Epigenetic priming of immune/inflammatory pathways activation and abnormal activity of cell cycle pathway in a perinatal model of white matter injury.

Prenatal inflammatory insults accompany prematurity and provoke diffuse white matter injury (DWMI), which is associated with increased risk of neurodevelopmental pathologies, including autism spectrum disorders. DWMI results from maturation arrest of oligodendrocyte precursor cells (OPCs), a process that is poorly understood. Here, by using a validated mouse model of OPC maturation blockade, we provide the genome-wide ID card of the effects of neuroinflammation on OPCs that reveals the architecture of global cell fate issues underlining their maturation blockade. First, we find that, in OPCs, neuroinflammation takes advantage of a primed epigenomic landscape and induces abnormal overexpression of genes of the immune/inflammatory pathways: these genes strikingly exhibit accessible chromatin conformation in uninflamed OPCs, which correlates with their developmental, stage-dependent expression, along their normal maturation trajectory, as well as their abnormal upregulation upon neuroinflammation. Consistently, we observe the positioning on DNA of key transcription factors of the immune/inflammatory pathways (IRFs, NFkB), in both unstressed and inflamed OPCs. Second, we show that, in addition to the general perturbation of the myelination program, neuroinflammation counteracts the physiological downregulation of the cell cycle pathway in maturing OPCs. Neuroinflammation therefore perturbs cell identity in maturing OPCs, in a global manner. Moreover, based on our unraveling of the activity of genes of the immune/inflammatory pathways in prenatal uninflamed OPCs, the mere suppression of these proinflammatory mediators, as currently proposed in the field, may not be considered as a valid neurotherapeutic strategy.

CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile hidden Markov models.

The arthropod cuticle is a composite, bipartite system, made of chitin filaments embedded in a proteinaceous matrix. The physical properties of cuticle are determined by the structure and the interactions of its two major components, cuticular proteins (CPs) and chitin. The proteinaceous matrix consists mainly of structural cuticular proteins. The majority of the structural proteins that have been described to date belong to the CPR family, and they are identified by the conserved R&R region (Rebers and Riddiford Consensus). Two major subfamilies of the CPR family RR-1 and RR-2, have also been identified from conservation at sequence level and some correlation with the cuticle type. Recently, several novel families, also containing characteristic conserved regions, have been described. The package HMMER v3.0 (http://hmmer.janelia.org/) was used to build characteristic profile Hidden Markov Models based on the characteristic regions for 8 of these families, (CPF, CPAP3, CPAP1, CPCFC, CPLCA, CPLCG, CPLCW, Tweedle). In brief, these families can be described as having: CPF (a conserved region with 44 amino acids); CPAP1 and CPAP-3 (analogous to peritrophins, with 1 and 3 chitin-binding domains, respectively); CPCFC (2 or 3 C-x(5)-C repeats); and four of five low complexity (LC) families, each with characteristic domains. Using these models, as well as the models previously created for the two major subfamilies of the CPR family, RR-1 and RR-2 (Karouzou et al., 2007), we developed CutProtFam-Pred, an on-line tool (http://bioinformatics.biol.uoa.gr/CutProtFam-Pred) that allows one to query sequences from proteomes or translated transcriptomes, for the accurate detection and classification of putative structural cuticular proteins. The tool has been applied successfully to diverse arthropod proteomes including a crustacean (Daphnia pulex) and a chelicerate (Tetranychus urticae), but at this taxonomic distance only CPRs and CPAPs were recovered.