Cnp1 is the fission-yeast CENP-A (CenH3), the centromere-specific histone H3 variant that replaces canonical histone H3 in centromeric nucleosomes and epigenetically defines centromere identity. It is restricted to the nonrepetitive central core/inner-repeat (cnt/imr) "central domain" of all three S. pombe centromeres, where it forms specialized CENP-A nucleosomes (a Cnp1-H4 heterotetramer together with H2A-H2B) that constitute the structural foundation of subkinetochore chromatin. Cnp1 is essential: it is required for recruitment and assembly of inner-kinetochore proteins, for mitotic progression, and for accurate chromosome segregation. Its centromeric deposition occurs in S and G2 phases and is mediated by the CENP-A receptor and chaperone system (the HJURP-related Scm3 receptor, the Sim3/NASP escort, and the Mis16/Mis18 complex), with centromeric retention dependent on the Mis6-Sim4 inner-kinetochore connector. Cnp1 thereby serves as the epigenetic mark that propagates centromere identity through replication and cell division.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0030527 structural constituent of chromatin | IBA GO_REF:0000033 | ACCEPT | Summary: Core molecular function. Cnp1/CENP-A is a centromere-specific histone H3 variant that replaces H3 as a structural component of centromeric nucleosomes; this is the principal molecular activity of the protein. Reason: Phylogenetically inferred across the CENP-A/H3 family and corroborated by experimental evidence that Cnp1 forms the specialized central-core nucleosomes that replace H3. Supporting Evidence: PMID:17677001 Within the central domain most histone H3 is replaced by the centromere-specific H3 variant CENP-ACnp1 to form the unusual chromatin that occupies most of the 10–12 kb comprising imr and cnt |
| GO:0051382 kinetochore assembly | IBA GO_REF:0000033 | ACCEPT | Summary: Core biological process. CENP-A chromatin is the platform on which the inner kinetochore is built; Cnp1 is essential for assembly of a functional kinetochore. Reason: Supported by phylogenetic inference and by experimental evidence that CENP-A is essential for kinetochore assembly in fission yeast. Supporting Evidence: PMID:17677001 CENP-A is essential for the assembly of a functional kinetochore and as such must represent a key component in establishing and/or maintaining the site of kinetochore assembly at the centromere |
| GO:0000776 kinetochore | IBA GO_REF:0000033 | ACCEPT | Summary: Core cellular component. Cnp1 forms the subkinetochore chromatin of the central core domain on which the inner kinetochore assembles. Reason: Phylogenetically inferred and supported by ChIP/IF evidence that Cnp1 and other inner-kinetochore proteins occupy the central domain. Supporting Evidence: PMID:26275423 Inner kinetochore proteins CENP-A, CENP-C, CENP-T, CENP-I, and Scm3 are highly enriched throughout the central domain except at tRNA genes |
| GO:0031507 heterochromatin formation | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: In fission yeast Cnp1/CENP-A occupies the central core (kinetochore) chromatin and is explicitly excluded from the flanking heterochromatin, which is instead occupied by Swi6/HP1 and assembled by the RNAi-Clr4 pathway. Attributing heterochromatin formation to CENP-A is misleading for S. pombe; the central core CENP-A domain is structurally and functionally distinct from heterochromatin. Reason: The IBA conflicts with experimental data showing Cnp1 binds central core DNA exclusively and not the flanking heterochromatic repeats, which are bound by Swi6. Supporting Evidence: PMID:11553715 The centromere-associated proteins, Mis6p and Cnp1p (SpCENP-A), associate exclusively with central core DNA, whereas the Swi6 protein binds the surrounding repeats |
| GO:0007080 mitotic metaphase chromosome alignment | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Chromosome alignment is a downstream consequence of having a functional CENP-A-based kinetochore; loss of Cnp1 causes missegregation. This is a real but indirect/peripheral role rather than the core molecular function. Reason: Downstream phenotypic consequence of kinetochore function; supported by the requirement of CENP-A for equal chromosome segregation. Supporting Evidence: PMID:10864871 the fission yeast homolog SpCENP-A is essential for establishing centromere chromatin associated with equal chromosome segregation |
| GO:0031492 nucleosomal DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: As a histone, Cnp1 wraps and binds DNA within the centromeric nucleosome. This is more informative than the generic DNA binding term and is consistent with the role of CENP-A in centromeric nucleosomes. Reason: Phylogenetically inferred for histones and consistent with the structural role of CENP-A in DNA-wrapping centromeric nucleosomes. Supporting Evidence: PMID:26275423 the central domain, which is occupied by centromere-specific H3 (cenH3 or CENP-A) nucleosomes with two H4s per particle |
