Gene expression is controlled through both transcriptional regulation and post-transcriptional events. Pre-mRNA alternative splicing (AS) represents a crucial post-transcriptional mechanism that regulates the spatial and temporal expression of genes. Despite its significance, the roles of AS in brain development remain largely unknown. The first chapter of this thesis is dedicated to examining the unproductive splicing events in neurodevelopment, through the use of RNA-Seq, which generated a long list of unproductive splicing events dynamically regulated during neurogenesis. Thereinto, an alternative 3' splice site (A3SS) located in the SYNGAP1 gene was identified as an important regulator of its expression, playing a vital role in neurodevelopment. The use of A3SS in non-neuronal cells results in nonsense-mediated decay (NMD) and guarantees neuron-specific expression of SYNGAP1 protein. This mammal-specific AS event is controlled by PTBP1 and PTBP2, which repress SYNGAP1 expression by promoting the usage of this A3SS. Manipulating this AS event through the use of splice-switching antisense oligonucleotides (SSOs) can restore SYNGAP1 expression, presenting a potential therapeutic strategy for non-syndromic intellectual disability (NSID) caused by SYNGAP1 haploinsufficiency. Overall, this part of the study sheds light on the previously unknown role and mechanism of cell-type-specific unproductive AS in brain development.On another level, DNA methylations, one type of main epigenetic modifications, usually serve as a repressive or activation mark for gene expression through transcriptional regulation. As the predominant DNA modification found in prokaryotic genomes, DNA N6-methyldeoxyadenosine (6mA) plays crucial roles in the restriction modification system, DNA repair, and also gene expression regulation. However, the frequency, dynamics, distribution patterns, effector proteins, and biological functions of 6mA in eukaryotic cells remain subject to controversy due to the extremely low abundance and the lack of effective and sensitive base-resolution detection approaches. The second chapter of this thesis presents an antibody-independent single-nucleotide-resolution 6mA sequencing method, namely Direct-Read 6mA Sequencing (DR-6mA-seq). This novel approach capitalizes on the misincorporation tendency of deoxythymidine triphosphate (dTTP) analog at 6mA sites, enabling quantitative mapping of 6mA in various genomic DNA species in a fast and cost-effective manner. By using this method, we were able to characterize the presence and elevated level of 6mA in the nuclear DNA of glioblastoma model cells. DR-6mA-seq can serve as a gold standard for quantitative Next Generation Sequencing (NGS) methods of 6mA, facilitating further biological studies and inspiring the development of new mapping methods for other DNA/RNA modifications.