FlyBase Gene Report: Dmel\Caf1-55

General Information

Symbol

Dmel\Caf1-55

Species

D. melanogaster

Name

Chromatin assembly factor 1, p55 subunit

Annotation Symbol

CG4236

Feature Type

protein_coding_gene

FlyBase ID

FBgn0263979

Gene Model Status

Current

Stock Availability

14 publicly available

Gene Summary

Chromatin assembly factor 1, p55 subunit (Caf1-55) encodes a subunit of the MuvB core complex. The MuvB core binds to the oncoprotein encoded by Myb and the Rbf-E2f2-Dp tumor suppressor complex, thereby controlling the expression of many genes, including critical regulators of the cell cycle. [Date last reviewed: 2019-03-21] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

p55, Caf1, NURF, NURF55, NURF-55

Key Links

Genomic Location

Cytogenetic map

88E3-88E3

Sequence location

3R:15,225,576..15,227,564 [+]

Recombination map

3-56

RefSeq locus

NT_033777 REGION:15225576..15227564

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (30 terms)

Molecular Function (6 terms)

Terms Based on Experimental Evidence (6 terms)

CV Term

Evidence

References

enables histone binding

inferred from direct assay

(Nowak et al., 2011)

enables histone deacetylase binding

inferred from direct assay

(Tyler et al., 1996)

contributes_to nucleosome binding

inferred from direct assay

(Nekrasov et al., 2005)

enables protein binding

inferred from physical interaction with FLYBASE:MBD-like; FB:FBgn0027950

(Marhold et al., 2004)

inferred from physical interaction with UniProtKB:Q9V464

(Tyler et al., 2001)

enables protein homodimerization activity

inferred from physical interaction with FLYBASE:Caf1-55; FB:FBgn0263979

(Marhold et al., 2004)

enables transcription cis-regulatory region binding

inferred from direct assay

(Yao et al., 2018)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables histone binding

inferred from biological aspect of ancestor with PANTHER:PTN000522733

(GO Reference Genome Project, 2011-)

enables histone deacetylase binding

inferred from sequence or structural similarity with UniProtKB:Q09028

(Tyler et al., 1996)

Biological Process (13 terms)

Terms Based on Experimental Evidence (10 terms)

CV Term

Evidence

References

involved_in chromatin organization

inferred from direct assay

(Martinez-Balbas et al., 1998, Bulger et al., 1995)

involved_in chromatin remodeling

inferred from direct assay

(Mizuguchi et al., 2001)

involved_in DNA replication-dependent chromatin assembly

inferred from direct assay

(Tyler et al., 1999, Ito et al., 1997, Tyler et al., 1996)

involved_in heterochromatin formation

inferred from physical interaction with FLYBASE:esc; FB:FBgn0000588

(Tie et al., 2001)

inferred from physical interaction with FLYBASE:E(z); FB:FBgn0000629

(Tie et al., 2001)

involved_in negative regulation of DNA-templated transcription

inferred from genetic interaction with FLYBASE:mrt; FB:FBgn0039507

(Yao et al., 2018)

involved_in negative regulation of transcription by RNA polymerase II

inferred from mutant phenotype

(Lewis et al., 2004)

involved_in nucleosome organization

inferred from direct assay

(Hamiche et al., 1999)

involved_in positive regulation of DNA-templated transcription

inferred from direct assay

(Mizuguchi et al., 2001)

involved_in regulation of mitotic cell cycle

inferred from mutant phenotype

(Pile et al., 2002)

involved_in segment specification

inferred from mutant phenotype

(Anderson et al., 2011)

Terms Based on Predictions or Assertions (6 terms)

CV Term

Evidence

References

involved_in chromatin organization

inferred from sequence or structural similarity with UniProtKB:Q09028

(Tie et al., 2005)

inferred from sequence or structural similarity with UniProtKB:Q16576

(Tie et al., 2005)

involved_in chromatin remodeling

inferred from biological aspect of ancestor with PANTHER:PTN000522733

(GO Reference Genome Project, 2011-)

involved_in eggshell chorion gene amplification

inferred by curator from GO:0031523

(Beall et al., 2002)

involved_in facultative heterochromatin formation

inferred by curator from GO:0035098

(Ohno et al., 2008, Muller et al., 2002)

involved_in heterochromatin formation

inferred by curator from GO:0035098

(Czermin et al., 2002)

involved_in regulation of DNA-templated transcription

inferred from biological aspect of ancestor with PANTHER:PTN000522733

(GO Reference Genome Project, 2011-)

Cellular Component (11 terms)

Terms Based on Experimental Evidence (11 terms)

CV Term

Evidence

References

part_of CAF-1 complex

inferred from direct assay

(Tyler et al., 1996)

part_of ESC/E(Z) complex

inferred from direct assay

(Herz et al., 2012, Ohno et al., 2008, Czermin et al., 2002, Muller et al., 2002)

part_of histone methyltransferase complex

inferred from physical interaction with FLYBASE:ash1; FB:FBgn0005386,FLYBASE:MRG15; FB:FBgn0027378

