The ENCODE and modENCODE consortia have generated a resource
containing large amounts of transcriptomic data, extensive mapping of
chromatin states, as well as the binding locations of >300
transcription factors (TFs) for human, worm and fly. We performed
extensive data integration by constructing genome-wide co-expression
networks and transcriptional regulatory models, revealing fundamental
principles of transcription conserved across the three highly divergent animals.
In particular, we found the gene expression levels in the organisms, both coding
and non-coding, can be predicted consistently based on their upstream
histone marks. In fact, a "universal model" with a single set of
cross-organism parameters can predict expression level for both protein
coding genes and ncRNAs. Carrying out the same type of "predictions" for TFs,
we found that information in their binding is more localized to near the TSS
region than that of histone marks but is largely redundant with that
of the marks.
Surprisingly, only a small number of TFs are necessary in the models
to successfully predict expression (e.g. ~5 of the >1000 in human).
hashtag #BCLgenetics for this event