Caf1-55 Chromatin assembly factor 1, p55 subunit [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: Caf1-55provided by FlyBase
Official Full Name: Chromatin assembly factor 1, p55 subunitprovided by FlyBase
Primary source: FLYBASE:FBgn0263979
Locus tag: Dmel_CG4236
See related: AllianceGenome:FB:FBgn0263979
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Drosophila melanogaster
Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as: 154659_at; 55; caf-1; Caf-1; CAF-1; CAF-1 p55; caf1; Caf1; CAF1; Caf1 (p55); caf1 p55; caf1-55; CAF1-55; Caf1-p55; CAF1-p55; Caf1/p55; Caf1p55; CAF1p55; CG4236; d-CAF1; dCAF-1; dCAF-1 p55; dCAF-1-p55; dCAF1; dCAF1-p55; Dmel\CG4236; dNURF; dp55; MSI1/RbAp48/CAC3/LIN-53; Nurf; NURF; Nurf 55; NURF 55; Nurf-55; NURF-55; nurf55; Nurf55; NURF55; p55; P55; p55 CAF1; p55/NURF-55; p55CAF1; RbAp46/48; RbAp48; RBAP48; S(ls)3
Summary: Enables several functions, including histone binding activity; histone deacetylase binding activity; and protein homodimerization activity. Contributes to nucleosome binding activity. Involved in several processes, including DNA replication-dependent chromatin assembly; nucleosome organization; and regulation of gene expression. Located in nucleus and polytene chromosome. Part of CAF-1 complex and nucleus. Is expressed in several structures, including adult head; embryonic/larval midgut primordium; ganglia; germline cell; and head epidermis primordium. Used to study azoospermia. Orthologous to several human genes including RBBP4 (RB binding protein 4, chromatin remodeling factor). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: 88E3-88E3; 3-56 cM

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	3R	NT_033777.3 (15225576..15227564)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	3R	NT_033777.2 (11051298..11053286)

Chromosome 3R - NT_033777.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Results of genetic interaction analyses revealed that Mi-2 and Caf1/p55, components of the Nucleosome Remodeling and Deacetylase (NuRD) complex, genetically antagonize the role of DREF in germline stem cell maintenance. Taken together, these data suggest that DREF contributes to intrinsic components of the germline stem cell regulatory network that maintains competence to self-renew.
Title: DREF Genetically Counteracts Mi-2 and Caf1 to Regulate Adult Stem Cell Maintenance.
CCR4 and CAF1, the two deadenylases in the CCR4-NOT complex, can remove 3' terminal non-A residues in an exonucleolytic manner.
Title: CCR4 and CAF1 deadenylases have an intrinsic activity to remove the post-poly(A) sequence.
CAF1-p180 and CAF1-p75 subunits mediate assembly of two different forms of chromatin.
Title: Subunits of the histone chaperone CAF1 also mediate assembly of protamine-based chromatin.
CAF-1 promotes Notch signaling through epigenetic control of target gene expression during Drosophila development.
Title: CAF-1 promotes Notch signaling through epigenetic control of target gene expression during Drosophila development.
these studies suggest that p55 is not crucial for PRC2-mediated gene silencing in vivo, and the vital function of p55 is probably not dependent on its interaction with histone H4.
Title: The biological function of the WD40 repeat-containing protein p55/Caf1 in Drosophila.
Chromatin-modifying complex component Nurf55/p55 associates with histones H3 and H4 and polycomb repressive complex 2 subunit Su(z)12 through partially overlapping binding sites.
Title: Chromatin-modifying complex component Nurf55/p55 associates with histones H3 and H4 and polycomb repressive complex 2 subunit Su(z)12 through partially overlapping binding sites.
analysis of Caf1 mutant tissue suggests that Caf1 plays important roles in cell survival and segment identity, and loss of Caf1 is associated with a reduction in the Polycomb Repressive Complex 2 (PRC2)-specific histone methylation mark H3K27me3
Title: The enhancer of trithorax and polycomb gene Caf1/p55 is essential for cell survival and patterning in Drosophila development.
spreading of heterochromatin is compromised in flies that have reduced CAF-1 p180. Furthermore, reduced CAF-1 p180 causes a defect in the dynamics of heterochromatic markers in early Drosophila embryos.
Title: Drosophila CAF-1 regulates HP1-mediated epigenetic silencing and pericentric heterochromatin stability.
results suggest that the ISWI-containing NURF complex functions as a co-activator of Armadillo to promote Wg-mediated transcription.
Title: The ISWI-containing NURF complex regulates the output of the canonical Wingless pathway.
larval endocycling cells lacking CAF-1 large subunit exhibit normal dynamics of progression through endocycles, although accumulating defects, such as perturbation of nucleosomal organisation, reduction of DNA replication and accumulation of DNA damage
Title: CAF-1 is required for efficient replication of euchromatic DNA in Drosophila larval endocycling cells.

