Genes in Hiding

Unrecognizable genes are an unsettling problem in genomics. Here, we survey the various types of cryptic genes and the corresponding deciphering strategies employed by cells. Encryption that renders genes substantially different from homologs in other species includes sequence substitution, insertion, deletion, fragmentation plus scrambling, and invasion by mobile genetic elements. Cells decode cryptic genes at the DNA, RNA or protein level. We will focus on a recently discovered case of unparalleled encryption involving massive gene fragmentation and nucleotide deletions and substitutions, occurring in the mitochondrial genome of a poorly understood protist group, the diplonemids. This example illustrates that comprehensive gene detection requires not only auxiliary sequence information – transcriptome and proteome data – but also knowledge about a cell's deciphering arsenal.

TrendsOmics technologies facilitate research into organisms beyond model systems, tapping into an underexploited wealth of information.Combination of genomics, transcriptomics, and proteomics is a potent means for uncovering hidden genes and genetic elements, assigning function to genomic regions thought to be ‘junk DNA’.Unconventional gene structures promise to reveal innovative strategies and novel molecular mechanisms in gene expression, and thus to expand our toolbox for synthetic biology, genetic engineering, and molecular therapy.