Lessons from modENCODE

The modENCODE (Model Organism Encyclopedia of DNA Elements) Consortium aimed to map functional elements-including transcripts, chromatin marks, regulatory factor binding sites, and origins of DNA replication-in the model organisms Drosophila melanogaster and Caenorhabditis elegans . During its five-...

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Bibliographic Details
Published in:Annual review of genomics and human genetics 2015-08, Vol.16 (1), p.31-53
Main Authors: Brown, James B, Celniker, Susan E
Format: Article
Language:English
Subjects:
Animals
BASIC BIOLOGICAL SCIENCES
Binding Sites
Caenorhabditis elegans
Caenorhabditis elegans - genetics
Chromatin - genetics
Chromatin - metabolism
Databases, Factual
DNA-Binding Proteins - genetics
Drosophila melanogaster
Drosophila melanogaster - genetics
epigenetics
Genome, Helminth
Genome, Insect
Genomics - methods
regulation of gene expression
replication
transcription
Transcriptome
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Summary:The modENCODE (Model Organism Encyclopedia of DNA Elements) Consortium aimed to map functional elements-including transcripts, chromatin marks, regulatory factor binding sites, and origins of DNA replication-in the model organisms Drosophila melanogaster and Caenorhabditis elegans . During its five-year span, the consortium conducted more than 2,000 genome-wide assays in developmentally staged animals, dissected tissues, and homogeneous cell lines. Analysis of these data sets provided foundational insights into genome, epigenome, and transcriptome structure and the evolutionary turnover of regulatory pathways. These studies facilitated a comparative analysis with similar data types produced by the ENCODE Consortium for human cells. Genome organization differs drastically in these distant species, and yet quantitative relationships among chromatin state, transcription, and cotranscriptional RNA processing are deeply conserved. Of the many biological discoveries of the modENCODE Consortium, we highlight insights that emerged from integrative studies. We focus on operational and scientific lessons that may aid future projects of similar scale or aims in other, emerging model systems.
ISSN:1527-8204
1545-293X
DOI:10.1146/annurev-genom-090413-025448