| GO:0043505 CENP-A containing nucleosome | IBA GO_REF:0000033 | ACCEPT | Summary: Core cellular component. Cnp1 is the defining histone of the CENP-A nucleosome at the central core domain. Reason: Phylogenetically inferred and directly supported by evidence that CENP-A nucleosomes occupy the central domain. Supporting Evidence: PMID:26275423 the central domain, which is occupied by centromere-specific H3 (cenH3 or CENP-A) nucleosomes with two H4s per particle |
| GO:0000775 chromosome, centromeric region | IEA GO_REF:0000044 | ACCEPT | Summary: Correct localization; Cnp1 localizes to the centromeric region. A more specific term (centromeric core domain) is also annotated. Reason: Supported by experimental IDA annotations to the same and more specific centromeric terms. Supporting Evidence: PMID:10864871 SpCENP-A binding to the nonrepetitious inner centromeres |
| GO:0000786 nucleosome | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Cnp1 is a component of nucleosomes (specifically CENP-A nucleosomes). Correct but more general than CENP-A containing nucleosome. Reason: True but a general parent of the more specific CENP-A containing nucleosome term that better captures the function. Supporting Evidence: PMID:17677001 Within the central domain most histone H3 is replaced by the centromere-specific H3 variant CENP-ACnp1 to form the unusual chromatin |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Generic DNA binding is uninformative for a histone. The more specific nucleosomal DNA binding (and centromeric DNA binding) terms are already annotated and better describe the activity. Reason: Overly general parent term superseded by nucleosomal DNA binding; provides little functional information for a centromeric histone. Supporting Evidence: PMID:26275423 the central domain, which is occupied by centromere-specific H3 (cenH3 or CENP-A) nucleosomes with two H4s per particle |
| GO:0005634 nucleus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Correct but generic. The functionally meaningful localization is the centromeric central core domain within the nucleus. Reason: True parent localization but uninformative relative to the specific centromeric annotations. Supporting Evidence: PMID:10864871 SpCENP-A binding to the nonrepetitious inner centromeres |
| GO:0006325 chromatin organization | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Very general process term. Cnp1 organizes centromeric chromatin, but the specific CENP-A containing chromatin assembly term captures this far better. Reason: Broad ARBA-derived parent term superseded by the specific CENP-A chromatin assembly annotation. Supporting Evidence: PMID:17677001 Within the central domain most histone H3 is replaced by the centromere-specific H3 variant CENP-ACnp1 to form the unusual chromatin |
| GO:0030527 structural constituent of chromatin | IEA GO_REF:0000002 | ACCEPT | Summary: Same core molecular function as the IBA annotation; supported by InterPro histone-fold assignment and by experimental evidence. Reason: Core structural histone function, consistent with the IBA annotation and with experimental data. Supporting Evidence: PMID:17677001 CENP-A is essential for the assembly of a functional kinetochore |
| GO:0046982 protein heterodimerization activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: As a histone-fold protein, Cnp1 heterodimerizes with histone H4 to form the Cnp1-H4 heterotetramer of the centromeric nucleosome. Supported but generic relative to its structural role. Reason: Histone-fold heterodimerization with H4 underlies nucleosome formation; a supporting molecular activity rather than the core function. Supporting Evidence: PMID:26275423 centromere-specific H3 (cenH3 or CENP-A) nucleosomes with two H4s per particle |
| GO:0005515 protein binding | IPI PMID:12773390 The role of Ppe1/PP6 phosphatase for equal chromosome segreg... | MARK AS OVER ANNOTATED | Summary: Bare protein binding is uninformative. This IntAct interaction is with the kinetochore protein Mis12 (Q9Y738), reflecting Cnp1 residence in the central centromere/kinetochore chromatin. The informative content is captured by the kinetochore and centromeric chromatin terms. Reason: Per curation guidance, bare protein binding should be replaced by informative terms; the kinetochore localization terms already capture this. Supporting Evidence: PMID:12773390 In fission yeast, spCENP-A is located to central centromere regions in a Mis6-dependent manner |
| GO:0005515 protein binding | IPI PMID:17627824 The kinetochore proteins Pcs1 and Mde4 and heterochromatin a... | MARK AS OVER ANNOTATED | Summary: Bare protein binding (IntAct interaction with Mis12, Q9Y738). Pcs1/Mde4 and Mis12 localize to the central core of centromeres where Cnp1 chromatin resides; the term itself is uninformative. Reason: Uninformative bare protein binding; underlying central-core kinetochore association is captured by the centromeric/kinetochore CC terms. Supporting Evidence: PMID:17627824 Both Pcs1 and Mde4 localize to the central core of centromeres. |
