NPAC (Cytokine-like nuclear factor N-PAC, also known as GLYR1/NDF/NP60) is a chromatin-associated nuclear protein in Anopheles gambiae that functions as a nucleosome-destabilizing factor facilitating RNA polymerase II transcription elongation through chromatin. The protein contains an N-terminal PWWP domain that reads histone H3K36me3 marks and binds DNA, and a C-terminal dehydrogenase-like Rossmann fold domain that is catalytically inert but mediates oligomerization. In orthologous species (Drosophila, human, mouse), NPAC is recruited to gene bodies of actively transcribed genes, destabilizes nucleosomes in an ATP-independent manner to facilitate Pol II passage, stimulates H3K56 acetylation by p300, and serves as a cofactor of the histone demethylase LSD2/KDM1B promoting H3K4me1/me2 demethylation. In Drosophila, it also interacts with the MSL histone acetyltransferase complex involved in dosage compensation. All functional annotations for the Anopheles protein are inferred by homology; no direct experimental studies exist for this organism.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: This IBA annotation is based on phylogenetic inference from the Drosophila ortholog CG4747 (Q8T079) and human GLYR1 (Q49A26). The PWWP domain of NPAC is known to strongly bind DNA in addition to reading histone marks. Reason: DNA binding via the PWWP domain is well-established for this protein family. UniProt CC states "The PWWP domain is a H3 reader and strongly binds DNA" (by similarity to Q49A26). The annotation is correct but somewhat generic; nucleosome binding (GO:0031491) is a more informative descriptor of the primary chromatin interaction. Supporting Evidence: PMID:29759984 NDF has a PWWP motif, interacts with nucleosomes near the dyad file:ANOGA/NPAC/NPAC-notes.md The PWWP domain is a H3 reader and strongly binds DNA |
| GO:0003682 chromatin binding | IEA GO_REF:0000117 | ACCEPT | Summary: This IEA annotation is from ARBA rule ARBA00027831. Chromatin binding is appropriate for this protein which localizes to and interacts with chromatin through the PWWP domain, but is less specific than the nucleosome binding annotation already present. Reason: Chromatin binding is correct. NPAC/NDF localizes to chromatin in a H3K36me3-dependent manner and directly interacts with nucleosomes. This is a broad but accurate annotation. Supporting Evidence: PMID:29759984 NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner PMID:33676077 Npac co-localizes with histone H3K36me3 in gene bodies of actively transcribed genes file:ANOGA/NPAC/NPAC-deep-research-bioreason-sft.md a chromatin-reading module that recognizes nucleosomal features |
| GO:0031491 nucleosome binding | IBA GO_REF:0000033 | ACCEPT | Summary: This IBA annotation is based on phylogenetic inference from Drosophila CG4747 and human GLYR1. Nucleosome binding is a core molecular function of this protein established in multiple studies. Reason: Nucleosome binding is one of the best-characterized functions of the NP60 subfamily. UniProt CC states "Binds to mononucleosomes" (by similarity to Q8T079). NDF interacts with nucleosomes near the dyad and destabilizes them to facilitate transcription. Supporting Evidence: PMID:29759984 NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner PMID:23260659 NPAC directly interacts with LSD2 and positively regulates its H3K4 demethylation activity both in vitro and in vivo |
| GO:0050661 NADP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: This InterPro2GO annotation derives from IPR006115 (6-phosphogluconate dehydrogenase, NADP-binding domain). The Rossmann fold in NPAC does contain conserved NAD(P)H-binding sites structurally, but the protein lacks a conserved active site and the dehydrogenase domain is catalytically inert. Reason: The structural capacity to bind NADP is plausible given the Rossmann fold architecture, but the dehydrogenase domain is catalytically inert. Fang et al. (2013) reported "attempts to identify the intrinsic enzymatic activity of NPAC as a potential dehydrogenase were unsuccessful." The binding may be structural or regulatory rather than catalytic, and the functional significance of NADP binding is unclear. This is not a core function of the protein. Supporting Evidence: PMID:23260659 attempts to identify the intrinsic enzymatic activity of NPAC as a potential dehydrogenase file:ANOGA/NPAC/NPAC-deep-research-bioreason-sft.md the active site is not conserved, the dehydrogenase domain seems to serve as a catalytically inert oligomerization module |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: This InterPro2GO annotation derives from IPR029154 (3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain). Same reasoning as for NADP binding -- the Rossmann fold is structurally present but catalytically inert. Reason: The structural NAD binding capacity is plausible given the conserved Rossmann fold, but the domain serves as "a catalytically inert oligomerization module" rather than performing redox chemistry. NAD binding is not a core function of this protein. Supporting Evidence: PMID:23260659 attempts to identify the intrinsic enzymatic activity of NPAC as a potential dehydrogenase |
