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R script to generate Figure 3B in Cid, Marquez-Galera et al., (2021) (https://doi.org/10.1016/j.celrep.2021.109229)., Peer reviewed

This data table is related to the published article Cid et al., (2021), doi: https://doi.org/10.1016/j.celrep.2021.109229., Table shows results of differential expression analysis of RNA-seq data from superficial and deep sublayers of the CA1 region of the dorsal hippocampus from the brain of healthy adult rats. Superficial and deep sublayers of the CA1 region were isolated by laser capture microdissection prior to RNA isolation and library construction for RNA-seq., Peer reviewed

This data table is related to the published article Cid et al., (2021), doi: https://doi.org/10.1016/j.celrep.2021.109229., Table shows results of differential expression analysis of RNA-seq data from superficial and deep sublayers of the CA1 region of the dorsal hippocampus from the brain of epileptic adult rats. Superficial and deep sublayers of the CA1 region were isolated by laser capture microdissection prior to RNA isolation and library construction for RNA-seq., Peer reviewed

This PDF file includes: Figs. S1 to S8. Legends for tables S1 to S3. Legends for movies S1 to S3 Other Supplementary Material includes (zip): Tables S1 to S3. Movies S1 and S2, Peer reviewed

Gene expression of human chemokines and their receptors analyzed by using RT² Profiler™ PCR Array Human Chemokines & Receptors (GeneGlobe ID - PAHS-022Z, Qiagen) on a CFX Connect Real-Time PCR System (Biorad, Hercules, CA) according to manufacturer instructions., Provided is raw data expressed as Ct values corresponding to gene expression of human chemokines and their receptors analyzed by using RT² Profiler™ PCR Array Human Chemokines & Receptors (GeneGlobe ID - PAHS-022Z, Qiagen) on a CFX Connect Real-Time PCR System (Biorad, Hercules, CA). Samples: Healthy, mildly and severely inflamed tissue biopsies were collected from all patients and preserved in RNAlater. Tissue samples were obtained from 20 patients of Cronh's disease, grouped by their treatment in 4 groups (untreated, adalimumab, ustekinumab and vedolizumab). Each treatment group has 5 patients associated, with 3 samples from each patient corresponding to the tissue's relative degree of inflammation (Healthy tissue, mildly inflamed tissue, severely inflamed tissue). Clinical and analytical characteristics of patients were recorded at inclusion in the study. Disease clinical activity was determined by Crohn’s disease activity index (CDAI)>150 and presence of clinical symptoms of relapse. Disease endoscopic activity was determined by Simple Endoscopic Score for Crohn Disease (SES-CD). All patients were Caucasian of Mediterranean ethnicity and were classified according to the Montreal classification. All included patients received diaries to record symptoms 1 week before inclusion and sample collection, and signed an informed consent to participate in the study. The study was approved by the Ethics Committee of Hospital General Universitario and performed in accordance with the ethical standards laid down in the 1964 Declaration of Helsinki and its later amendments. All patients gave their informed consent prior to their inclusion in the study., Peer reviewed

The supporting information: Figure S1. Differentiating CBPf/f neurospheres infected with Cre-recombinase-encoding viruses do not express CBP. Representative images of differentiating secondary neurospheres infected with control (DsRed) or Cre-recombinase-encoding Lentiviruses stained with antibodies specific for CBP and counterstained with DAPI. Scale bars: 100 µm; Figure S2. Sensitivity analysis of snRNA-seq. Violin plots show the distribution of the number of transcripts (left, scored by UMIs) and genes (right) detected per cell for differentiating neurospheres from control (CTRL), CBPf/f (CBP), and p300f/f (P300) neurospheres. UMIs: unique molecular identifiers; Video S1. Time-lapse culture over 2 days of a control differentiating neurosphere infected with control plasmids; Video S2. Time-lapse culture over 2 days of a differentiating CBPf/f neurosphere infected with Cre plasmids; Video S3. Time-lapse culture over 2 days of a differentiating p300f/f neurosphere infected with Cre plasmids; Table S1. Gene markers for individual clusters of snRNA-seq data identified by differential expression testing using the Wilcoxon rank sum test (see methods); ; Table S2. Differential expression analysis between Crebbpf/f + Cre and control neurosphere for cluster 0 and cluster 5, using the Wilcoxon rank sum test (see methods)., Peer reviewed

