Modulo (mod, CG2050) is the Drosophila nucleolin-like protein, a 542-residue nuclear phosphoprotein with an acidic, disordered N-terminal region, four RNA recognition motifs and a basic C-terminal tail. It binds both RNA and DNA: the central RRM region recognises a specific RNA motif class, while the basic terminal regions bind DNA, an interaction that is down-regulated by phosphorylation. The phosphorylated pool resides in the nucleolus within a ribonucleoprotein particle, and the unphosphorylated pool associates with condensed chromatin, heterochromatin and repetitive DNA; in mitosis Modulo moves to the chromosome periphery and cytoplasm. Modulo is a dominant suppressor of position-effect variegation, a direct dMyc target needed for growth of proliferating cells, and is required for embryonic morphogenesis, male germline transcription of spermatid-differentiation genes, neuroblast maintenance, piRNA-directed transposon silencing in the ovary and centromere integrity. It interacts with the coactivator dCBP (nejire), the CENP-A assembly factor CAL1 and Piwi. Null mutants are recessive lethal with melanotic tumours.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000381 regulation of alternative mRNA splicing, via spliceosome | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Phylogenetic transfer of splicing regulation from SR-protein/RBM-type members of the RRM-protein family; no Modulo evidence for a role in splicing. Reason: The PTN009063129 node is grounded by splicing regulators such as SRSF6 (Q13247), RBM4 (Q9BWF3) and fly SR-type proteins. Modulo is a nucleolin-like protein (acidic N-terminus, four RRMs, basic tail, no RS domain) whose characterised functions are nucleolar RNA binding and chromatin association. Neither the RIP-seq study nor any other Modulo paper reports a splicing role, so transfer of this process rests only on shared RRM ancestry within a very large family. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE ROLE CONFLATION Sources checked: PANTHER:PTN009063129 SUPPORTS SOURCE BUT NOT TARGET Node grounded by SR proteins and RBM-type splicing regulators; Modulo belongs to the nucleolin-like lineage with no splicing evidence. Supporting Evidence: PMID:10037720 in vivo nucleolar Modulo is highly phosphorylated and belongs to a ribonucleoprotein particle, whereas chromatin-associated protein is not modified file:DROME/mod/mod-uniprot.txt DOMAIN 175..251 FT /note="RRM 1" file:DROME/mod/mod-deep-research-manual.md PANTHER places it in the very large PTHR24012 |
| GO:0003676 nucleic acid binding | IEA GO_REF:0000002 | MODIFY | Summary: Correct but general; Modulo has experimentally shown binding to both RNA and DNA. Reason: The RBD superfamily signature supports nucleic acid binding, but direct experiments show both DNA binding (already IDA on this gene) and RNA binding (IEA row here, supported by PMID:10037720 and RIP-seq). Both more specific descendants are listed. Proposed replacements: RNA binding DNA binding Supporting Evidence: PMID:10037720 two basic terminal domains independently contact DNA without sequence specificity, whereas a central RNA Recognition Motif (RRM)-containing domain allows recognition of a novel sequence-/motif-specific RNA class |
| GO:0003677 DNA binding | IDA PMID:1425581 Cell lineage-specific expression of modulo, a dose-dependent... | ACCEPT | Summary: Direct DNA binding by Modulo, consistent with its chromatin and heterochromatin association. Reason: Shown directly (PMID:1425581) and mapped to the basic terminal domains (PMID:10037720). Specificity is disputed, so the general DNA binding term is the precision the combined evidence warrants. Supporting Evidence: PMID:1425581 The mod protein directly binds DNA, which indicates that it may serve to anchor multimeric complexes promoting chromatin compaction and silencing. PMID:10037720 two basic terminal domains independently contact DNA without sequence specificity |
| GO:0003723 RNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: RNA binding via the RRM domains; supported experimentally. Reason: Four RRM domains; in vitro selection shows motif-specific RNA recognition by the central RRM-containing domain, nucleolar Mod is part of an RNP particle, and RIP-seq identifies bound transcripts in larval brain. Core activity. Supporting Evidence: PMID:10037720 a central RNA Recognition Motif (RRM)-containing domain allows recognition of a novel sequence-/motif-specific RNA class PMID:39700092 Mod targets were identified using RNA immunoprecipitation coupled to Sequencing (RiP-Seq) |
