A,B,X deletrion. Hi-C in mOSNs from zone1 and zone4/5, iOSNs from zone1 and zone4/5, and cells from NFI knockout and wt zone4/5 shows differences in nuclear architecture in cells from different zones, and changes upon NFI A,B,X knockout. Dip-C in zone1 and zone4/5 mOSNs shows nuclear architecture of single cells. Hi-C in OSNs expressing a transgenic knock in teto-Olfr17 allele and Gng8-tTA driver shows nuclear architecture in cells that received a pulse of Olfr17 during the progenitor stage.