The human transcriptome: an unfinished story

Abstract

Despite recent technological advances, the study of the human transcriptome is still in its early stages. Here we provide an overview of the complex human transcriptomic landscape, present the bioinformatics challenges posed by the vast quantities of transcriptomic data, and discuss some of the studies that have tried to determine how much of the human genome is transcribed. Recent evidence has suggested that more than 90% of the human genome is transcribed into RNA. However, this view has been strongly contested by groups of scientists who argued that many of the observed transcripts are simply the result of transcriptional noise. In this review, we conclude that the full extent of transcription remains an open question that will not be fully addressed until we decipher the complete range and biological diversity of the transcribed genomic sequences.

Figure 1

Composition of the human transcriptome. (a) Venn diagram of the number of loci containing mRNA transcripts (green), long ncRNAs (blue), and small ncRNAs (red); (b) Base pair coverage of the transcriptome by the three categories of transcripts.

Figure 2

The size of the transcriptome, computed as the fraction of the total number of base pairs in the human genome covered by the assembled transcripts, for 16 normal human tissues included in the Illumina Body Map [98]. Each RNA-seq data set was mapped to the genome with TopHat [78] and assembled with Cufflinks [41]. Note that except for adrenal tissue, in which transcripts cover 5.3% of the human genome, all other reconstructed transcriptomes are smaller in size than the currently annotated transcriptome.