Npas4: Linking Neuronal Activity to Memory

Immediate-early genes (IEGs) are rapidly activated after sensory and behavioral experience and are believed to be crucial for converting experience into long-term memory. Neuronal PAS domain protein 4 (Npas4), a recently discovered IEG, has several characteristics that make it likely to be a particularly important molecular link between neuronal activity and memory: it is among the most rapidly induced IEGs, is expressed only in neurons, and is selectively induced by neuronal activity. By orchestrating distinct activity-dependent gene programs in different neuronal populations, Npas4 affects synaptic connections in excitatory and inhibitory neurons, neural circuit plasticity, and memory formation. It may also be involved in circuit homeostasis through negative feedback and psychiatric disorders. We summarize these findings and discuss their implications.National Institutes of Health (U.S.) (Grant MH091220-01

PstI-MspI SNP table - UNEAK - 23 worldwide populations

Generated with mnC=0.8, minCov=1 and a MAF=0.01. Use this file as input to generate the “UNEAK-PstI/MspI” SNP tables with different parameters (mnC, minCov and MAF) using the countCleaner script found at https://bitbucket.org/mimeeb/gbs (Windows-based software)

Supplemental Figure 1

Relationship between the median coverage (median number of reads/locus/population supporting each SNP) and the number of SNPs retained by the two pipelines at a minimum allele frequency of 1% (MAF = 0.01) and 5% (MAF = 0.05)

Supplemental Figure 2

Number of SNPs retained by UNEAK and PoPoolation2 pipelines at different parameter values on an ApeKI library from 23 worldwide populations of Globodera rostochiensis. ‘MAF’ is the minimum allele frequency; ‘minCov’ is the minimum number of reads/locus/population required to accept a SNP; ‘mnC’ is the minimum proportion of populations in which a locus must have been scored to be accepted. PoPoolation2 does not allow missing data (mnC = 1.0). *The number of SNPs identified by UNEAK was not influenced by the ‘mnC’ value when the minimum allele frequency was set to 5% (MAF = 0.05)

UNEAK PstI-MspI allele frequencies - Validation assay - 28 Quebec populations from 2 fields + 1 outgroup

Allele frequencies calculated from UNEAK exact counts (mnC=1, minCov=20 and MAF=0.01) and used for principal component analysis (PCA) of Globodera rostochiensis populations from two fields of the province of Quebec, Canada and an unrelated population from France

Supplemental Figure 3

Principal component analyses of 23 worldwide populations of Globodera rostochiensis from different pathotypes (Ro1, Ro2, Ro3, Ro4, Ro5 and a mixed population of Ro2/Ro3). Calculated with the prcomp() function in R. Based on genome-wide allele frequencies of different number of loci obtained from the PstI/MspI library supported by six different minimum coverage values (minCov = 5, 10, 20, 30, 40 or 50 reads/locus/population). Computed by the PoPoolation2 pipeline with a minimum allele frequency of 1% (MAF = 0.01) and no missing data allowed (mnC = 1.0)

Supplemental Figure 4

Principal component analysis of 23 worldwide populations of Globodera rostochiensis. Calculated with the prcomp() function in R. Based on genome-wide allele frequencies of 1,277 loci obtained from the PstI/MspI library, and computed by the PoPoolation2 pipeline with a minimum allele frequency of 1% (MAF = 0.01), no missing data allowed (mnC = 1.0) and a minimum coverage of 20 reads/SNP/population (minCov = 20). Colors represent the different pathotypes: Black = Ro1; Yellow = Ro2; Green = Ro3; Red = Ro4; Blue = Ro5 and Grey is the mixed Ro2/3 sample

Sample description

Details about the origin (Country, province and field) of the samples, which experiment and figures they were used in and accession numbers (bioproject and biosample numbers)

nGr.v1.0.iprscan.xml

inter pro scan as gzipped xm

nGr.v1.0.iprscan.xml

interproscan as ts