| GO:0003729 mRNA binding | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: mRNA binding inherited across the RRM-protein node; consistent with RIP-seq recovery of mRNAs bound by Modulo. Reason: RIP-seq shows Modulo associates with protein-coding transcripts (proneural, ribosomal protein, mitochondrial transcripts), so mRNA binding is plausible. However, the best-characterised RNA association of Modulo is nucleolar (RNP particle, motif-specific RNA class) and the RIP data do not separate direct from indirect binding; mRNA binding is therefore kept as non-core rather than replacing the general RNA binding core function. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN009063129 SUPPORTS TRANSFER Broad RRM-protein node; mRNA binding is consistent with Modulo RIP-seq data. Supporting Evidence: PMID:39700092 Mod also bound transcripts of genes involved in fundamental cellular processes including metabolic enzyme function (COX1, COX3, CYTB) and peptide synthesis (svr, eIF4E7, RpL41). |
| GO:0005515 protein binding | IPI PMID:11854460 The interaction between the coactivator dCBP and Modulo, a c... | MODIFY | Summary: Interaction with the coactivator dCBP (nejire), mapped by two-hybrid, GST pulldown and co-IP. Reason: Bare protein binding is uninformative. The partner FBgn0261617 (nej, dCBP) is a transcriptional coactivator, and the paper maps the binding to Mod residues 219-493 and to the dCBP C/H3 plus activation domain, so transcription coactivator binding describes the interaction. Proposed replacements: transcription coactivator binding Supporting Evidence: PMID:11854460 We also found that amino acids 219–493 of Modulo are sufficient to PMID:11854460 We demonstrate that dCBP and Modulo bind in vitro and in vivo |
| GO:0005634 nucleus | IDA PMID:16877538 Transcriptional regulation by Modulo integrates meiosis and ... | ACCEPT | Summary: Nuclear localization; consistent across all studies. Reason: Modulo is a nuclear protein in embryos, cultured cells, neuroblasts and germ cells; the nucleolus row gives the main sub-compartment. Supporting Evidence: file:DROME/mod/mod-uniprot.txt SUBCELLULAR LOCATION: Nucleus. PMID:1425581 The protein is first detected before the blastoderm cellularization in all somatic nuclei |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to nucleus; correct. Reason: Consistent with the IDA nucleus row and all localization studies. Supporting Evidence: PMID:1425581 The protein is first detected before the blastoderm cellularization in all somatic nuclei |
| GO:0005730 nucleolus | IDA PMID:11854460 The interaction between the coactivator dCBP and Modulo, a c... | ACCEPT | Summary: Modulo is predominantly nucleolar in embryonic nuclei; confirmed in S2 cells and neuroblasts by Fibrillarin co-staining. Reason: Nucleolus is the major interphase location of Modulo and the compartment where its RNP association and its CAL1 partnership are observed. Core location. Supporting Evidence: PMID:23028777 In interphase, we confirmed that Modulo accumulates at the nucleolus and has a weaker staining on DNA PMID:39700092 Mod was most prominently detected in a subnuclear compartment of interphase NBs overlapping with Fibrillarin (Fib), consistent with nucleolar localization |
| GO:0005737 cytoplasm | IDA PMID:16877538 Transcriptional regulation by Modulo integrates meiosis and ... | KEEP AS NON CORE | Summary: Cytoplasmic signal in germ cells (abstract-only paper); Modulo is also cytoplasmic in mitotic cells after nucleolar breakdown. Reason: The cytoplasmic observation cannot be checked in the abstract, but independent full-text data show cytoplasmic Mod during mitosis in neuroblasts. This is a peripheral, cell-cycle-dependent location, not where the core activities act. Supporting Evidence: PMID:39700092 During mitosis, Mod was localized to the peri-chromosomal regions as well as throughout the cytoplasm |
