nurf-1 Bromo domain-containing protein;Bromodomain-containing protein;DDT domain-containing protein;Nucleosome-remodeling factor subunit NURF301;Nucleosome-remodeling factor subunit NURF301-like [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: nurf-1
Official Full Name: Bromo domain-containing protein;Bromodomain-containing protein;DDT domain-containing protein;Nucleosome-remodeling factor subunit NURF301;Nucleosome-remodeling factor subunit NURF301-like
Primary source: WormBase:WBGene00009180
Locus tag: CELE_F26H11.2
See related: AllianceGenome:WB:WBGene00009180
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and methylated histone binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of NURF complex. Is expressed in several structures, including head; pharyngeal-intestinal valve; pharynx; reproductive system; and tail. Human ortholog(s) of this gene implicated in Kaposi's sarcoma; alcohol dependence; and neurodevelopmental disorder with dysmorphic facies and distal limb anomalies. Orthologous to human BPTF (bromodomain PHD finger transcription factor). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See nurf-1 in Genome Data Viewer

Location:: chromosome: II

Exon count:: 28

Sequence:: Chromosome: II; NC_003280.10 (14390713..14407911)

Chromosome II - NC_003280.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003280.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Using CRISPR-Cas9 genome editing and transgenic rescue, the authors demonstrate that in Caenorhabditis elegans, nurf-1 has split into two, largely non-overlapping isoforms (NURF-1.D and NURF-1.B, which they call Yin and Yang, respectively) that share only two of 26 exons. Both isoforms are essential for normal gametogenesis but have opposite effects on male/female gamete differentiation.
Title: Evolution of Yin and Yang isoforms of a chromatin remodeling subunit precedes the creation of two genes.
Given the previous discovery that this same nurf-1 variation was central for hermaphrodite laboratory adaptation, the evolution of reduced male sperm size in LSJ strains likely reflects a pleiotropic consequence. Together, our results provide a comprehensive quantification of natural variation in C. elegans sperm size and first insights into the genetic determinants of Caenorhabditis sperm size
Title: Natural Variation and Genetic Determinants of Caenorhabditis elegans Sperm Size.
We propose that chromatin remodeling, acting through nurf-1, is a pleiotropic regulator of life history trade-offs underlying the evolution of multiple traits across different species.
Title: Selection on a Subunit of the NURF Chromatin Remodeler Modifies Life History Traits in a Domesticated Strain of Caenorhabditis elegans.
there is a link between RBR-2 activity, H3K4me3 levels, the NURF complex and the expression of WSP-1
Title: The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

F26H11.3 (e-PCR)
- UniSTS:317480

F26H11.2 (e-PCR)
- UniSTS:306593

F26H11.1 (e-PCR)
- UniSTS:316647

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of NURF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NURF complex	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Bromo domain-containing protein;Bromodomain-containing protein;DDT domain-containing protein;Nucleosome-remodeling factor subunit NURF301;Nucleosome-remodeling factor subunit NURF301-like

NP_001022117.2

Confirmed by transcript evidence

NP_001022119.1

Partially confirmed by transcript evidence

NP_001022120.1

Partially confirmed by transcript evidence

NP_001254428.1

Confirmed by transcript evidence

NP_001254429.1

Confirmed by transcript evidence

NP_001254430.1

Partially confirmed by transcript evidence

NP_001300538.1

Confirmed by transcript evidence

NP_001300539.1

Confirmed by transcript evidence

NP_001300540.1

Confirmed by transcript evidence

NP_001300541.1

Confirmed by transcript evidence

NP_001300542.1

Confirmed by transcript evidence

NP_001364539.1

Confirmed by transcript evidence

NP_001379249.1

Confirmed by transcript evidence

NP_001380247.1

Confirmed by transcript evidence

NP_001380248.1

Confirmed by transcript evidence

NP_496994.3

Confirmed by transcript evidence

NP_496995.3

Confirmed by transcript evidence

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

NC_003280.10 Reference assembly

Range

14390713..14407911

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001267500.3 → NP_001254429.1 DDT domain-containing protein [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001254429.1

Status: REVIEWED

UniProtKB/TrEMBL

B6VQ92

Conserved Domains (5) summary

smart00249
Location:350 → 389

PHD; PHD zinc finger

smart00571
Location:196 → 256

DDT; domain in different transcription and chromosome remodeling factors

PHA03247
Location:4 → 107

PHA03247; large tegument protein UL36; Provisional

pfam09606
Location:1163 → 1576

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam15613
Location:410 → 470

WSD; Williams-Beuren syndrome DDT (WSD), D-TOX E motif
NM_064593.4 → NP_496994.3 Nucleosome-remodeling factor subunit NURF301-like [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_496994.3

Status: REVIEWED

UniProtKB/Swiss-Prot

Q6BER5

Conserved Domains (2) summary

smart00249
Location:350 → 389

PHD; PHD zinc finger

smart00571
Location:196 → 256

DDT; domain in different transcription and chromosome remodeling factors
NM_064594.9 → NP_496995.3 Nucleosome-remodeling factor subunit NURF301-like [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_496995.3

Status: REVIEWED

UniProtKB/Swiss-Prot

Q6BER5

Conserved Domains (6) summary

cd05509
Location:2052 → 2137

Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...

smart00249
Location:350 → 389

PHD; PHD zinc finger

smart00571
Location:196 → 256

DDT; domain in different transcription and chromosome remodeling factors

COG5034
Location:1745 → 1953

TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

cd15560
Location:1964 → 2010

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

cl22851
Location:1904 → 1950

PHD_SF; PHD finger superfamily
NM_001377899.3 → NP_001364539.1 DDT domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9MQ08

