WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00019947 Gene Name  htz-1
Sequence Name  ? R08C7.3 Brief Description  htz-1 encodes the C. elegans ortholog of the H2A.Z histone variant; htz-1 is an essential gene and during development, HTZ-1 functions with the PHA-4/FoxA transcription factor and the MYS-1/TIP60-SSL-1/SWR1 remodeling complex to regulate gene expression during pharyngeal (foregut) organogenesis; a YFP::HTZ-1 fusion protein localizes to pharyngeal gene promoters at the onset of transcription, in a manner that requires PHA-4.
Organism  Caenorhabditis elegans Automated Description  Predicted to be a structural constituent of chromatin. Involved in negative regulation of DNA-templated transcription and negative regulation of cell fate specification. Located in chromatin; condensed chromosome; and nucleus. Expressed in several structures, including distal tip cell and somatic gonad. Is an ortholog of human H2AZ1 (H2A.Z variant histone 1) and H2AZ2 (H2A.Z variant histone 2).
Biotype  SO:0001217 Genetic Position  IV :0.275282 ±0.008597
Length (nt)  ? 784
Paste the following link
Quick Links:
SummaryGenomicsOther
 
Quick Links:
SummaryGenomicsOther
 
Lists
This Gene is in one list:
metrics_list_union (10192)

1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00019947

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:R08C7.3.1 R08C7.3.1 734   IV: 4446216-4446999
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:R08C7.3 R08C7.3 423   IV: 4446236-4446405

35 RNAi Result

WormBase ID
WBRNAi00064791
WBRNAi00026065
WBRNAi00073604
WBRNAi00072596
WBRNAi00068669
WBRNAi00064673
WBRNAi00073599
WBRNAi00073601
WBRNAi00069044
WBRNAi00069043
WBRNAi00069046
WBRNAi00069045
WBRNAi00069047
WBRNAi00017579
WBRNAi00113545
WBRNAi00081788
WBRNAi00081822
WBRNAi00081852
WBRNAi00065166
WBRNAi00034742
WBRNAi00065158
WBRNAi00064813
WBRNAi00051535
WBRNAi00073598
WBRNAi00073600
WBRNAi00073603
WBRNAi00062049
WBRNAi00065155
WBRNAi00027436
WBRNAi00073602

11 Allele

Public Name
gk963722
gk963908
gk946027
tm2469
gk200133
gk375145
gk723588
gk589980
ok3100
ok3099
gk898742

1 Chromosome

WormBase ID Organism Length (nt)
IV Caenorhabditis elegans 17493829  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00019947 4446216 4446999 1

4 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  
C. elegans genomic annotations (GFF3 Gene)  
Panther orthologue and paralogue predictions  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIV_4447000..4447330   331 IV: 4447000-4447330 Caenorhabditis elegans

248 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  oocyte proteins identified by two or more unique peptides during proteomics study. In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide. WBPaper00038289:oocyte_protein
  Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. DESeq. False discovry rate (FDR) < 0.1. WBPaper00048988:neuron_expressed
adult vs dauer larva Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C. N.A. WBPaper00050488:adult_vs_dauer_regulated_N2_20C
Osmotic stress Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present DESeq(version 1.10.1), FDR < 0.05. WBPaper00050726:OsmoticStress_regulated_Food
Osmotic stress Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present DESeq(version 1.10.1), FDR < 0.05. WBPaper00050726:OsmoticStress_regulated_NoFood
  Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rifampicin-Allantoin_upregulated
  Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc). DESeq2, fold change >= 2, FDR <= 0.01. WBPaper00056826:SGP_biased
  Proteins detected in isolated mitochondria. N.A. WBPaper00067939:mitochondria_expressed_protein
  Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:arcade_intestinal-valve_expressed
  Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:body-muscle_expressed
  Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:GABAergic-neuron_expressed
  Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. N.A. WBPaper00064071:NHR-49_interacting
  Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:hypodermis_expressed
  Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:intestine_expressed
  Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:NMDA-neuron_expressed
  Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:pharynx_expressed
  Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 hours at 24 centigrade). For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). WBPaper00040858:eQTL_age_regulated_aging
  Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:seam_expressed
  Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
  Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
  Transcripts that showed significantly increased expression in hda-1(RNAi) embryos comparing to control animals. DESeq2, fold change > 2, FDR < 0.05. WBPaper00067044:hda-1(RNAi)_upregulated
Bacteria diet: Escherichia coli HB101. Fed for 30 generations. Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50. DESeq2 fold change > 2, p-value < 0.01. WBPaper00061007:HB101_downregulated
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations. Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50. DESeq2 fold change > 2, p-value < 0.01. WBPaper00061007:S.aquatilis_downregulated
  Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. All three experiments have CPM >= 1. WBPaper00067147:germline_expressed
  Proteins interacting with GST-FBXA-210(C-terminal) via IP-MS in young adult animals. Proteins shown here are enriched in GST Fold change > 2 and p-value < 0.1 were defined as threshold for significance. WBPaper00068277:FBXA-210(C-terminal)_interacting_YoungAdult
  Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. Sleuth WBPaper00051558:aging_regulated
  Transcripts that showed significantly increased expression after 24-hour exposure to 10uM benzyl butyl phthalate (BBP) in col-121(nx3) animals. DESeq2v1.38.3, FDR < 0.05 WBPaper00067417:benzyl-butyl-phthalate_regulated
  Genes down regulated by mir-243(n4759). RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243. WBPaper00036130:mir-243_down_regulated
  Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy. Cufflinks WBPaper00065120:body-muscle-transcriptome
  Genes with increased RNA expression after 24 hours rotenone treatment EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed. WBPaper00044426:rotenone_24h_upregulated

