Part 6:Mapping The Epigenomic And Transcriptomic Interplay During Memory Formation And Recall in The Hippocampal Engram Ensemble

Mar 22, 2022

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Pls click here to Part 5

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Fig. 1. Temporal and spatial identification of activated and reactivated engram cells.

(a) Schematic representation of the experimental design. TRAP mice were initially exposed to training in which a conditioned (context) and unconditioned (foot shock, FS) stimulus were paired together within a brief window of 4-Hydroxytamoxifen (TAM) exposure. Four different neuronal populations (Basal, Activated –early, Activated –late and Reactivated) were sorted by flow cytometer and subjected to library preparation for nRNA-seq, ATAC- seq, Hi-C and pc-HiC.

(b) Representative images (DG) and whole hippocampus quantifications of eYFP+ neurons after TAM treatment in home cage (naïve, n = 4 mice/6 slices per animal), 1.5 h (Activated – early, n = 4 mice/4 slices per animal) and 5 days (Activated –late, n = 4 mice/8 slices per animal) after exposure after FS. The scale bar represents 200 μm. The dot-plot indicates the mean and error bars (SEM), one-way ANOVA (parametric, unpaired), F (2, 70) = 240.3, P<0.0001. Bonferroni’s multiple comparisons test; HC vs. Early ***P = 0.0007, HC vs. Late****P < 0.0001, Early vs. Late ****P < 0.0001.

(c) Quantifications ofActivated –late and Reactivated neurons in the hippocampus in two experimental groups; CFC with (CFC+TAM, n = 4 mice/8 slices per animal) or without (CFC NO-TAM, n = 4 mice/6 slices per animal) tamoxifen administration. The dot-plot indicates the mean and error bars (SEM), two-sided unpaired Student’s t-test, Activated – late; t=25.65, df=47, Reactivated; t=11.00, df=52, ****P < 0.0001.

(d) Representative images and quantifications from different regions ofthe hippocampus. Number of positive nuclei were analyzed using IMARIS (see methods) from the DG, CA1 and CA3. The scale bar represents 100 μm. n = 5 mice/ Activated –early: 6 slices per animal, n = 6 mice/ Activated –late: 6 Reactivated: 6 slices per animal. The dot-plot indicates the mean and error bars (SEM), one-way ANOVA (parametric, unpaired), Early; F (2, 42) = 13.46. Late; F (2, 95) = 556.3. Reactivated; F (2, 89) = 83.53. All Ps < 0.0001. Bonferroni’s multiple comparisons test, *P= 0.029, **P= 0.0075, ***P= 0.0009, ****P< 0.0001. (e) Valuation of context effects on the number and the distribution of hippocampal memory traces.

(f) Quantifications ofActivated -late and Reactivated neurons in the A-B (n = 6 mice/ 6 slices per animal), compared to the A-A (n = 5 mice/ 6 slices per animal) group. The dot- plot indicates the mean and error bars (SEM), two-sided unpaired Student’s t-test, Activated –late; t=0.08292, df=59, P = 0.9342. Reactivated; t=8.385, df=57, ****P< 0.0001.n.s = non-significant.


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Fig. 2. Chromatin accessibility landscape during memory formation and recall.

(a) Differential accessible regions (DAR)s are shown in a volcano plot (Pairwise comparisons, FDR < 0.01; fold changes > 1.5), n = 3 biologically independent samples. (b) Analysis of common gained- accessible region (stable), acquired 90 min after the FS (Activated -early), that remain accessible in the late state of consolidation (Activated -late) and recall (Reactivated). Overlapping stable DARs were only considered if they appeared in at least 2 biological replicates in a given condition.

(c) Representative IGV genome browser tracks of the Arc locus.

(d) Annotation analysis (HOMER tools) for all the DARs. Numbers on the y-axis indicate the Log2 ratio values of observed loci (number of DARs) over expected (total size (bp)) of the TTS, exons, introns, intergenic and promoters. P-value were calculated by HOMER

tools; Basal vs. Activated -early (Intergenic *P = 1.73 × 10−103), Activated -early vs. Activated -late (TTS *P = 0.0339, Promoter *P = 1.48 × 10−39), Activated -late vs. Reactivated (Promoter *P = 2.48 × 10−6), stable (Intergenic *P = 0.0358).

