Fei et al. (2018) PMID:29759984 identified the Drosophila ortholog CG4747 and human GLYR1 as NDF, "a nucleosome-destabilizing factor that facilitates transcription through nucleosomes." Key findings:
- NDF interacts with nucleosomes near the dyad
- Destabilizes nucleosomes in an ATP-independent manner
- Facilitates Pol II transcription through nucleosomes
- Stimulates H3K56 acetylation by p300 on nucleosomal substrates
- Recruited to transcribed regions of thousands of genes upon transcriptional induction
- Colocalizes with H3K36me3-enriched regions
- The PWWP domain recognizes H3K36me3, but H3K36me3 is "necessary but not sufficient" for localization
- Essential in human stem cells
- Overexpressed in ~21% of breast cancers
Fang et al. (2013) PMID:23260659 showed NPAC/GLYR1 is a cofactor of LSD2/KDM1B:
- Stimulates H3K4me1 and H3K4me2 demethylation
- The minimal functional segment is a dodecapeptide (residues 214-225)
- Residue F217 stabilizes enzyme-substrate interaction
- Crystal structures of LSD2 alone and LSD2-NPAC complex were determined
Yu et al. (2021) PMID:33676077 showed in mouse ESCs:
- Npac co-localizes with H3K36me3 in gene bodies of actively transcribed genes
- Interacts with p-TEFb (positive transcription elongation factor b)
- Interacts with Ser2-phosphorylated and Ser5-phosphorylated RNA Pol II
- Depletion disrupts transcriptional elongation of pluripotency genes (Nanog, Rif1)
- Required for mESC pluripotency maintenance
UniProt CC for Q7Q161 states (by similarity to Q8T079):
- "Binds to mononucleosomes"
- "Interacts with male-specific lethal (MSL) histone acetyltransferase complex at least composed of mof, msl-1, msl-2 and msl-3"
The MSL complex in Drosophila acetylates H4K16 for dosage compensation on the male X chromosome.
Fang et al. (2013) PMID:23260659: "attempts to identify the intrinsic enzymatic activity of NPAC as a potential dehydrogenase...were unsuccessful." The dehydrogenase domain instead serves as "a catalytically inert oligomerization module" that forms a stable tetramer.
UniProt CC for Q7Q161: "the active site is not conserved, the dehydrogenase domain seems to serve as a catalytically inert oligomerization module"
UniProt CC (by similarity to Drosophila Q8T079): "Localization to open chromatin depends on H3K36 trimethylation by Set2."
| GO ID | Term | Qualifier | Evidence | Reference |
|---|---|---|---|---|
| GO:0003677 | DNA binding | enables | IBA | GO_REF:0000033 |
| GO:0003682 | chromatin binding | enables | IEA | GO_REF:0000117 (ARBA) |
| GO:0031491 | nucleosome binding | enables | IBA | GO_REF:0000033 |
| GO:0050661 | NADP binding | enables | IEA | GO_REF:0000002 (InterPro:IPR006115) |
| GO:0051287 | NAD binding | enables | IEA | GO_REF:0000002 (InterPro:IPR029154) |
| GO:0140673 | transcription elongation-coupled chromatin remodeling | involved_in | IBA | GO_REF:0000033 |
| GO:0000785 | chromatin | is_active_in | IBA | GO_REF:0000033 |
| GO:0005694 | chromosome | located_in | IEA | GO_REF:0000044 |
Two InterPro2GO annotations:
- IPR006115 -> GO:0050661 (NADP binding): Based on the 6-phosphogluconate dehydrogenase NADP-binding domain
- IPR029154 -> GO:0051287 (NAD binding): Based on the 3-hydroxyisobutyrate dehydrogenase-like NAD-binding domain
These are technically correct structurally (the Rossmann fold does bind NAD(P)), but the dehydrogenase domain is catalytically inert. The NAD(P) binding may be structural/regulatory rather than enzymatic.
NPAC/GLYR1/NDF is a multifunctional chromatin-associated protein whose core biology is well-characterized in human and Drosophila but entirely inferred by homology for the Anopheles ortholog. The protein reads H3K36me3 marks via its PWWP domain, destabilizes nucleosomes to facilitate RNA Pol II transcription elongation, cofactors LSD2-mediated H3K4 demethylation, and stimulates H3K56 acetylation by p300. The dehydrogenase-like C-terminal domain is catalytically inert but serves as an oligomerization platform. In Drosophila, it also interacts with the MSL dosage compensation complex.