Extended Data: Figure 1-1 RNA-seq samples generated in this study. Download Figure 1-1, XLSX file. Figure 1-2 Two sheets. a, Downregulated genes in the CBP-ifKO RNA-seq. b, Upregulated genes in the CBP-ifKO RNA-seq (see attached Excel file)., Figure 1: CBP, but not p300, is necessary for the normal expression of neuronal plasticity-related genes. a, Scheme presenting the genetic strategy for the generation of CBP-ifKOs and p300-ifKOs illustrated with the immunostaining of sagittal brain slices of control and ifKOs that demonstrate the loss of CBP or p300 in areas where the Camk2a-creERT2 transgene is expressed. b, IHC analysis demonstrated the loss of CBP in pyramidal and granular cells in the hippocampus of young adult (3- to 6-month-old) ifKO mice. Gene ablation is also appreciable in amygdala and cortex, but not in brain areas where the Cre recombinase is not expressed. Scale bar, 500 µm. c, WB of CBP-ifKO (green bars) and control (WT, black bars) hippocampal protein extracts confirmed the loss of CBP expression in young adult (3- to 6-month-old) CBP-ifKOs using two different antibodies against CBP. No upregulation of p300 was observed. d, RNA-seq was used for the differential expression profiling of CBP-ifKOs and control littermates (Extended Data Figs. 1-1, 1-2, additional details). Heatmap representations of upregulated and downregulated genes in young adult (3- to 6-month-old) CBP-ifKOs (top panel) and p300-ifKOs (bottom panel) referred to their respective control littermates. The creERT2 driver-related genes Esr1 and Arsi are the only genes differentially expressed in p300-ifKOs. e, GO analysis of downregulated genes in CBP-ifKOs. The top 20 GO biological process terms are shown. f, IGV profiles of two representative genes downregulated in CBP-ifKOs. g, qRT-PCR assays confirmed the downregulation of CBP target genes in the hippocampi of CBP-ifKOs. h, Comparison of DEG sets in dKAT3-ifKOs (p-adjusted < 0.05; no fold cutoff) and CBP-ifKOs. i, Overlap between the sets of genes downregulated in dKAT3-ifKOs (p-adjusted < 0.05; no cutoff) and CBP-ifKOs. j, The comparison of differential expression profiles in CBP-ifKO and Crebbp+/− mice revealed a gene dose effect and showed that many DEGs in CBP-ifKOs were also reduced in heterozygous mice, although did not reach the threshold for significance. *p-value < 0.05; **p-value < 0.01; ***p-value < 0.001., Peer reviewed

Extended Data: Figure 2-1. Extended information on statistical analysis of behavioral experiments in Figure 2. XLSX file., The loss of CBP, but not p300, in forebrain principal neurons causes cognitive deficits. a, Scheme indicating the age at the time of TMX administration to trigger gene ablation, the interval until behavioral testing, and the battery of behavioral tasks (Extended Data Fig. 2-1, additional detail). Experiments were performed in young adult (3- to 6-month-old) mice. b, Behavior in an open field evaluated as total distance traveled. c, No difference in time spent in the center, closed and open arms in the elevated plus maze test. d, Latency to fall in the RotaRod test. e, Percentage of immobility time in the Porsolt forced swimming task. f, Number of balls buried in the marble-burying task. g, Discrimination index during training and testing in the novel object recognition memory task. h, The sociability index reflects the preference of the animal for interacting with another mouse rather than an object, whereas the social recognition index reflects the preference of the animal for interacting with an unfamiliar mouse in the social recognition memory task. i, Graph presents the daily average latency to find the platform in the MWM task. V, Visible platform; H, hidden platform. j, Performance in the contextual and cued fear-conditioning tasks measured as freezing 24 h after training. k, l, Normal behavior of p300-ifKOs in an open field, no differences in overall activity (a) or anxiety measured as time near the wall (b). m, Normal behavior of p300-ifKOs in the RotaRod. n, Normal behavior of p300-ifKOs in the Porsolt forced swimming task. o, Normal behavior of p300-ifKOs in marble-burying task. p, Normal performance of p300-ifKOs in the novel object recognition task. q, Normal performance of p300-ifKOs in the sociability and social recognition task. r, p300-ifKOs show no differences in learning and memory in the MWM. The panel shows only the latency curve, but similarly no difference was observed in different parameters during the visible and hidden platform tasks and the probe trials. s, Normal performance of p300-ifKOs in the fear conditioning task. ns: non significant; *p-value < 0.05; **0.001 < p-value < 0.01; ***p-value < 0.001., Peer reviewed