(Huang et al., 2017)

inferred from direct assay

(Ketel et al., 2005)

part_of Myb complex

inferred from direct assay

(Korenjak et al., 2004, Lewis et al., 2004, Beall et al., 2002)

located_in nucleus

inferred from direct assay

(Czermin et al., 2002, Tie et al., 2001, Martinez-Balbas et al., 1998, Tyler et al., 1996)

part_of NuRD complex

inferred from direct assay

(Reddy et al., 2010, Marhold et al., 2004)

part_of NURF complex

inferred from direct assay

(Kwon et al., 2009)

inferred from physical interaction with FLYBASE:Iswi; FB:FBgn0011604

(Martinez-Balbas et al., 1998)

located_in polytene chromosome

inferred from direct assay

(Martinez-Balbas et al., 1998)

part_of RNA polymerase II transcription regulator complex

inferred from direct assay

(Beall et al., 2007)

part_of Sin3-type complex

inferred from direct assay

(Spain et al., 2010)

part_of transcription regulator complex

inferred from physical interaction with FLYBASE:Trf2; FB:FBgn0261793

(Hochheimer et al., 2002)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

part_of ESC/E(Z) complex

inferred from biological aspect of ancestor with PANTHER:PTN001110116

(GO Reference Genome Project, 2011-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000522733

(GO Reference Genome Project, 2011-)

part_of NuRD complex

inferred from biological aspect of ancestor with PANTHER:PTN001110116

(GO Reference Genome Project, 2011-)

part_of NURF complex

traceable author statement

(Badenhorst et al., 2002, Gdula et al., 1998)

Gene Group (FlyBase)

NUCLEOSOME REMODELING FACTOR

POLYCOMB REPRESSIVE COMPLEX 2, PCL VARIANT

CHROMATIN ASSEMBLY FACTOR 1

NUCLEOSOME REMODELING DEACETYLASE COMPLEX

POLYCOMB REPRESSIVE COMPLEX 2, JARID2-JING VARIANT

DREAM TRANSCRIPTIONAL REPRESSOR COMPLEX, RBF VARIANT

TESTIS-SPECIFIC MEIOTIC ARREST COMPLEX

DREAM TRANSCRIPTIONAL REPRESSOR COMPLEX, RBF2 VARIANT

MUVB CORE SUBUNITS

MYB-MUVB TRANSCRIPTIONAL ACTIVATION COMPLEX

Protein Family (UniProt)

Belongs to the WD repeat RBAP46/RBAP48/MSI1 family. (Q24572)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Group (FlyBase)

NUCLEOSOME REMODELING FACTOR -: Nucleosome Remodeling Factor (NURF) is an ISWI ATPase-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. (Adapted from FBrf0228922 and FBrf0228920).
POLYCOMB REPRESSIVE COMPLEX 2, PCL VARIANT -: The Polycomb repressive complex 2 (PRC2) is a Polycomb group complex. Histone-lysine N-methyltransferase which trimethylates catalyzes the trimethylation of K27 of histone H3 (H3K27me3) which serves to recruit PRC1 and K9 of histone H3 (H3K9me3) and promotes heterochromatin formation. The PRC2 core may preferentially interact with Pcl or Jarid2 giving rise to variants. (Adapted from FBrf0188105 & FBrf0252799).
CHROMATIN ASSEMBLY FACTOR 1 -: Chromatin assembly factor 1 (CAF-1) is a highly conserved three-subunit histone chaperone in eukaryotes, which facilitates chromatin assembly by depositing histone H3 and H4 onto newly synthesized DNA. CAF-1 is also implicated in epigenetic regulation. (Adapted from FBrf0222414).
NUCLEOSOME REMODELING DEACETYLASE COMPLEX -: The nucleosome remodelling and deacetylase (NuRD) complex couples chromatin remodelling and histone deacetylation to mediate transcriptional repression. (Adapted from FBrf0228973 and FBrf0228920).
POLYCOMB REPRESSIVE COMPLEX 2, JARID2-JING VARIANT -: The Polycomb repressive complex 2 (PRC2) is a Polycomb group complex. Histone-lysine N-methyltransferase which trimethylates catalyzes the trimethylation of K27 of histone H3 (H3K27me3) which serves to recruit PRC1 and K9 of histone H3 (H3K9me3) and promotes heterochromatin formation. he PRC2 core may preferentially interact with Pcl or Jarid2 giving rise to variants. (Adapted from FBrf0188105 & FBrf0252799).
DREAM TRANSCRIPTIONAL REPRESSOR COMPLEX, RBF VARIANT -: The DREAM complex is a MuvB-type transcriptional repressor complex containing multiple site-specific DNA-binding proteins, including E2f2 and Rbf. (Adapted from PMID:35468940 and FBrf0258562.)
TESTIS-SPECIFIC MEIOTIC ARREST COMPLEX -: The testis-specific meiotic arrest complex (tMAC) is a MuvB-type transcriptional activator complex required for meiosis and spermiogenesis. (Adapted from FBrf0238569.)
DREAM TRANSCRIPTIONAL REPRESSOR COMPLEX, RBF2 VARIANT -: The DREAM complex is a MuvB-type transcriptional repressor complex containing multiple site-specific DNA-binding proteins, including E2f2 and Rbf2. (Adapted from PMID:35468940 and FBrf0258562.)
MUVB CORE SUBUNITS -: The MuvB core subunits are a conserved assembly of five proteins that form the central scaffold of several transcription regulatory complexes. The MuvB core interacts with other factors, many sequence-specific DNA transcription factors, to form different transcription regulatory complexes. The exact composition of the complex dictates the genes targeted and the mechanism of regulation. (Adapted from PMID:35468940.)
MYB-MUVB TRANSCRIPTIONAL ACTIVATION COMPLEX -: The Myb-MuvB transcriptional activation complex (MMC) is formed from the interaction of the MuvB core with the transcription factor Myb. (Adapted from FBrf0236039.)