Submit: New GeneRIF Correction See all GeneRIFs (16)

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase binding	IDA Inferred from Direct Assay more info	PubMed
enables histone deacetylase binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
contributes_to nucleosome binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA replication-dependent chromatin assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin organization	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin organization	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in eggshell chorion gene amplification	IC Inferred by Curator more info	PubMed
involved_in facultative heterochromatin formation	IC Inferred by Curator more info	PubMed
involved_in heterochromatin formation	IC Inferred by Curator more info	PubMed
involved_in heterochromatin formation	IPI Inferred from Physical Interaction more info	PubMed
involved_in negative regulation of DNA-templated transcription	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleosome organization	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in segment specification	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of CAF-1 complex	IDA Inferred from Direct Assay more info	PubMed
part_of ESC/E(Z) complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ESC/E(Z) complex	IDA Inferred from Direct Assay more info	PubMed
part_of Myb complex	IDA Inferred from Direct Assay more info	PubMed
part_of NURF complex	IDA Inferred from Direct Assay more info	PubMed
part_of NURF complex	IPI Inferred from Physical Interaction more info	PubMed
part_of NURF complex	TAS Traceable Author Statement more info	PubMed
part_of NuRD complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NuRD complex	IDA Inferred from Direct Assay more info	PubMed
part_of RNA polymerase II transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed
part_of Sin3-type complex	IDA Inferred from Direct Assay more info	PubMed
part_of histone methyltransferase complex	IDA Inferred from Direct Assay more info	PubMed
part_of histone methyltransferase complex	IPI Inferred from Physical Interaction more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in polytene chromosome	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: chromatin assembly factor 1, p55 subunit

Names: CG4236-PA; CG4236-PB; Caf1-55-PA; Caf1-55-PB; Nurf55/CAF1; chromatin assembly Factor-1; chromatin assembly factor 1; chromatin assembly factor 1 subunit; chromatin associated factor-1 subunit; nucleosome remodeling factor; nucleosome remodeling factor - 55kD; p55

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NT_033777.3 Reference assembly

Range

15225576..15227564

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_079630.4 → NP_524354.1 chromatin assembly factor 1, p55 subunit, isoform A [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_524354.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A0AP04, Q24572, Q9VFB4

UniProtKB/TrEMBL

C0MJE4

Related

FBpp0082511

Conserved Domains (3) summary

sd00039
Location:132 → 179

7WD40; WD40 repeat [structural motif]

pfam12265
Location:23 → 92

CAF1C_H4-bd; Histone-binding protein RBBP4 or subunit C of CAF1 complex

cl29593
Location:127 → 408

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001170146.2 → NP_001163617.1 chromatin assembly factor 1, p55 subunit, isoform B [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001163617.1

Status: REVIEWED

UniProtKB/TrEMBL

E1JIL4

Conserved Domains (3) summary

sd00039
Location:131 → 178

7WD40; WD40 repeat [structural motif]

pfam12265
Location:22 → 91

CAF1C_H4-bd; Histone-binding protein RBBP4 or subunit C of CAF1 complex

cl29593
Location:126 → 407

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...