Extended Data Fig. 6: Neuron subtype-specific activation programs, hypothesized protein–protein interactions and upstream regulatory motifs.
From: Persistent transcriptional programmes are associated with remote memory
a, Fraction of cells in each neuron subtype that are induced with the transcriptional program (that is, DEGs) from a neuron subtype. Overall, the activation program of each TRAPed neuron subtype is found to be more specific to it than the inactive population, or other subtypes. b, Left, de novo regulator motif discovery: analysis was performed using HOMER on the subset of 99 remote-memory-associated DEGs by looking at the sequences -400 to +100 bp from the TSS. 12 de novo and 2 known motifs were found (only motifs with an enrichment P value <10−2) were kept). Heat map depicts the ‘motif score’ of each DEG for each motif, and genes and motifs were clustered via the ward.D method. Right, bar graph depicting the percentage of the DEGs (target sequences) that possess a match for the motif within -400 to +100 bp from the TSS, vs the percentage of background sequences. For de novo motifs, the best match gene is listed on the right. HIF1b and HIF1a are matches to known motifs. c, Left, hypothesized protein–protein interactions of a subset of recall-dependent DEGs (TRAPed FR/NF) using the STRING database (https://string-db.org/). Only genes that are connected at a confidence level of 0.4 (medium) are shown. Connections indicate a possible existence of an interaction between two proteins. Genes are coloured by up of downregulation in FR/NF. Right, same network plot, with nodes coloured by the neuron subtype which differentially regulates the DEG.