(e) Histone modification emission states (left) and enrichment analysis offers over emissions using ChromHMM. Fold enrichment scale (FE) 0–30. The and p-value was determined by the z-score value (as calculated in Extended Data Fig. 2c), Full analysis is reported in supplement table 3. *P < 0.00001, reported only for enriched values (not depleted)

(f) Chip-qPCR. Samples were immunoprecipitated with antibodies against H3K27ac or H3K4me1 and subjected to real-time PCR with two sets of primers for identified putative enhancers. H3K27ac: n = 4, H3K4me1 n = 3, The dot-plot indicates the mean and error bars (SEM), one-way ANOVA (parametric, unpaired) with Dunnett’s multiple comparisons test, Enhancer 1; H3K27ac - F (3, 12) = 4.664, P = 0.02, (Basal versus Activated-late *P = 0.0246, Basal versus Reactivated *P = 0.0232), H3K4me1 - F (3, 8) = 0.845, P = 0.506. Enhancer 2; H3K27ac - F (3, 12) = 5.221, P = 0.0155, (Basal vs. Activated -late **P = 0.0059), H3K4me1 - F (3, 8) = 1.719, P = 0.24. Enhancer 3; H3K27ac - F (3, 12) = 29.91, P < 0.0001, H3K4me1 - F (3, 8) = 10.39, P = 0.0039, (Basal vs. Activated -early *P = 0.0298, Basal vs. Activated -late **P = 0.0021, Basal vs. Reactivated **P = 0.0063). Enhancer 4; H3K27ac - F (3, 12) = 6.273, P = 0.0083, (Basal vs. Activated -late **P = 0.007, Basal vs. Reactivated *P = 0.0152), H3K4me1 - F (3, 8) = 9.901, P = 0.0045, (Basal vs. Reactivated **P = 0.0016).


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Fig. 3. Sub-compartment switching across the different phases of memory formation and recall.

(a) Hi-C correlation heatmap represents compartmentalization of chr6 for Basal, Activated - early and Activated -late cells. Compartments calculated by Juicer at 500 kb resolution (observed–expected normalized).

Activated -late). Compartment switch was only considered if a negative value was transformed to a positive value and vice versa.

(c) Representative images from IGV browser that shows stable compartment switch from A to B (upper panel) and B to A (lower panel) across different memory phases.

(d) Overlap analysis between DARs in the early phase (Basal vs. Activated –early) and stable switched compartment. Left Venn diagram shows gained DARs and stable compartment switched from B to A. Right, Venn diagram shows lost DARs and stable compartment switched from A to B.

(e) Illustration of activity-induced compartment switch and specific promoter-enhancers interactions.

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Fig. 4. Promoters interact more frequently with a distinct subset of enhancers during each

(a) Heatmap represent the interaction score as defined by Chicago, for each population. Basal: n = 3, Activated -early, Activated -late and Reactivated: n = 4 biologically independent samples.

(b) Violin plots show the distribution and the intensity (log10 scale) of interaction that were either unique or shared by at least 3 populations (common). One-way ANOVA (parametric, unpaired), F (4, 57922) = 2364, P < 0.0001. Bonferroni’s multiple comparisons test, n.s = non-significant (P = 0.7659), *P < 0.0001.

(c) Frequency of promoter-enhancer interaction as measured by 3C-qPCR for selected loci. Four sets of primers encompassing interaction between promoter-enhancer (P/E), and three random loci inside the loop (P/Ein), outside the loop (P/Eout), and on the promoter (P/Pin).

Reads were normalized to promoter-enhancer interaction values of the housekeeping gene βActin. n = 3 biologically independent samples. Data are presented as mean values with error bars indicate the SEM, two-way ANOVA. Eif3d; population × interaction location (F

(9, 32) = 1.917, P=0.0851), effect of interaction location only (F (3, 32) = 22.64, P < 0.0001). Grik3; population × interaction location F (9, 32) = 0.1716. Bonferroni’s multiple comparisons test, P/E Basal vs. Reactivated **P = 0.0019.

(d) Representative priming events of the Eif5a locus. IGV Genome browser tracks presenting chromatin accessibility dynamics (colored tracks) on the promoter (gray rectangle) and enhancers (blue rectangle). WashU browser tracks present significant promoter-enhancer interaction via arcs (purple - Basal, light green - Activated -early, dark green - Activated - late, and orange - Reactivated).