| GO:0005634 nucleus | EXP PMID:10864871 Requirement of Mis6 centromere connector for localizing a CE... | KEEP AS NON CORE | Summary: Experimentally confirmed nuclear localization, but generic; the meaningful site is the centromeric central core within the nucleus. Reason: Correct experimental localization but superseded by specific centromeric annotations. Supporting Evidence: PMID:10864871 SpCENP-A binding to the nonrepetitious inner centromeres |
| GO:0000779 condensed chromosome, centromeric region | IDA PMID:17035632 Reconstruction of the kinetochore during meiosis in fission ... | ACCEPT | Summary: Cnp1 (a Mis6-like-group protein) remains at the centromere of condensed chromosomes throughout meiosis, supporting localization to the centromeric region of condensed chromosomes. Reason: Direct cytological observation that Cnp1 persists at centromeres throughout meiotic divisions. Supporting Evidence: PMID:17035632 Mis6-like group proteins remain at the centromere throughout meiosis |
| GO:0005515 protein binding | IPI PMID:10864871 Requirement of Mis6 centromere connector for localizing a CE... | MARK AS OVER ANNOTATED | Summary: Bare protein binding (interaction with Mis6, SPAC1687.20c). Mis6 is the inner-kinetochore connector required to localize Cnp1 to the central core; the term itself is uninformative but reflects a key dependency. Reason: Uninformative bare protein binding; the Mis6 dependency is better represented by the centromeric localization and chromatin assembly terms. Supporting Evidence: PMID:10864871 SpCENP-A binding to the nonrepetitious inner centromeres depended on Mis6, an essential centromere connector protein acting during G1-S phase |
| GO:0061638 CENP-A containing chromatin | IDA PMID:17677001 Plasticity of fission yeast CENP-A chromatin driven by relat... | ACCEPT | Summary: Core cellular component. Cnp1 is the histone that defines CENP-A chromatin at the central domain, directly demonstrated by ChIP. Reason: Directly supported by ChIP showing endogenous Cnp1/CENP-A chromatin across the central domain. Supporting Evidence: PMID:17677001 Within the central domain most histone H3 is replaced by the centromere-specific H3 variant CENP-ACnp1 to form the unusual chromatin that occupies most of the 10–12 kb comprising imr and cnt |
| GO:0005515 protein binding | IPI PMID:29194511 Prolyl isomerization of the CENP-A N-terminus regulates cent... | MARK AS OVER ANNOTATED | Summary: Bare protein binding (interaction with the CENP-A escort chaperone Sim3, SPBC577.15c). Sim3 binds the Cnp1 N-terminal GRANT motif and escorts CENP-A for centromeric deposition; the GO term itself is uninformative. Reason: Uninformative bare protein binding; the Sim3 chaperone interaction is better represented by the CENP-A chromatin assembly process. Supporting Evidence: PMID:29194511 we further identified the SpCENP-A-localizing chaperone Sim3 as a SpCENP-A NTD interacting protein that is dependent on GRANT proline residues |
| GO:0000775 chromosome, centromeric region | IDA PMID:18077559 Biphasic incorporation of centromeric histone CENP-A in fiss... | ACCEPT | Summary: Directly demonstrated centromeric localization of Cnp1/CENP-A across the cell cycle (S and G2 deposition phases). Reason: Direct experimental evidence of Cnp1 incorporation at centromeres. Supporting Evidence: PMID:18077559 CENP-A is normally localized to centromeres in S phase in an Ams2-dependent manner |
| GO:0000785 chromatin | IDA PMID:23314747 Myb-domain protein Teb1 controls histone levels and centrome... | KEEP AS NON CORE | Summary: Cnp1 is a chromatin component; demonstrated by ChIP of centromeric Cnp1. Correct but general relative to the CENP-A chromatin term. Reason: True but a general parent of the specific CENP-A containing chromatin annotation. Supporting Evidence: PMID:23314747 we examined localization of the centromeric histone H3 variant Cnp1 and found reduced centromeric binding along with reduced centromeric silencing |
| GO:0005515 protein binding | IPI PMID:19217404 Fission yeast Scm3: A CENP-A receptor required for integrity... | MARK AS OVER ANNOTATED | Summary: Bare protein binding (interaction with Scm3, SPAPB1A10.02). Scm3 is the HJURP-related CENP-A receptor that physically binds Cnp1 and mediates its assembly into central-core chromatin; the GO term itself is uninformative. Reason: Uninformative bare protein binding; the Scm3 receptor interaction is better represented by the CENP-A chromatin assembly process. Supporting Evidence: PMID:19217404 Scm3(Sp) coaffinity purifies with CENP-A(Cnp1) and associates with CENP-A(Cnp1) in vitro |
| GO:0000775 chromosome, centromeric region | IDA PMID:26275423 Inner Kinetochore Protein Interactions with Regional Centrom... | ACCEPT | Summary: Directly mapped Cnp1/CENP-A nucleosomes occupying the centromeric central domain by native ChIP and cleavage mapping. Reason: Direct genomic mapping of CENP-A nucleosomes at the centromere. Supporting Evidence: PMID:26275423 the central domain, which is occupied by centromere-specific H3 (cenH3 or CENP-A) nucleosomes |
