FlyBase Gene Report: Dmel\Chd1

General Information

Symbol

Dmel\Chd1

Species

D. melanogaster

Name

Chromodomain-helicase-DNA-binding protein 1

Annotation Symbol

CG3733

Feature Type

protein_coding_gene

FlyBase ID

FBgn0250786

Gene Model Status

Current

Stock Availability

17 publicly available

Gene Summary

Chromodomain-helicase-DNA-binding protein 1 (Chd1) encodes an ATPase involved in the remodeling and assembly of chromatin. Its biological functions include regulation of gene transcription, incorporation of the histone variant H3.3 into paternal chromatin at fertilization and regulation of intestinal immunity and microbiota. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

CHD-1, Chromodomain-helicase-DNA-binding protein, dCHD1

Key Links

Genomic Location

Cytogenetic map

23C4-23C4

Sequence location

2L:2,979,562..2,987,723 [-]

Recombination map

2-8

RefSeq locus

NT_033779 REGION:2979562..2987723

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 (14 terms)

Molecular Function (6 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables chromatin binding

inferred from direct assay

(Stokes et al., 1996)

Terms Based on Predictions or Assertions (6 terms)

CV Term

Evidence

References

enables ATP binding

inferred from electronic annotation with InterPro:IPR000330

(InterPro Project Members, 2004-)

enables ATP hydrolysis activity

inferred from biological aspect of ancestor with PANTHER:PTN002473914

(GO Reference Genome Project, 2011-)

enables ATP-dependent chromatin remodeler activity

inferred from biological aspect of ancestor with PANTHER:PTN002473914

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with UniProtKB:P32657

(Gene Ontology Curators, 2002-)

enables chromatin binding

inferred from biological aspect of ancestor with PANTHER:PTN002473914

(GO Reference Genome Project, 2011-)

enables DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN002473914

(GO Reference Genome Project, 2011-)

enables histone binding

inferred from biological aspect of ancestor with PANTHER:PTN002473914

(GO Reference Genome Project, 2011-)

Biological Process (4 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

involved_in imaginal disc-derived wing morphogenesis

inferred from mutant phenotype

(McDaniel et al., 2008)

involved_in oogenesis

inferred from mutant phenotype

(McDaniel et al., 2008)

involved_in sperm DNA decondensation

inferred from mutant phenotype

(Konev et al., 2007)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in nucleosome organization

inferred from biological aspect of ancestor with PANTHER:PTN001326511

(GO Reference Genome Project, 2011-)

Cellular Component (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in polytene chromosome interband

inferred from direct assay

(Stokes et al., 1996)

located_in polytene chromosome puff

inferred from direct assay

(Stokes et al., 1996)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in chromatin

inferred from biological aspect of ancestor with PANTHER:PTN002473914

(GO Reference Genome Project, 2011-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN002473914

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

SNF2-LIKE CHROMATIN REMODELERS

Protein Family (UniProt)

Belongs to the SNF2/RAD54 helicase family. (Q7KU24)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

ATP hydrolysis activity
RHEA 13065:

Summaries

Gene Snapshot

Gene Group (FlyBase)

SNF2-LIKE CHROMATIN REMODELERS -: Snf2-like chromatin remodelers are a family of helicase-like proteins that direct energy derived from ATP hydrolysis into the mechanical remodelling of chromatin structure. They are so-called due to the presence of a domain homologous to the helicase-like ATPase domain of the S. cerevisiae Snf2 protein. This domain, the Snf2 domain, consists of two tandem RecA-like folds and contains seven conserved helicase-related sequence motifs that classify it as part of the helicase superfamily 2 (SF2). However, Snf2 proteins are not bona fide helicases, lacking the ability to separate nucleic acid strands. Instead, Snf2 proteins are DNA translocases that apply an ATP-dependent torsional strain to DNA, which provides the necessary force to remodel nucleosomes or in some cases other DNA-protein complexes. (Adapted from PMID:21862382.)

Protein Function (UniProtKB)

ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin remodeling, but also required to maintain a specific chromatin configuration across the genome (By similarity). Involved in assembly of active chromatin. Required for maintaining open chromatin and pluripotency in embryonic stem cells and is important for wing development and fertility. Is essential for the incorporation of histone H3.3 and assembly of paternal chromatin. Required for replication-independent nucleosome assembly in the decondensing male pronucleus.

