Summary: Centromere protein H (CENP-H)

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CENPH Edit Wikipedia article

Centromere protein H

Identifiers

Symbols

CENPH; NNF1; PMF1

External IDs

OMIM: 605607 MGI: 1349448 HomoloGene: 32519 GeneCards: CENPH Gene

Gene Ontology
Molecular function	• protein binding • kinetochore binding
Cellular component	• kinetochore • kinetochore • kinetochore • condensed chromosome kinetochore • nucleus • nucleoplasm • chromosome • cytosol
Biological process	• M phase of mitotic cell cycle • mitotic prometaphase • mitotic cell cycle • nucleosome assembly • chromosome segregation • CenH3-containing nucleosome assembly at centromere • cell division • kinetochore organization
Sources: Amigo / QuickGO

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 5:
68.49 – 68.51 Mb

Chr 13:
101.53 – 101.55 Mb

PubMed search

[1]

[2]

CENP-H

Identifiers

Symbol

CENP-H

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Centromere protein H is a protein that in humans is encoded by the CENPH gene.^[1]^[2]^[3]

[edit] Function

Centromere and kinetochore proteins play a critical role in centromere structure, kinetochore formation, and sister chromatid separation. The protein encoded by this gene colocalizes with inner kinetochore plate proteins CENP-A and CENP-C in both interphase and metaphase. CENP-H is required for the localisation of CENP-C, but not CENP-A, to the centromere. However, it may be involved in the incorporation of newly synthesised CENP-A into centromeres via its interaction with the CENP-A/CENP-HI complex.^[4] CENP-H localizes outside of centromeric heterochromatin, where CENP-B is localized, and inside the kinetochore corona, where CENP-E is localized during prometaphase. It is thought that this protein can bind to itself, as well as to CENP-A, CENP-B or CENP-C. Multimers of the protein localize constitutively to the inner kinetochore plate and play an important role in the organization and function of the active centromere-kinetochore complex.^[5] CENP-H contains a coiled-coil structure and a nuclear localisation signal.^[5]

Studies show that CENP-H may be associated with certain human cancers.^[6]^[7]

CENP-H shows sequence similarity to the Schizosaccharomyces pombe kinetochore protein Fta3 which is a subunit of the Sim4 complex. This complex is required for loading the DASH complex onto the kinetochore via interaction with dad1. Fta2, Fta3 and Fta4 associate with the central core and inner repeat region of the centromere.^[8]

[edit] Other Protein Interactions

CENPH has also been shown to interact with KIAA0090.^[9] The significance of this interaction is unclear.

[edit] References

^ Sugata N, Li S, Earnshaw WC, Yen TJ, Yoda K, Masumoto H, Munekata E, Warburton PE, Todokoro K (Jan 2001). "Human CENP-H multimers colocalize with CENP-A and CENP-C at active centromere--kinetochore complexes". Hum Mol Genet 9 (19): 2919–26. doi:10.1093/hmg/9.19.2919. PMID 11092768.
^ Obuse C, Iwasaki O, Kiyomitsu T, Goshima G, Toyoda Y, Yanagida M (Nov 2004). "A conserved Mis12 centromere complex is linked to heterochromatic HP1 and outer kinetochore protein Zwint-1". Nat Cell Biol 6 (11): 1135–41. doi:10.1038/ncb1187. PMID 15502821.
^ "Entrez Gene: CENPH centromere protein H". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=64946.
^ Fukagawa, T.; Mikami, Y.; Nishihashi, A.; Regnier, V.; Haraguchi, T.; Hiraoka, Y.; Sugata, N.; Todokoro, K. et al (2001). "CENP-H, a constitutive centromere component, is required for centromere targeting of CENP-C in vertebrate cells". The EMBO Journal 20 (16): 4603–4617. doi:10.1093/emboj/20.16.4603. PMC 125570. PMID 11500386. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=125570. edit
^ ^a ^b Sugata N, Munekata E, Todokoro K (September 1999). "Characterization of a novel kinetochore protein, CENP-H". J. Biol. Chem. 274 (39): 27343–6. PMID 10488063.
^ Guo XZ, Zhang G, Wang JY, Liu WL, Wang F, Dong JQ, Xu LH, Cao JY, Song LB, Zeng MS (2008). "Prognostic relevance of Centromere protein H expression in esophageal carcinoma". BMC Cancer 8: 233. doi:10.1186/1471-2407-8-233. PMC 2535782. PMID 18700042. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2535782.
^ Liao WT, Song LB, Zhang HZ, Zhang X, Zhang L, Liu WL, Feng Y, Guo BH, Mai HQ, Cao SM, Li MZ, Qin HD, Zeng YX, Zeng MS (January 2007). "Centromere protein H is a novel prognostic marker for nasopharyngeal carcinoma progression and overall patient survival". Clin. Cancer Res. 13 (2 Pt 1): 508–14. doi:10.1158/1078-0432.CCR-06-1512. PMID 17255272.
^ Liu X, McLeod I, Anderson S, Yates JR, He X (August 2005). "Molecular analysis of kinetochore architecture in fission yeast". EMBO J. 24 (16): 2919–30. doi:10.1038/sj.emboj.7600762. PMC 1187945. PMID 16079914. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1187945.
^ Prieto C, De Las Rivas J (July 2006). "APID: Agile Protein Interaction DataAnalyzer". Nucleic Acids Res. 34 (Web Server issue): W298–302. doi:10.1093/nar/gkl128. PMC 1538863. PMID 16845013. http://bioinfow.dep.usal.es/apid/html/home.htm.

