Transcriptional state transition of loci in various gene ontologies.
(A) Loci with an annotated in multicellular organismal development (GO:0007275) are more likely than the whole genome to start paused and have a greater number of loci (15.4% vs 11.9% overall) transitioning state. (B) Loci annotated for translation elongation (GO:0006414), a housekeeping function, tend to start and end as active, with no loci changing state. (C) Loci annotated for being in the ATP generating proton-pump (GO:0046961), another housekeeping function, also are greatly enriched for those starting and ending as active. A small number of loci (5.3% in this ontogeny) are transcriptionally activating from paused to active. (D) Loci annotated as regulators of heart contraction (GO:0008016), are highly enriched for those starting paused, with loci transcriptionally activating or priming for mesodermal or later productive transcription. (E) Loci annotated for neurotransmitter receptor activity (GO:0030594) also tend to start paused, but those loci transitioning are instead archiving to silent, reflecting a commitment away from ectodermal lineages, such as neurons. (F) Loci annotated for keratinization (GO:0031424) also tend to start paused, with those transitioning archiving to silent, reflecting a commitment away from ectodermal lineages, such as skin.