title: Chemoproteomic discovery of cysteine-containing human short open reading frames.
abstract: The application of ribosome profiling and mass spectrometry technologies has recently revealed that the human proteome is larger than previously appreciated. Short open reading frames (sORFs), which are difficult to identify using traditional gene-finding algorithms, constitute a significant fraction of unknown protein-coding genes. Thus, experimental approaches to identify sORFs provide invaluable insight into the protein-coding potential of genomes. Here, we report an affinity-based approach to enrich and identify cysteine-containing human sORF-encoded polypeptides (ccSEPs) from cells. This approach revealed 16 novel ccSEPs, each derived from an uncharacterized sORF, demonstrating its potential for discovering new genes. We validated expression of a SEP from its endogenous RNA, and demonstrated the specificity of our labeling approach using synthetic SEP. The discovery of additional human SEPs and their conservation indicate the potential importance of these molecules in biology.
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
authors.forename: Adam G
authors.initials: AG
authors.lastname: Schwaid
authors.affiliation: Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA.
authors.forename: D Alexander
authors.initials: DA
authors.lastname: Shannon
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
authors.forename: Jiao
authors.initials: J
authors.lastname: Ma
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Slavoff
authors.affiliation: Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.affiliation: Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA.
authors.forename: Eranthie
authors.initials: E
authors.lastname: Weerapana
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Saghatelian
mesh_terms: D000595:Amino Acid Sequence; D003545:Cysteine / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010455:Peptides / Q000737:chemistry / Q000235:genetics*; D020543:Proteome / Q000235:genetics*; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides; D020543:Proteome; D003545:Cysteine