[edit] Further reading

Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=139241.
Saffery R, Sumer H, Hassan S, et al. (2003). "Transcription within a functional human centromere.". Mol. Cell 12 (2): 509–16. doi:10.1016/S1097-2765(03)00279-X. PMID 14536089.
Obuse C, Yang H, Nozaki N, et al. (2004). "Proteomics analysis of the centromere complex from HeLa interphase cells: UV-damaged DNA binding protein 1 (DDB-1) is a component of the CEN-complex, while BMI-1 is transiently co-localized with the centromeric region in interphase.". Genes Cells 9 (2): 105–20. doi:10.1111/j.1365-2443.2004.00705.x. PMID 15009096.
Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=528928.
Mikami Y, Hori T, Kimura H, Fukagawa T (2005). "The functional region of CENP-H interacts with the Nuf2 complex that localizes to centromere during mitosis.". Mol. Cell. Biol. 25 (5): 1958–70. doi:10.1128/MCB.25.5.1958-1970.2005. PMC 549355. PMID 15713649. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=549355.
Tomonaga T, Matsushita K, Ishibashi M, et al. (2005). "Centromere protein H is up-regulated in primary human colorectal cancer and its overexpression induces aneuploidy.". Cancer Res. 65 (11): 4683–9. doi:10.1158/0008-5472.CAN-04-3613. PMID 15930286.
Foltz DR, Jansen LE, Black BE, et al. (2006). "The human CENP-A centromeric nucleosome-associated complex.". Nat. Cell Biol. 8 (5): 458–69. doi:10.1038/ncb1397. PMID 16622419.
Okada M, Cheeseman IM, Hori T, et al. (2006). "The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres.". Nat. Cell Biol. 8 (5): 446–57. doi:10.1038/ncb1396. PMID 16622420.
Izuta H, Ikeno M, Suzuki N, et al. (2006). "Comprehensive analysis of the ICEN (Interphase Centromere Complex) components enriched in the CENP-A chromatin of human cells.". Genes Cells 11 (6): 673–84. doi:10.1111/j.1365-2443.2006.00969.x. PMID 16716197.
Orthaus S, Ohndorf S, Diekmann S (2006). "RNAi knockdown of human kinetochore protein CENP-H.". Biochem. Biophys. Res. Commun. 348 (1): 36–46. doi:10.1016/j.bbrc.2006.06.187. PMID 16875666.
Liao WT, Song LB, Zhang HZ, et al. (2007). "Centromere protein H is a novel prognostic marker for nasopharyngeal carcinoma progression and overall patient survival.". Clin. Cancer Res. 13 (2 Pt 1): 508–14. doi:10.1158/1078-0432.CCR-06-1512. PMID 17255272.
Ewing RM, Chu P, Elisma F, et al. (2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry.". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1847948.

This article on a gene on chromosome 5 is a stub. You can help Wikipedia by expanding it.

Genetics: chromosomes

General

Karyotype · Ploidy · Meiosis

Classification

Autosome · Sex chromosome · Microchromosome

Evolution

Chromosomal inversion · Chromosomal translocation · Polyploidy · Paleopolyploidy

Structure

Nucleosome

Telomere: Telomere-binding protein (TINF2)

Chromatid

Chromatin	Euchromatin · Heterochromatin

Histone	H1 · H2A · H2B · H3 · H4

Centromere	A · B · C1 · C2 · E · F · H · I · J · K · M · N · O · P · Q · T

B strc: edmb (perx), skel (ctrs), epit, cili, mito, nucl (chro)

This article incorporates text from the public domain Pfam and InterPro IPR008426

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Centromere protein H (CENP-H) Provide feedback

This family consists of several eukaryotic centromere protein H (CENP-H) sequences. Macromolecular centromere-kinetochore complex plays a critical role in sister chromatid separation, but its complete protein composition as well as its precise dynamic function during mitosis has not yet been clearly determined. CENP-H contains a coiled-coil structure and a nuclear localisation signal. CENP-H is specifically and constitutively localised in kinetochores throughout the cell cycle. CENP-H may play a role in kinetochore organisation and function throughout the cell cycle [1]. This the C-terminus of the region, which is conserved from fungi to humans.