(UniProt, Q7KU24)

Summary (Interactive Fly)

chromodomain protein in the SNF2-like family of ATPases - functions in assembly of active chromatin

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Chd1 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 Q7KU24)

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

Comments on Gene Model

Gene model reviewed during 5.40

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.45

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Chd1-RA

FBtr0077674

NM_057849

6332

1883

Chd1-RB

FBtr0305980

NM_001258922

6216

1900

Chd1-RC

FBtr0331654

NM_001273046

6463

1881

Additional Transcript Data and Comments

Reported size (kB)

7 (northern blot)

(Stokes 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

Chd1-PA

FBpp0077358

211.8

1883

6.30

FBpp0297122

213.9

1900

6.41

FBpp0304044

211.5

1881

6.26

M9PEB2

NP_001259975

AGB92512

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

1883 (aa); 200~210 (kD observed); 211 (kD predicted)

(Stokes et al., 1996)

Comments

External Data

Subunit Structure (UniProtKB)

Monomer (PubMed:15643425). Component of the SAGA complex (By similarity). Interacts with SSRP1.

(UniProt, Q7KU24)

Domain

The 2 chromodomains are involved in the binding to the histone H3 methyllysine at position 4 (H3K4me3).

The CHD1 helical C-terminal domain (CHCT) binds DNA and nucleosomes.

(UniProt, Q7KU24)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Chd1 using the Feature Mapper tool.

External Data

Crossreferences

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

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).

-0.07

Transcript Expression

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage & adult stage

(Stokes et al., 1996)

Additional Descriptive Data

Chd1 transcripts are observed in late embryo and adult RNA on northern blots.

(Stokes et al., 1996)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

day 5 of adulthood | male -- day 7 of adulthood | male

spermatozoon

(Wasbrough et al., 2010)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in polytene chromosome interband

inferred from direct assay

(Stokes et al., 1996)

located_in polytene chromosome puff

inferred from direct assay

(Stokes et al., 1996)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Chd1 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Chd1

View exonic expression by tissue for Dmel\Chd1

Bulk Downloads

RNA-Seq RPKM values for all genes

Reference

See Gelbart and Emmert, 2013 for analysis details and data files for all genes.

Developmental Proteome: Life Cycle

Developmental Proteome: Embryogenesis

External Data and Images

Linkouts

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

33505/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0250786

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0250786

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG3733

Flygut - An atlas of the Drosophila adult midgut

FBgn0250786

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 11 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 16 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Chd1

Transgenic constructs containing regulatory region of Chd1

Aberrations (Deficiencies and Duplications) ( 16 )

Inferred from experimentation ( 16 )

Gene disrupted in

Df(2L)AS2

(Ferro, 2002.12)

Df(2L)Exel7014

(Ryder, 2004.4.26)

Df(2L)JS17

(Ferro, 2002.12, Eeken, 2000.2.29)

Gene not disrupted in

(Ferro, 2002.12)

(Ferro, 2002.12)

(Ferro, 2002.12)

(Ferro, 2002.12)

(Ferro, 2002.12)

(Ferro, 2002.12)

(Ferro, 2002.12, Eeken, 2000.2.29)

Df(2L)C144

(McDaniel, 2006.10.11)

Df(2L)JS7

(Eeken, 2000.2.29)

Df(2L)JS25

(Ferro, 2002.12)

Df(2L)JS27

(Ferro, 2002.12)

Gene partially disrupted in

Df(2L)Chd1¹

(Konev et al., 2007)

Df(2L)Chd1²

(Konev et al., 2007)

Inferred from location ( 8 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal | male limited, with Scer\GAL4^Act5C.PI

Chd1^EP

lethal | recessive

Chd1^A7-4

lethal - all die during embryonic stage | non-rescuable maternal effect (with Df(2L)Exel7014)

lethal - all die during embryonic stage | non-rescuable maternal effect | recessive

Chd1^unspecified

lethal - all die during P-stage, with Scer\GAL4^Mef2.PR

Chd1^GD11058

partially lethal (with Df(2L)Exel7014)

partially lethal - majority live (with Df(2L)Exel7014)

Chd1^unspecified

partially lethal - majority live (with Df(2L)JS17)

Chd1^unspecified

viable

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Chd1^GD11058

viable, with Scer\GAL4^pnr-MD237

Chd1^GD11058

viable, with Scer\GAL4^tin.CΔ4

Chd1^GD11058

viable (with Chd1⁴)

Chd1⁵

viable (with Chd1⁵)