| GO:0140673 transcription elongation-coupled chromatin remodeling | IBA GO_REF:0000033 | ACCEPT | Summary: This IBA annotation is based on phylogenetic inference from Drosophila CG4747 and human GLYR1. This is one of the most precisely characterized functions of the protein. Reason: Transcription elongation-coupled chromatin remodeling is the central biological process of NPAC/NDF. The protein destabilizes nucleosomes to facilitate Pol II transcription through chromatin, interacts with p-TEFb and phosphorylated Pol II, and is recruited to gene bodies upon transcriptional induction. This is a core function. Supporting Evidence: PMID:29759984 NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes PMID:33676077 Npac is essential for the transcriptional elongation of pluripotency genes by recruiting p-TEFb and interacting with RNA Pol II Ser2P and Ser5P |
| GO:0000785 chromatin | IBA GO_REF:0000033 | ACCEPT | Summary: This IBA annotation places NPAC as active in chromatin, based on the Drosophila and human orthologs which localize to chromatin. Reason: NPAC localizes to chromatin in a H3K36me3-dependent manner. In Drosophila, it localizes to polytene chromosome interbands (open chromatin). The protein is active at chromatin where it destabilizes nucleosomes and facilitates transcription. Supporting Evidence: PMID:33676077 Npac co-localizes with histone H3K36me3 in gene bodies of actively transcribed genes PMID:29759984 Upon transcriptional induction, NDF is recruited to the transcribed regions of thousands of genes and colocalizes with a subset of H3K36me3-enriched regions |
| GO:0005694 chromosome | IEA GO_REF:0000044 | ACCEPT | Summary: This IEA annotation is derived from UniProt subcellular location "Chromosome" (by similarity to Q8T079). NPAC localizes to chromosomes. Reason: Chromosome localization is correct and consistent with the protein's chromatin association. This is a broad but accurate annotation; the more specific "chromatin" (GO:0000785) annotation is also present. Supporting Evidence: file:ANOGA/NPAC/NPAC-notes.md Localization to open chromatin depends on H3K36 trimethylation by Set2 |
| GO:0140003 histone H3K36me3 reader activity | ISS PMID:29759984 NDF, a nucleosome-destabilizing factor that facilitates tran... | NEW | Summary: NPAC reads H3K36me3 marks via its PWWP domain, which is the primary mechanism for its recruitment to actively transcribed gene bodies. This is a more specific and informative annotation than general chromatin binding. Reason: H3K36me3 reader activity via the PWWP domain is a core molecular function that drives the chromatin localization and biological activity of the protein. This is well-established in both Drosophila and mammalian orthologs and should be annotated for the Anopheles ortholog by sequence similarity. Supporting Evidence: PMID:29759984 NDF has a PWWP motif...colocalizes with a subset of H3K36me3-enriched regions PMID:33676077 Npac, a "reader" of histone H3 lysine 36 trimethylation (H3K36me3), is required to maintain mouse ESC |
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Download this section (compressed HTML)Q: Does the Anopheles NPAC ortholog interact with the MSL dosage compensation complex in vivo, as predicted by homology to the Drosophila ortholog?
Q: Does the Anopheles NPAC dehydrogenase domain retain any capacity for NAD(P) binding, and if so, does this have a regulatory role?
Q: Is NPAC involved in any mosquito-specific chromatin regulation processes related to malaria vector biology (e.g., during blood feeding or parasite infection)?
Experiment: ChIP-seq of NPAC in Anopheles gambiae cell lines to determine whether it co-localizes with H3K36me3 marks as in orthologs, confirming the conserved chromatin targeting mechanism.
Hypothesis: NPAC localizes to H3K36me3-enriched gene bodies of actively transcribed genes in Anopheles, consistent with its ortholog function.
Experiment: Co-immunoprecipitation of NPAC with components of the Anopheles MSL complex (MOF) to validate the predicted interaction.
Hypothesis: NPAC interacts with the MSL complex in Anopheles as it does in Drosophila.
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