Extended information on statistical analysis of behavioral experiments in Figure 3. XLSX file., Aging worsens the neurologic deficits in CBP-ifKO mice. a, Average weight in young adult and aged mice of both sexes. b, qRT-PCR assays show the dysregulation of LRGs in aged (15- to 20-month-old) CBP-ifKOs, as previously shown in younger animals (compare Fig. 1g, results). c, qRT-PCR assays show that several IEGs were not significantly downregulated at the basal state (Fig. 6a, Extended Data Fig. 1-2). d, Representative coronal MR brain images of aged control and CBP-ifKO mice (top) and graph showing the comparison of hippocampal areas between both genotypes (bottom). e, Immunostaining against GFAP and NeuN in the dentate gyrus (DG) and CA1 area of 15- to 20-month-old CBP-ifKOs and control littermates, revealed a normal histology and cellular composition, indicating no apparent gliosis or neurodegeneration in CBP-ifKOs. Scale bars, 100 µm. f, qRT-PCR assay shows comparable levels of Gfap transcripts in 15- to 20-month-old CBP-ifKOs and control littermates, consistent with the absence of active gliosis in aged CBP-ifKOs. g, Gait analysis in young adult and aged control and CBP-ifKO mice. h, MWM escape latency graph in aged CBP-ifKOs and control littermates (Extended Data Fig. 3-1, additional detail). i, Memory in the contextual FC (CFC) and cued FC tasks measured as freezing 24 h after training. j, Fear conditioning and extinction in young adult (left) and aged (right) CBP-ifKOs and control littermates. ns: non significant; *p-value < 0.05; **0.001 < p-value < 0.01; ***p-value < 0.001., Peer reviewed

Extended Data: ChIP-seq samples generated in this study. Figure 4, XLSX file., H2B lysine acetylation deficits. a, WB against different core histone acetylations in hippocampal protein extract of CBP-ifKOs and control littermates (n = 4). The quantification of the signal is shown on the right. *p-value < 0.05; **0.001 < p-value < 0.01; ***p-value < 0.001. A significant decrease in H2A-ac, H2B-ac, and H3K27ac was observed. H3K9,14ac and H4-ac were unaffected by the loss of CBP. b, ChIP-seq was used for the analysis of differential histone acetylation in CBP-ifKOs and control littermates (Extended Data Fig. 4-1, additional detail). Metagene ChIP-seq signal for H2B-ac in the sets of no-DEGs and downregulated genes in CBP-ifKOs. c, IHC for acetylation of H2B in CBP-ifKOs and control littermates. The field shows the nucleus of an interneuron in which creERT2 is not expressed, and therefore there was no loss of CBP immunoreactivity. d, ChIP-qPCR assays on chromatin extracts confirm a global decrease in H2Bac in CBP-ifKOs in all the assessed regions, including intergenic chromatin. e, WB against acetylation of different lysine residues in the N-tail of histone H2B. All the acetylated residues investigated were significantly decreased. The quantification of the signal referred to total H2B is shown in the right bar graph. f, WB against other post-translational modifications of the tail of histone H2B in hippocampal protein extract of CBP-ifKO and control littermates. The quantification of the signal is shown in the bar graph. g, WB against the acetylated form of different core histones (top) and the acetylation of specific lysine residues in the H2B N-tail (bottom) in hippocampal protein extracts of Crebbp+/− and wild-type littermates. The quantification of the signal is shown on the right bar graphs. h, ChIP-seq density graph for H2Bac in Crebbp+/− and wild-type littermates., Peer reviewed