Chd1⁴

viable (with Df(2L)Exel7014)

Sterility

Allele

female semi-sterile (with Chd1⁴)

Chd1⁵

female semi-sterile (with Chd1⁵)

Chd1⁴

female sterile (with Df(2L)Exel7014)

female sterile (with Df(2L)JS17)

Chd1^unspecified

male sterile (with Chd1⁴)

Chd1⁵

male sterile (with Chd1⁵)

Chd1⁴

male sterile (with Df(2L)Exel7014)

Chd1^unspecified

male sterile (with Df(2L)JS17)

Chd1^unspecified

Other Phenotypes

Allele

abnormal developmental rate

abnormal developmental rate (with Chd1⁴)

Chd1⁵

abnormal developmental rate (with Chd1⁵)

Chd1⁴

abnormal developmental rate (with Df(2L)Exel7014)

abnormal pain response | adult stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Chd1^GD11058

enhancer of variegation, with Dp(?;2)bw^D, Scer\GAL4^GMR.PF

Chd1^EP

some die during embryonic stage | recessive

Chd1^unspecified

visible, with Scer\GAL4^pnr-MD237

Chd1^GD11058

visible (with Chd1⁴)

Chd1⁵

visible (with Chd1⁵)

Chd1⁴

visible (with Df(2L)Exel7014)

Phenotype manifest in

Allele

male pronucleus (with Df(2L)Exel7014)

Chd1¹

trichogen cell, with Scer\GAL4^pnr-MD237

Chd1^GD11058

wing (with Chd1⁴)

Chd1⁵

wing (with Chd1⁵)

Chd1⁴

wing (with Df(2L)Exel7014)

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (31)

Hsap\CHD2

13 of 14

Yes

Hsap\CHD1

12 of 14

Yes

Hsap\C17orf64

2 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Hsap\ERCC6L2

1 of 14

Yes

Hsap\ERCC6L

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (29)

Rnor\Chd2

13 of 14

Yes

Rnor\Chd1

12 of 14

Yes

Rnor\Chd6

2 of 14

Rnor\Chd7

2 of 14

Rnor\RGD1310166

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Rnor\Ercc6l

1 of 14

Yes

Rnor\Ercc6

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (28)

Mmus\Chd1

12 of 14

Yes

Mmus\Chd2

12 of 14

Yes

Mmus\1700125H20Rik

2 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Mmus\Ercc6l

1 of 14

Yes

Mmus\Ercc6

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (19)

Xtro\chd2

11 of 13

Yes

Xtro\chd1

10 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Xtro\ercc6l

1 of 13

Yes

Xtro\ercc6

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (27)

Drer\chd2

12 of 14

Yes

Drer\chd1

11 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Drer\ercc6l2

1 of 14

Yes

Drer\ercc6l

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (26)

Cele\chd-1

14 of 14

Yes

Cele\chd-7

3 of 14

Cele\btf-1

1 of 14

Cele\C25F9.4

1 of 14

Yes

Cele\C25F9.5

1 of 14

Yes

Cele\chd-3

1 of 14

Cele\csb-1

1 of 14

Cele\F19B2.5

1 of 14

Yes

Cele\F53H4.6

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Cele\M04C3.2

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (15)

Agam\AgaP_AGAP008698

11 of 12

Yes

3 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (39)

Atha\CHR5

12 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\SYD

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (14)

Scer\CHD1

11 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (10)

Spom\hrp1

10 of 12

Yes

Spom\hrp3

10 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Yes

Spom\rhp54

1 of 12

Spom\snf21

1 of 12

Spom\snf22

1 of 12

Escherichia coli (enterobacterium) (1)

Ecol\rapA

1 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Chd1. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (16)

Chd3

5 of 13

kis

5 of 13

Mi-2

5 of 13

Hel89B

4 of 13

brm

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

lds

3 of 13

okr

3 of 13

XNP

3 of 13

CG7376

2 of 13

dom

2 of 13

Ino80

2 of 13

Marcal1

2 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

autism spectrum disorder, susceptibility to, CHD1,2-related

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

Chd1¹

model of autism spectrum disorder

CEA

(Genç et al., 2020)

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

CHD2; chromodomain helicase DNA binding protein 2

model of developmental and epileptic encephalopathy 94

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 3 )

