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

doi:10.1016/j.celrep.2023.113311

Molecular and functional characterization of the Drosophila melanogaster conserved smORFome

Cell Rep. 2023 Nov 28;42(11):113311. doi: 10.1016/j.celrep.2023.113311. Epub 2023 Oct 26.

Authors

Affiliations

¹ Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
² 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.
³ Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
⁴ Laboratory of Invertebrate Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
⁵ 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. Electronic address: jbbrown@lbl.gov.
⁶ Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA. Electronic address: perrimon@genetics.med.harvard.edu.
⁷ Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: secelniker@lbl.gov.

Abstract

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.

Keywords: CP: Genomics; CRISPR; Drosophila; gene function; gene knockout; peptide; ribosome profiling; smORF.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Drosophila melanogaster* / genetics
Drosophila melanogaster* / metabolism
Genome
Humans
Open Reading Frames / genetics
Peptides* / metabolism

Substances

Peptides

Abstract

Publication types

MeSH terms

Substances

Grants and funding