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Fig. 5. Transcriptional signature of reactivated engram neurons

(a) Pairwise analysis of DEGs from the hippocampus trap mice that were exposed to CFC are shown in a volcano plot (FDR<0.01; log2FC > 2). n = 3 biologically independent samples.

unpaired), followed by Bonferroni’s multiple-comparison test. Dw–Late; F (3, 1032) = 42.19, Up-Late; F (3, 280) = 752.5, Stable; F (3, 764) = 92.28, Reactivation; F (3, 1744) =597.4. All Ps < 0.0001. multiple comparisons test, n.s = non-significant, ***P < 0.0001. (d) Gene ontology (GO) analysis (ToppFun) for DEGs that were identified in each cluster. (e) Representative DEGs from each cluster. log2FC from the basal-state is presented in three biological replicates. Line represent calculated average. n = 3 biologically independent samples, one-way ANOVA (parametric, unpaired) with Dunnett’s multiple comparisons test, n.s = non-significant. Gad1; F (3, 8) = 4.387, P= 0.04. *P = 0.0268. Gabrb3; F (3, 8) = 6.184, P=0.0177. *P = 0.0441. Rest; F (3, 8) = 23.23, P=0.0003. ***P = 0.0268. Map4k4; F (3, 8) = 6.244, P=0.0172. *P = 0.0151. Nefl;F (3, 8) = 12.06, P=0.0024. **P = 0.0059, **P = 0.0014. Nefh; F (3, 8) = 21.50, P=0.0003. *P = 0.016, ***P = 0.0008, ***P = 0.0002. Eif5a; F (3, 8) = 8.482, P=0.0072. **P = 0.004. Eif4h; F (3, 8) = 26.58, P=0.0002. ***P =0.0001.

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(f) Representative images and quantification of Eif4e protein levels from Activated -early, Activated -late, and Reactivated. For quantification, two separate surfaces were built on IMARIS; cell soma and dendritic shaft. The number ofEif4e puncta were measured only in those surfaces boundaries. Data for dendritic shaft is presented as a ratio between number and the length (μM). The scale bar represents 10 μm. n = 4 mice /5 section per animal, boxplot indicates the mean, interquartile range and the minimum and maximum, one-way ANOVA (parametric, unpaired), Shaft; F (2, 28) = 5.113, P=0.0128. Soma; F (2, 43) = 3.026, P=0.0589. Bonferroni’s multiple comparisons test; Shaft; Activated -early vs. Reactivated *P = 0.0324, Activated -late vs. Reactivated *P = 0.0324

(g) Representative images (left panel) and quantification (right panel) of the Gria1 protein levels, during different phases of memory. Three populations of neurons (Activated -early, Activated -late, and Reactivated) were analyzed, based on the immunoreactivity of eYFP and endogenous Arc. For quantification, MARIS surfaces were built on the dendritic shaft and the number ofGRIA1 puncta were measured only in the boundaries of the surface (<1μm threshold). Data is presented as a ratio between several puncta and the shaft length. The scale bar represents 10 μm. n = 4 mice /5 section per animal, boxplot indicates the mean, interquartile range, and the minimum and maximum, one-way ANOVA, F (2, 16) = 15.22, P = 0.0002. Bonferroni’s multiple comparisons test, **P = 0.002, ***P = 0.0005.


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Fig. 6. Sequential reprogramming of chromatin accessibility, promoter-enhancer interactions and

Line graphs for each K-means cluster show the average (log2 scale) of (a) transcriptional changes (p-values as reported in Fig. 5c, mean of n = 3 biologically independent samples) (b) chromatin accessibility (normalized RPKM values, mean of n = 3 biologically independent samples) and (c) promoter-enhancer interaction scores (as calculated by Chicago, mean basal: n = 3, Activated -early, Activated -late and Reactivated: n = 4 biologically independent samples) Repeated measures one-way ANOVA (between groups).

638.7. Stable; F (2.437, 4504) = 717.9. Reactivation; F (2.434, 8481) = 1425. All Ps < 0.0001. Interaction scores; Dw-Late; F (2.833, 7054) = 46.86. Up-Late; F (2.94, 5442) = 14.87. Stable; F (2.91, 5702) = 21.5. Reactivation; F (2.86, 11188) = 44.94. All Ps < 0.0001. Bonferroni’s multiple comparisons test, ***P < 0.0001.

(d-e) Characterization of motif enrichment on interacting enhancers, in each cluster. ChromHMM was used to build the emission states using the HOEMR motif database (Egr1, Ap1, Slug, Plagl1, Hic2, Rest, CTCF, Yy1, Mecp2) and previously published ChIP-seq data (Ap1-Junb12, CTCF47, Mecp248). Four states were identified as i) control – random genome sampling, ii) strong repressors iii) bivalent iv) strong activator. Fold enrichment scale (FE)

0.15–20.







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