9 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr4261   YFP::HTZ-1 associates with chromatin in cells during metaphase and anaphase. YFP::HTZ-1 is non-randomly distributed in cells during interphase.
Picture: Figure 2.   Expr8333 HTZ-1 protein is present in all cell types throughout all stages of development. HTZ-1 protein levels are low in early embryos (1 to 12 cell), but increase as development progresses. HTZ-1 protein becomes detectably incorporated into chromosomes by the four-cell stage, coincident with the onset of zygotic transcription. This occurs in both wild-type and M+Z- embryos. In wild-type adults, HTZ-1 protein is observed in both somatic and germline precursor cells. No HTZ-1 protein was observed by immunofluorescence in M+Z- adult gonads or their M-Z- embryos.
    Expr11467 YFP::HTZ-1 was expressed in somatic gonadal cells (SGCs) including DTCs. In nine out of nine wild-type animals, puncta of YFP::HTZ-1 were observed in the nuclei of SGCs.  
    Expr1038662 Tiling arrays expression graphs  
    Expr1155212 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr2012642 Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).  
    Expr2040804 Translational efficiency and RNA abundance/Ribosome occupancy across early embryonic stages (1-cell to 8-cell). For each developmental stage, translational efficiency was calculated as the ratio between ribosome footprint reads and mRNA abundance after normalization. A detailed description of the experimental methods and analysis can be found in: Shukla Y, Ghatpande V, Hu CF, Dickinson DJ, Cenik C. Landscape and regulation of mRNA translation in the early C. elegans embryo. Cell Rep. 2025 June 24;44(6):115778. doi: 10.1016/j.celrep.2025.115778. PMID: 40450690  
    Expr1015131 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
    Expr2030878 Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).  

20 GO Annotation

Annotation Extension Qualifier
  located_in
  located_in
existence_starts_and_ends_during(GO:0000278) located_in
  located_in
  located_in
  located_in
existence_overlaps(GO:0051325) located_in
  located_in
  enables
  enables
  enables
  enables
  enables
occurs_in(WBbt:0007815) involved_in
  involved_in
has_input(WB:WBGene00000445),occurs_in(WBbt:0007815) involved_in
  located_in
  part_of
  part_of
  part_of

14 Homologues

Type
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
least diverged orthologue
least diverged orthologue
least diverged orthologue
least diverged orthologue
least diverged orthologue

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00019947 4446216 4446999 1

20 Ontology Annotations

Annotation Extension Qualifier
  located_in
  located_in
existence_starts_and_ends_during(GO:0000278) located_in
  located_in
  located_in
  located_in
existence_overlaps(GO:0051325) located_in
  located_in
  enables
  enables
  enables
  enables
  enables
occurs_in(WBbt:0007815) involved_in
  involved_in
has_input(WB:WBGene00000445),occurs_in(WBbt:0007815) involved_in
  located_in
  part_of
  part_of
  part_of

2 Regulates Expr Cluster

Regulated By Treatment Description Algorithm Primary Identifier
  mRNAs that showed significantly decreased expression in htz-1(ok3099) comparing to in N2. DESeq2 WBPaper00046509:htz-1(ok3099)_downregulated
  mRNAs that showed significantly increased expression in htz-1(ok3099) comparing to in N2. DESeq2 WBPaper00046509:htz-1(ok3099)_upregulated

1 Sequence

Length
784

1 Sequence Ontology Term

Identifier Name Description
gene  

3 Strains

WormBase ID
WBStrain00037309
WBStrain00037355
WBStrain00007140

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIV_4445741..4446215   475 IV: 4445741-4446215 Caenorhabditis elegans