Transcriptome sequencing allows for analysis of mature RNAs at base pair 
resolution. Here we show that RNA-seq can also be used for studying nascent RNAs 
undergoing transcription. We sequenced total RNA from human brain and liver and 
found a large fraction of reads (up to 40%) within introns. Intronic RNAs were 
abundant in brain tissue, particularly for genes involved in axonal growth and 
synaptic transmission. Moreover, we detected significant differences in intronic 
RNA levels between fetal and adult brains. We show that the pattern of intronic 
sequence read coverage is explained by nascent transcription in combination with 
co-transcriptional splicing. Further analysis of co-transcriptional splicing 
indicates a correlation between slowly removed introns and alternative splicing. 
Our data show that sequencing of total RNA provides unique insight into the 
transcriptional processes in the cell, with particular importance for normal 
brain development.