Conserved Domains (7) summary

cd05509
Location:2054 → 2139

Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...

smart00249
Location:350 → 389

PHD; PHD zinc finger

smart00571
Location:196 → 256

DDT; domain in different transcription and chromosome remodeling factors

cd15560
Location:1966 → 2012

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

pfam09606
Location:1358 → 1579

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam15613
Location:410 → 459

WSD; Williams-Beuren syndrome DDT (WSD), D-TOX E motif

cl22851
Location:1906 → 1952

PHD_SF; PHD finger superfamily
NM_001267499.2 → NP_001254428.1 DDT domain-containing protein [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001254428.1

Status: REVIEWED

UniProtKB/TrEMBL

H2FLJ6

Conserved Domains (5) summary

smart00249
Location:350 → 389

PHD; PHD zinc finger

smart00571
Location:196 → 256

DDT; domain in different transcription and chromosome remodeling factors

PHA03247
Location:4 → 107

PHA03247; large tegument protein UL36; Provisional

pfam09606
Location:1165 → 1578

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam15613
Location:410 → 470

WSD; Williams-Beuren syndrome DDT (WSD), D-TOX E motif
NM_001026946.4 → NP_001022117.2 Nucleosome-remodeling factor subunit NURF301-like [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022117.2

Status: REVIEWED

UniProtKB/Swiss-Prot

B1Q274, O45407, O45409, O45410, Q5WRM3, Q6BER5, Q95ZU8, Q9NLC1

Conserved Domains (6) summary

cd05509
Location:2049 → 2134

Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...

smart00249
Location:350 → 389

PHD; PHD zinc finger

smart00571
Location:196 → 256

DDT; domain in different transcription and chromosome remodeling factors

COG5034
Location:1733 → 1950

TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

cd15560
Location:1961 → 2007

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

cl22851
Location:1901 → 1947

PHD_SF; PHD finger superfamily
NM_001313611.3 → NP_001300540.1 DDT domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3AR10

Conserved Domains (6) summary

cd05509
Location:2051 → 2136

Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...

smart00249
Location:350 → 389

PHD; PHD zinc finger

smart00571
Location:196 → 256

DDT; domain in different transcription and chromosome remodeling factors

COG5034
Location:1735 → 1952

TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

cd15560
Location:1963 → 2009

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

cl22851
Location:1903 → 1949

PHD_SF; PHD finger superfamily
NM_001313609.3 → NP_001300538.1 Nucleosome-remodeling factor subunit NURF301 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3ARK1

Conserved Domains (6) summary

cd05509
Location:1930 → 2015

Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...

smart00249
Location:229 → 268

PHD; PHD zinc finger

smart00571
Location:75 → 135

DDT; domain in different transcription and chromosome remodeling factors

COG5034
Location:1614 → 1831

TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

cd15560
Location:1842 → 1888

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

cl22851
Location:1782 → 1828

PHD_SF; PHD finger superfamily
NM_001313610.3 → NP_001300539.1 Nucleosome-remodeling factor subunit NURF301 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3ATY3

Conserved Domains (6) summary

cd05509
Location:1928 → 2013

Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...

smart00249
Location:229 → 268

PHD; PHD zinc finger

smart00571
Location:75 → 135

DDT; domain in different transcription and chromosome remodeling factors

COG5034
Location:1612 → 1829

TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

cd15560
Location:1840 → 1886

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

cl22851
Location:1780 → 1826

PHD_SF; PHD finger superfamily
NM_001393235.1 → NP_001380248.1 Nucleosome-remodeling factor subunit NURF301-like [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A486WW91
NM_001393233.1 → NP_001379249.1 Nucleosome-remodeling factor subunit NURF301-like [Caenorhabditis elegans]

Status: REVIEWED

Conserved Domains (4) summary

cd05509
Location:663 → 748

Bromo_gcn5_like; Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long ...

COG5034
Location:347 → 564

TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

cd15560
Location:575 → 621

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

cl22851
Location:515 → 561

PHD_SF; PHD finger superfamily
NM_001393234.1 → NP_001380247.1 Nucleosome-remodeling factor subunit NURF301-like [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A486WWS1
NM_001313612.3 → NP_001300541.1 Bromodomain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3AUK7

Conserved Domains (4) summary

COG5034
Location:107 → 324

TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

cd15560
Location:335 → 381

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

cl02556
Location:423 → 508

Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

cl22851
Location:275 → 321

PHD_SF; PHD finger superfamily
NM_001313613.3 → NP_001300542.1 Bromodomain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3AWW5

Conserved Domains (3) summary

cd15560
Location:219 → 265

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

cl02556
Location:307 → 392

Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

cl22851
Location:159 → 205

PHD_SF; PHD finger superfamily
NM_001026948.6 → NP_001022119.1 Nucleosome-remodeling factor subunit NURF301-like [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022119.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q6BER5

Conserved Domains (3) summary

cd15560
Location:172 → 218

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

cl02556
Location:260 → 345

Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

cl22851
Location:112 → 158

PHD_SF; PHD finger superfamily
NM_001026949.5 → NP_001022120.1 Nucleosome-remodeling factor subunit NURF301-like [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022120.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q6BER5

Conserved Domains (3) summary

cd15560
Location:277 → 323

PHD2_3_BPTF; PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF)

cl02556
Location:365 → 450

Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

cl22851
Location:217 → 263

PHD_SF; PHD finger superfamily
NM_001267501.3 → NP_001254430.1 Bromo domain-containing protein [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001254430.1

Status: REVIEWED

UniProtKB/TrEMBL

F5GUF5

Conserved Domains (1) summary

cl02556
Location:1 → 84

Bromodomain; Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.