| GO:0034506 chromosome, centromeric core domain | IDA PMID:11553715 The domain structure of centromeres is conserved from fissio... | ACCEPT | Summary: Core cellular component. Cnp1 associates exclusively with the central core domain, distinct from the flanking heterochromatin repeats. Reason: Directly demonstrated exclusive association of Cnp1 with central core DNA. Supporting Evidence: PMID:11553715 The centromere-associated proteins, Mis6p and Cnp1p (SpCENP-A), associate exclusively with central core DNA, whereas the Swi6 protein binds the surrounding repeats |
| GO:0000775 chromosome, centromeric region | IDA PMID:10864871 Requirement of Mis6 centromere connector for localizing a CE... | ACCEPT | Summary: Foundational direct evidence that SpCENP-A localizes to the nonrepetitive inner centromere. Reason: Original direct demonstration of Cnp1 centromeric localization. Supporting Evidence: PMID:10864871 SpCENP-A binding to the nonrepetitious inner centromeres |
| GO:0034080 CENP-A containing chromatin assembly | IMP PMID:10864871 Requirement of Mis6 centromere connector for localizing a CE... | ACCEPT | Summary: Core biological process. Cnp1 is required to establish centromeric CENP-A chromatin; mutant analysis demonstrates its essential role in assembling this specialized chromatin. Reason: Mutant phenotype (IMP) shows Cnp1 is essential for establishing centromere chromatin. Supporting Evidence: PMID:10864871 the fission yeast homolog SpCENP-A is essential for establishing centromere chromatin associated with equal chromosome segregation |
| GO:0000779 condensed chromosome, centromeric region | IDA PMID:23166349 Csi1 links centromeres to the nuclear envelope for centromer... | ACCEPT | Summary: Cnp1 is used as a centromere marker localizing to centromeres clustered at the nuclear envelope; supports centromeric localization on condensed chromosomes. Reason: Direct cytological localization of Cnp1 at clustered centromeres. Supporting Evidence: PMID:23166349 the centromeres of each chromosome are clustered together and attached to the nuclear envelope near the site of the spindle pole body during interphase |
| GO:0034506 chromosome, centromeric core domain | IDA PMID:18077559 Biphasic incorporation of centromeric histone CENP-A in fiss... | ACCEPT | Summary: Core cellular component. Direct evidence of Cnp1 incorporation into the centromeric central core domain across the cell cycle. Reason: Direct experimental localization to the centromeric core domain. Supporting Evidence: PMID:18077559 CENP-A is normally localized to centromeres in S phase in an Ams2-dependent manner |
| GO:0005634 nucleus | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | KEEP AS NON CORE | Summary: High-throughput YFP localization confirms nuclear localization; generic relative to the specific centromeric annotations. Reason: Correct but uninformative parent localization from a genome-wide localization screen. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome, by tagging each ORF with the yellow fluorescent protein |
| GO:0019237 centromeric DNA binding | ISM GO_REF:0000050 | KEEP AS NON CORE | Summary: Cnp1 occupies and binds DNA of the centromeric central core. Note that in fission yeast CENP-A deposition is sequence-independent (epigenetic), so this reflects centromeric occupancy rather than sequence-specific recognition. Acceptable as a non-core descriptor of its DNA association at the centromere. Reason: Cnp1 binds DNA within centromeric nucleosomes (ChIP-enriched at the central core), though binding is sequence-independent rather than sequence-specific. Supporting Evidence: PMID:11553715 Cnp1 ( S. pombe CENP-A) and Mis6 proteins both bind to the central core region but not the flanking regions |
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Download this section (compressed HTML)Q: Does fission yeast CENP-A truly bind centromeric DNA in a sequence-specific manner, or is the GO:0019237 centromeric DNA binding annotation better interpreted purely as epigenetic, sequence-independent occupancy?
Q: What is the precise stoichiometry and composition of the S. pombe CENP-A nucleosome in vivo (octameric vs. alternative particles, H2A/H2B content)?
Q: How do the S-phase (Ams2-dependent) and G2 deposition pathways divide the labor of CENP-A loading, and which is the primary maintenance pathway?
Experiment: Genome-wide native-ChIP and cleavage mapping of Cnp1 across the cell cycle to quantify CENP-A nucleosome positioning, density, and the relative contributions of S-phase vs G2 deposition.
Experiment: In vitro reconstitution of S. pombe CENP-A nucleosomes with Scm3, Sim3, and Mis16/Mis18 to define the minimal assembly machinery and the particle composition (H2A/H2B content) of central-core nucleosomes.
Experiment: Targeted degron depletion of Cnp1 followed by quantitative imaging of inner-kinetochore protein recruitment and chromosome segregation fidelity to dissect the order of kinetochore assembly downstream of CENP-A.
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