Literature references

Sugata N, Munekata E, Todokoro K; , J Biol Chem 1999;274:27343-27346.: Characterization of a novel kinetochore protein, CENP-H. PUBMED:10488063 EPMC:10488063
Fukagawa T, Mikami Y, Nishihashi A, Regnier V, Haraguchi T, Hiraoka Y, Sugata N, Todokoro K, Brown W, Ikemura T; , EMBO J 2001;20:4603-4617.: CENP-H, a constitutive centromere component, is required for centromere targeting of CENP-C in vertebrate cells. PUBMED:11500386 EPMC:11500386

External database links

PANDIT:	PF05837
Pseudofam:	PF05837
SYSTERS:	CENP-H

This tab holds annotation information from the InterPro database.

InterPro entry IPR008426

Chromosome segregation in eukaryotes requires the kinetochore, a multi-protein structure that assembles on centromeric DNA, and which acts to link chromosomes to spindle microtubules. Kinetochore structure and composition is highly conserved among vertebrates. The inner kinetochore is essential for kinetochore assembly, and is involved in chromosome segregation via regulation of the spindle. Inner kinetochore components include the multi-subunit CENP-H/I complex, which may function, in part, in directing centromere protein A (CENP-A) deposition to centromeres, where CENP-A is a centromere-specific histone H3 variant required for the organisation of centromeric chromatin during interphase. The CENP-H/I complex contains three functional classes of proteins [PUBMED:16622420, PUBMED:18094054]:

CENP-H class (includes CENP-H, -I, -K, -L)
CENP-M class (includes CENP-M)
CENP-O class (includes CENP-O, -P, -Q, -R, -50)

CENP-H is required for the localisation of CENP-C, but not CENP-A, to the centromere. However, it may be involved in the incorporation of newly synthesised CENP-A into centromeres via its interaction with the CENP-A/CENP-HI complex. CENP-H contains a coiled-coil structure and a nuclear localisation signal. CENP-H is specifically and constitutively localised in kinetochores throughout the cell cycle, and may play a role in kinetochore organisation and function throughout the cell cycle [PUBMED:10488063].

Studies show that CENP-H may be associated with certain human cancers [PUBMED:18700042, PUBMED:17255272].

This entry also includes Kinetochore protein Fta3 which is a subunit of the Sim4 complex. This complex is required for loading the DASH complex onto the kinetochore via interaction with dad1. Fta2, Fta3 and Fta4 associate with the central core and inner repeat region of the centromere [PUBMED:16079914].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component	nucleus (GO:0005634)
Cellular component	condensed chromosome kinetochore (GO:0000777)
Molecular function	kinetochore binding (GO:0043515)
Biological process	chromosome segregation (GO:0007059)
Biological process	cell division (GO:0051301)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

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You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (16)	Full (119)	Representative proteomes				NCBI (130)	Meta (1)
	Seed (16)	Full (119)	RP15 (18)	RP35 (34)	RP55 (60)	RP75 (88)	NCBI (130)	Meta (1)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (16)	Full (119)	Representative proteomes				NCBI (130)	Meta (1)
	Seed (16)	Full (119)	RP15 (18)	RP35 (34)	RP55 (60)	RP75 (88)	NCBI (130)	Meta (1)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (16)	Full (119)	Representative proteomes				NCBI (130)	Meta (1)
	Seed (16)	Full (119)	RP15 (18)	RP35 (34)	RP55 (60)	RP75 (88)	NCBI (130)	Meta (1)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Pfam-B_8705 (release 8.0)

Previous IDs:

none

Type:

Domain

Author:

Moxon SJ

Number in seed:

16

Number in full:

119

Average length of the domain:

106.20 aa

Average identity of full alignment:

27 %

Average coverage of the sequence by the domain:

46.14 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	23.0	23.0
Trusted cut-off	25.3	25.0
Noise cut-off	22.9	22.9

Model length:

106

Family (HMM) version:

7

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: CENP-H (PF05837)

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