Molecular and functional characterization of the Drosophila melanogaster conserved smORFome
Justin A. Bosch,
Nathan Keith,
Felipe Escobedo,
William W. Fisher,
James Thai LaGraff,
Jorden Rabasco,
Kenneth H. Wan,
Richard Weiszmann,
Yanhui Hu,
Shu Kondo,
James B. Brown,
Norbert Perrimon,
Susan E. Celniker
Affiliations
Justin A. Bosch
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
Nathan Keith
Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Felipe Escobedo
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
William W. Fisher
Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
James Thai LaGraff
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
Jorden Rabasco
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
Kenneth H. Wan
Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Richard Weiszmann
Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Yanhui Hu
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
Shu Kondo
Laboratory of Invertebrate Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
James B. Brown
Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Corresponding author
Norbert Perrimon
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Corresponding author
Susan E. Celniker
Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Corresponding author
Summary: Short polypeptides encoded by small open reading frames (smORFs) are ubiquitously found in eukaryotic genomes and are important regulators of physiology, development, and mitochondrial processes. Here, we focus on a subset of 298 smORFs that are evolutionarily conserved between Drosophila melanogaster and humans. Many of these smORFs are conserved broadly in the bilaterian lineage, and ∼182 are conserved in plants. We observe remarkably heterogeneous spatial and temporal expression patterns of smORF transcripts—indicating wide-spread tissue-specific and stage-specific mitochondrial architectures. In addition, an analysis of annotated functional domains reveals a predicted enrichment of smORF polypeptides localizing to mitochondria. We conduct an embryonic ribosome profiling experiment and find support for translation of 137 of these smORFs during embryogenesis. We further embark on functional characterization using CRISPR knockout/activation, RNAi knockdown, and cDNA overexpression, revealing diverse phenotypes. This study underscores the importance of identifying smORF function in disease and phenotypic diversity.