| GO:0016607 nuclear speck | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Speckle localization transferred from SR proteins (SRSF1/2/3/4/6 etc.); Modulo localizes to the nucleolus and chromatin, not to speckles. Reason: The node donors are SR splicing factors (Q07955 SRSF1, Q01130 SRSF2, P84103 SRSF3, Q08170 SRSF4, Q13247 SRSF6). Every Modulo localization study (embryos, polytene chromosomes, S2 cells, larval brain) places it in the nucleolus and on chromatin; none reports a speckle pattern. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000567445 SUPPORTS SOURCE BUT NOT TARGET Node grounded by SR-protein speckle localizations; Modulo is a nucleolar nucleolin-like protein. Supporting Evidence: PMID:9718368 While actually associated to condensed chromatin and heterochromatin sites, the protein is also abundantly found at nucleolus. PMID:23028777 In interphase, we confirmed that Modulo accumulates at the nucleolus and has a weaker staining on DNA |
| GO:0032991 protein-containing complex | IPI PMID:11854460 The interaction between the coactivator dCBP and Modulo, a c... | KEEP AS NON CORE | Summary: Co-immunoprecipitation with dCBP from Kc cell extracts places both in a common complex. Reason: The co-IP supports a complex with dCBP, but its identity is undefined and no more specific complex term is supported by this evidence. The generic term is as precise as the data allow and peripheral to core function. Supporting Evidence: PMID:11854460 indicating that both proteins are part of the same complex in |
| GO:0043565 sequence-specific DNA binding | IDA PMID:16877538 Transcriptional regulation by Modulo integrates meiosis and ... | KEEP AS NON CORE | Summary: Modulo purified as the protein binding the Sdic promoter; sequence specificity conflicts with earlier in vitro analysis. Reason: The full text is not cached; the abstract states specific binding to the Sdic promoter, and the curator had the full text, so the row is retained. However PMID:10037720 found the DNA-binding basic domains to bind without sequence specificity and assigned motif specificity to RNA binding instead, so sequence-specific DNA binding is not adopted as the core activity. Supporting Evidence: PMID:16877538 we purified the protein that specifically binds to the promoter of spermatid-differentiation gene Sdic and identified it as Modulo |
| GO:0000792 heterochromatin | IDA PMID:9718368 Dynamics of the sub-nuclear distribution of Modulo and the r... | NEW | Summary: Modulo associates with condensed chromatin and heterochromatin sites, and its DNA targets are repetitive elements. Reason: Shown by immunolocalisation on mitotic and polytene chromosomes and by cross-linking/IP of genomic DNA targets (PMID:9718368), and independently by polytene staining in PMID:11854460 (full text). Not captured in GOA, which has only nucleus/nucleolus rows. Fits the PEV-suppressor phenotype and chromatin-level DNA binding. Supporting Evidence: PMID:9718368 While actually associated to condensed chromatin and heterochromatin sites, the protein is also abundantly found at nucleolus. PMID:9718368 repetitive elements instead of rDNA constitute Modulo DNA targets, indicating that the protein directly contacts DNA in heterochromatin but not at the nucleolus |
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Download this section (compressed HTML)Q: Does Modulo bind DNA sequence-specifically (as the Sdic promoter purification suggested) or non-specifically (as in vitro domain mapping indicated), and is specificity conferred by partners?
Q: Which molecular step does Modulo perform in CAL1 nucleolar retention and centromeric CID maintenance, and in Piwi-directed H3K9me3 deposition at transposons, i.e. does it act as an RNA-binding scaffold, a histone chaperone like nucleolin, or indirectly through ribosome biogenesis?
Q: Is Modulo a functional nucleolin ortholog in ribosome biogenesis (pre-rRNA binding/processing), given the Minute-like clone phenotype and the lack of a GAR domain?
Experiment: Map direct RNA targets of Modulo in S2 cells and ovaries to test binding to pre-rRNA, centromeric and transposon transcripts.
Type: CLIP-seq / iCLIP
Experiment: Test whether recombinant Modulo binds histones or CID-H4 and assists nucleosome assembly, as described for nucleolin.
Type: In vitro histone chaperone assay
modulo (mod) encodes a nucleolar protein that is required for growth of proliferative cells through its association with the proto-oncogene Myc. The mod protein is essential for transcription of spermatid-differentiation genes and for high expression of meiotic arrest genes. The product of mod is phosphorylated, which in turn regulates its localization.
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