Protein Function (UniProtKB)

Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the nucleosome remodeling and deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the nucleosome remodeling factor (NURF) complex, which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin; and the polycomb group (PcG) repressor complex ESC-E(Z), which promotes repression of homeotic genes during development. Also required for transcriptional repression of E2F target genes by E2f2 and Rbf or Rbf2.

(UniProt, Q24572)

Summary (Interactive Fly)

A histone chaperone protein - mediates nucleosome assembly on both the leading and lagging strands immediately after passage of the DNA replication fork - maintenance of heterochromatin CAF-1 requires its interaction with HP1a through a conserved motif

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Caf1-55 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q24572)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

PDB - An information portal to biological macromolecular structures

Comments on Gene Model

Gene model reviewed during 5.48

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Caf1-55-RA

FBtr0083052

NM_079630

1828

430

Caf1-55-RB

FBtr0301845

NM_001170146

1825

429

Additional Transcript Data and Comments

Reported size (kB)

2.1 (northern blot)

(Tyler et al., 1996)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Caf1-55-PA

FBpp0082511

48.6

430

4.52

FBpp0291059

48.6

429

4.52

E1JIL4

NP_001163617

ACZ94913

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

430 (aa); 55 (kD observed); 48 (kD predicted)

(Tyler et al., 1996)

Comments

External Data

Subunit Structure (UniProtKB)

Probably binds directly to helix 1 of the histone fold of histone H4, a region that is not accessible when H4 is in chromatin (Probable). Self associates (PubMed:15516265). Associates with chromatin (PubMed:9419341). Component of the CAF-1 complex, composed of Caf1-55, Caf1-105 and Caf1-180; within the CAF-1 complex, Caf1-180 interacts directly with both Caf1-55 and Caf1-105 (PubMed:11533245). Component of the NuRD complex, composed of at least Caf1-55, Mi-2, MTA1-like and HDAC1/Rpd3 (PubMed:15516265). Within the NuRD complex, Caf1-55 may interact directly with Mi-2, MTA1-like and HDAC1/Rpd3. The NuRD complex may also associate with the methyl-DNA binding protein MBD-like via Caf1-55 and Mi-2. Component of the NURF complex, composed of Caf1-55, E(bx), Nurf-38 and Iswi (PubMed:9419341, PubMed:9784495). Component of the polycomb repressive complex 2 (PRC2, also known as the Esc/E(Z) complex), composed of Caf1-55, esc, E(z), Su(z)12, and possibly pho (PubMed:11124122, PubMed:12408863, PubMed:12408864, PubMed:12533794, PubMed:12697833). PRC2 associates with the accessory components Jarid2 and jing to form the PRC2 Jarid2-jing variant (PRC2.2) (PubMed:22354997). PRC2 may also associate with Pcl and HDAC1/Rpd3 during early embryogenesis (PubMed:11124122, PubMed:12408863, PubMed:12408864, PubMed:12533794, PubMed:12697833). Interacts with Rbf and Rbf2 (PubMed:15456884). Component of the DREAM complex at least composed of Myb, Caf1-55, mip40, mip120, mip130, E2f2, Dp, Rbf, Rbf2, lin-52, HDAC1/Rpd3 and l(3)mbt (PubMed:12490953, PubMed:15479636, PubMed:15545624).

(UniProt, Q24572)

Crossreferences

InterPro - A database of protein families, domains and functional sites

PDB - An information portal to biological macromolecular structures

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Caf1-55 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Caf1_1

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.17

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism | ubiquitous

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

antennal primordium