modENCODE

modENCODE, short for Model Organism ENCODE, is a project within the ENCODE consortium that aimed to identify and characterize functional genomic elements in the genomes of model organisms. The project focused on Drosophila melanogaster (fruit fly) and Caenorhabditis elegans (nematode), with the goal of producing reference maps of regulatory elements and transcriptional activity to complement the human ENCODE data. The effort sought to illuminate promoters, enhancers, transcription start sites, chromatin states, transcription factor binding, and noncoding RNAs across development and tissues.

To achieve these goals, modENCODE generated genome-wide data using high-throughput assays such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) for histone modifications and transcription factor binding, and RNA sequencing (RNA-seq) to profile transcripts. Additional assays covered chromatin accessibility and small RNAs. All data were processed with standardized pipelines and integrated into public resources.

Data were released through the modENCODE Data Coordinating Center and the ENCODE data portals, with deposition in public repositories such as GEO. The datasets supported genome annotation, comparative analyses, and studies of regulatory evolution in model organisms.

Impact and legacy: modENCODE produced reference epigenomes for multiple developmental stages in Drosophila and for C. elegans, improving gene models and enabling cross-species comparisons. The project helped set data standards and contributed to the broader ENCODE effort to annotate functional elements in diverse genomes. It operated in the late 2000s and early 2010s under funding from NHGRI and collaborating institutions.