Allele

Disease

Interaction

References

Chd1^HMS01142

exacerbates amyotrophic lateral sclerosis type 10

modeled by Hsap\TARDBP^UAS.cEa

(Berson et al., 2017)

modeled by Hsap\TARDBP^{M.UAS.Tag:FLAG}

(Azpurua et al., 2021)

ameliorates amyotrophic lateral sclerosis type 10

modeled by Hsap\TARDBP^{M.UAS.Tag:FLAG}

(Azpurua et al., 2021)

Chd1¹

model of autism spectrum disorder

is exacerbated by Pdk1³³

(Genç et al., 2020)

is exacerbated by Rim¹⁰³

(Genç et al., 2020)

is exacerbated by wrd¹⁰⁴

(Genç et al., 2020)

Chd1^UAS.cMa

ameliorates amyotrophic lateral sclerosis type 10

modeled by Hsap\TARDBP^UAS.cEa

(Berson et al., 2017)

Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

CHD2; chromodomain helicase DNA binding protein 2

13 of 14

602119

DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 94; DEE94

developmental and epileptic encephalopathy 94

CHD1; chromodomain helicase DNA binding protein 1

12 of 14

602118

PILAROWSKI-BJORNSSON SYNDROME; PILBOS

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Chd1 - Hira

anti tag coimmunoprecipitation, western blot

(Konev et al., 2007)

Chd1 - His3

pull down, molecular weight estimation by staining

(Morettini et al., 2011)

Chd1 - Hsap\TARDBP

anti tag coimmunoprecipitation, western blot

(Berson et al., 2017)

Chd1 - mof

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Mendjan et al., 2006)

Chd1 - su(Hw)

anti bait coimmunoprecipitation, western blot

(Vorobyeva et al., 2021)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

Chd1

(Schneiderman et al., 2010)

dom

enhanceable

Chd1

(Ellis et al., 2015)

suppressible

Chd1

(Iyer et al., 2016)

External Data

Subunit Structure (UniProtKB)

Monomer (PubMed:15643425). Component of the SAGA complex (By similarity). Interacts with SSRP1.

(UniProt, Q7KU24 )

Linkouts

BioGRID - A database of protein and genetic interactions.

59725

DroID - A comprehensive database of gene and protein interactions.

FBgn0250786

MIST (protein-protein) - An integrated Molecular Interaction Database

33505

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-8

Cytogenetic map

23C4-23C4

Sequence location

2L:2,979,562..2,987,723 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

23C4-23C4

Limits computationally determined from genome sequence between P{PZ}lilli⁰⁰⁶³² and P{PZ}toc⁰¹³⁶¹

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

23C-24A

(determined by in situ hybridisation)

(Stokes et al., 1996)

Experimentally Determined Recombination Data

Location

2-8

(FlyBase, 2016)

2-6.6

(Comeron et al., 2012)

(Stokes et al., 1996)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (17)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

5727

Chd1^A7-4 cn¹ bw¹/CyO

28436

y¹ w^*; P{EP}Chd1^G2213

58248

y¹ v¹; P{TRiP.HMJ22269}attP40/CyO

78985

y¹ w^*; TI{CRIMIC.TG4.0}Chd1^{CR00688-TG4.0}/SM6a

Kyoto

108390

Chd1^A7-4 cn¹ bw¹/CyO

NIG-Fly

3733R-2

P{NIG.3733R}2

3733R-3

P{NIG.3733R}3

HMJ22269

y¹ v¹; P{TRiP.HMJ22269}attP40/CyO

M2L-0402

y¹ w¹¹¹⁸; Chd1^SK1 P{neoFRT}40A/CyO-Tb

GL00126

y¹ sc^* v¹ sev²¹; P{TRiP.GL00126}attP2

VDRC

v103640

P{KK101875}VIE-260B

v26277

w¹¹¹⁸; P{GD11058}v26277

More stocks available...

Genomic Clones (19)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (27)

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

FBgn0250786

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

GM20615

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0250786

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Mazina et al., 2018, Stokes et al., 1996)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from S2-ThermoFischer : Stable S2 cell lines were created to study chromatin remodeling. The base S2[OsTir1] was created and selected core proteins from the four main sub-families of ATP-dependent chromatin remodelers (Snr1, Iswi, Ino80, and Chd1) as well as SWI/SNF component Brd7-9 were inserted to create S2OsTir1-Snr1-AID, S2OsTir1-Iswi-AID, S2OsTir1-Ino80-AID, S2OsTir1-Chd1-AID, and S2OsTir1-Brd7-AID for component depletion studies.
(Hendy et al., 2022)

Other Comments

Chd1 is required for incorporation of His3.3A protein into the male pronucleus.

