Transcriptome profiling of mouse brain and lung under Dip2a regulation using RNA-sequencing

Abstract

Disconnected interacting protein 2 homolog A (DIP2A) is highly expressed in nervous system and respiratory system of developing embryos. However, genes regulated by Dip2a in developing brain and lung have not been systematically studied. Transcriptome of brain and lung in embryonic 19.5 day (E19.5) were compared between wild type and Dip2a -/- mice. An average of 50 million reads per sample was mapped to the reference sequence. A total of 214 DEGs were detected in brain (82 up and 132 down) and 1900 DEGs in lung (1259 up and 641 down). GO enrichment analysis indicated that DEGs in both Brain and Lung were mainly enriched in biological processes ‘DNA-templated transcription and Transcription from RNA polymerase II promoter’, ‘multicellular organism development’, ‘cell differentiation’ and ‘apoptotic process’. In addition, COG classification showed that both were mostly involved in ‘Replication, Recombination, and Repair’, ‘Signal transduction and mechanism’, ‘Translation, Ribosomal structure and Biogenesis’ and ‘Transcription’. KEGG enrichment analysis showed that brain was mainly enriched in ‘Thyroid cancer’ pathway whereas lung in ‘Complement and Coagulation Cascades’ pathway. Transcription factor (TF) annotation analysis identified Zinc finger domain containing (ZF) proteins were mostly regulated in lung and brain. Interestingly, study identified genes Skor2 , Gpr3711 , Runx1 , Erbb3 , Frmd7 , Fut10 , Sox11 , Hapln1 , Tfap2c and Plxnb3 from brain that play important roles in neuronal cell maturation, differentiation, and survival; genes Hoxa5 , Eya1 , Errfi1 , Sox11 , Shh , Igf1 , Ccbe1 , Crh , Fgf9 , Lama5 , Pdgfra , Ptn , Rbp4 and Wnt7a from lung are important in lung development. Expression levels of the candidate genes were validated by qRT-PCR. Genome wide transcriptional analysis using wild type and Dip2a knockout mice in brain and lung at embryonic day 19.5 (E19.5) provided a genetic basis of molecular function of these genes.

Transcriptomic profiling of Dip2a in the neural differentiation of mouse embryonic stem cells

“…The mutant mice have defects in spine morphology and synaptic transmission, and autism-like behaviors such as excessive repetitive self-grooming and defective social novelty [5] , [27] . Those results indicate that DIP2A is required for the maintenance of neural development of mice [28] . Since the neural differentiation is a decisive step in normal neural development, we hypothesized that DIP2A may play a role in the neural differentiation.…”

“…In this study, mESCs were used as an in vitro model, N2B27 (monolayer culture) and KSR (three-dimensional culture) culture were performed as two neural differentiation methods to systemically investigate the role of Dip2a in the process of neural differentiation. In previous studies, depletion of DIP2A was found to lead to significantly altered expression of multiple genes associated with lung development in mice, including the genes Crh and Pdgfra , which are essential for cell proliferation [28] . In our experiments, we found that knockout of Dip2a does not affect the mESCs pluripotency, but reduced cell proliferation and prolonged the G1 phase under 2iL culture condition.…”

“… [26] . Analysis of embryonic brain and lung of DIP2A knockout mice discovered significant number of genes that may be affected by DIP2A [28] . In consistence with those findings, our RNA-sequencing-based transcriptome analysis uncovered thousands of genes that were affected by knockout of Dip2a in mESCs during neural differentiation.…”

Impact of vitamin C supplementation on placental DNA methylation changes related to maternal smoking: association with gene expression and respiratory outcomes

“…The DIP2 family members ( DIP2A , DIP2B , and DIP2C ) are highly conserved, and DIP2B and DIP2C are both expressed in human lung and placenta (Human Protein Atlas available from http://www.proteinatlas.org ) [ 63 ]. Transcriptome profiling in lungs from Dip2a −/− versus wild-type mice revealed dysregulation of genes critical to vasculogenesis, alveologenesis, and branching morphogenesis [ 64 ], while loss of Dip2b in mice results in embryonic lethality due to abnormal lung development [ 65 , 66 ], suggesting a likely role for DIP2 members in human lung development. Further, an EWAS of lung function in a Korean COPD cohort identified one significant DMC in DIP2C (cg03559389) associated with FEV1/FVC ratio, strengthening the potential relevance of this gene in lung development and function [ 67 ].…”