(Konev et al., 2007)

Embryos lacking Chd1 function cannot incorporate His3.3A protein into the male pronucleus, rendering the paternal genome unable to participate in zygotic mitoses and leading to haploid embryos.

(Konev et al., 2007)

cDNA clones that encode the Drosophila CHD1 homologue are isolated and antibodies raised against a portion demonstrate the protein is concentrated in transcriptionally active regions of the genome.

(Stokes et al., 1996)

Relationship to Other Genes

Source for database merge of

Source for merge of: Chd1 l(2)23Cd

(Konev et al., 2007)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (15)

Reported As

Symbol Synonym

CG3733

(National Institute of Genetics Fly Stocks, 2022-, Ni et al., 2011.7.19, Ni et al., 2010.12.1, Schneiderman et al., 2010, Keleman et al., 2009.8.5, Schneiderman et al., 2009, Konev et al., 2007, Spellman and Rubin, 2002)

CHD-1

(Khattak et al., 2002, Eissenberg, 2001, Tsukiyama and Wu, 1997, Stokes, 1996.8.13)

CHD1

(Krasnov et al., 2023, McCarthy et al., 2022, Pennemann et al., 2021, Schoberleitner et al., 2021, Vorobyeva et al., 2021, Mazina et al., 2017, Ellis et al., 2015, Emelyanov et al., 2014, Orsi et al., 2013, Mills, 2010, Podhraski et al., 2010, Clapier and Cairns, 2009, Eissenberg et al., 2007, Konev et al., 2007, Polo and Almouzni, 2006, Lusser et al., 2005, Brehm et al., 2004)

CHD1,2

(Schuettengruber et al., 2011)

Chd1

(Justice et al., 2025, Ding et al., 2022, Hendy et al., 2022, National Institute of Genetics Fly Stocks, 2022-, Azpurua et al., 2021, Layalle et al., 2021, Sureka and Mishra, 2021, Jiang et al., 2019, Gene Disruption Project members, 2018-, Berson et al., 2017, Transgenic RNAi Project members, 2017-, Konev et al., 2016, Sebald et al., 2016, Kavi et al., 2015, Kwong et al., 2015, Nikalayevich and Ohkura, 2015, Mueller-Planitz et al., 2013, Torigoe et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Radman-Livaja et al., 2012, Davis et al., 2011, Morettini et al., 2011, Podhraski et al., 2010, Schneiderman et al., 2010, Wasbrough et al., 2010, Schneiderman et al., 2009, Doheny et al., 2008, Petesch and Lis, 2008, Vázquez et al., 2008, Eissenberg et al., 2007, Konev et al., 2007, Marfella and Imbalzano, 2007, Mendjan et al., 2006, Spellman and Rubin, 2002)

DmCHD1

(Woodage et al., 1997)

chd1

(Vicars et al., 2021, Kim et al., 2015, Armstrong et al., 2008, Levine and Begun, 2008, McDaniel et al., 2008, Armstrong et al., 2007, McDaniel, 2006.10.11, Lasko, 2000)

dCHD1

(Kelley et al., 1999, Stokes et al., 1996)

dChd1

(Torigoe et al., 2013)

l(2)23Cd

Name Synonyms

Chromodomain-helicase-DNA-binding protein

(Davis et al., 2011)

Chromodomain-helicase-DNA-binding protein 1

chromo-ATPase/helicase-DNA-binding domain

(Stokes et al., 1996)

chromo-ATPase/helicase-DNA-binding protein 1

(Lusser et al., 2005)

lethal (2) 23Cd

Secondary FlyBase IDs

FBgn0016132
FBgn0040118

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 57 )

Sequence Crossreferences

NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

33505

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q7KU24

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q7KU24

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q7KU24

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

33505/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0250786

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0250786

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

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG3733

MARRVEL_MODEL - MARRVEL (model organism gene)

33505

Linkouts

BioGRID - A database of protein and genetic interactions.

59725

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0250786

DroID - A comprehensive database of gene and protein interactions.

FBgn0250786

DRSC - Results frm RNAi screens

FBgn0250786

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

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0250786

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG3733

Flygut - An atlas of the Drosophila adult midgut

FBgn0250786

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC010805

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

MIST (protein-protein) - An integrated Molecular Interaction Database

33505

References (113)

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

-0.07

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