WormMine: Gene WBGene00003656

• WormBase Gene ID: WBGene00003656
• Gene Name: nhr-66
• Sequence Name: T09A12.4
• Brief Description: nhr-66 encodes a member of the superfamily of nuclear receptors, which is one of the most abundant class of transcriptional regulators; nuclear receptors have a well conserved DNA binding domain and a less conserved C-terminal ligand binding domain; expression studies using GFP fusions indicate that nhr-66 is expressed in several neuronal and nonneuronal cells; microarray analysis indicates that expression of nhr-66 in neurons and seam cells is upregulated in response to exposure to cholesterol.
• Organism: Caenorhabditis elegans
• Automated Description: Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Expressed in several structures, including head ganglion; hypodermis; neurons; terminal bulb; and ventral nerve cord.
• Biotype: SO:0001217
• Genetic Position: IV :3.69466 ±0.00382
• Length (nt): 10272

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003656

Genomics

10 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T09A12.4a.1	T09A12.4a.1	2146	IV: 8226331-8231697
Transcript:T09A12.4c.1	T09A12.4c.1	2619	IV: 8226331-8236582
Transcript:T09A12.4b.1	T09A12.4b.1	4472	IV: 8226336-8231838
Transcript:T09A12.4f.1	T09A12.4f.1	2627	IV: 8226337-8236602
Transcript:T09A12.4j.1	T09A12.4j.1	2173	IV: 8226380-8229577
Transcript:T09A12.4e.1	T09A12.4e.1	1560	IV: 8226743-8229327
Transcript:T09A12.4i.1	T09A12.4i.1	1554	IV: 8226743-8229327
Transcript:T09A12.4h.1	T09A12.4h.1	1740	IV: 8226743-8231697
Transcript:T09A12.4d.1	T09A12.4d.1	1980	IV: 8226743-8236050
Transcript:T09A12.4g.1	T09A12.4g.1	1974	IV: 8226743-8236050

Other

10 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T09A12.4c	T09A12.4c	2202	IV: 8226743-8226979
CDS:T09A12.4f	T09A12.4f	2196	IV: 8226743-8226979
CDS:T09A12.4e	T09A12.4e	1560	IV: 8226743-8226979
CDS:T09A12.4i	T09A12.4i	1554	IV: 8226743-8226979
CDS:T09A12.4a	T09A12.4a	1734	IV: 8226743-8226979
CDS:T09A12.4b	T09A12.4b	1581	IV: 8226743-8226979
CDS:T09A12.4d	T09A12.4d	1980	IV: 8226743-8226979
CDS:T09A12.4g	T09A12.4g	1974	IV: 8226743-8226979
CDS:T09A12.4h	T09A12.4h	1740	IV: 8226743-8226979
CDS:T09A12.4j	T09A12.4j	1587	IV: 8226743-8226979

8 RNAi Result

• WBRNAi00052913
• WBRNAi00008244
• WBRNAi00018483
• WBRNAi00115816
• WBRNAi00064842
• WBRNAi00092012
• WBRNAi00084692
• WBRNAi00084679

141 Allele

• gk964278
• gk964500
• gk962765
• gk963722
• gk963417
• WBVar02121210
• WBVar00240589
• WBVar02020961
• WBVar02020960
• WBVar01853913
• WBVar01853912
• WBVar01853911
• WBVar01853910
• gk206915
• gk206916
• WBVar01853909
• ttTi39010
• WBVar01853908
• WBVar01730069
• WBVar01688020
• WBVar00191001
• WBVar00191002
• WBVar01831816
• WBVar01831815
• otn3218
• ttTi15462
• WBVar02049116
• tm11320
• gk932620
• gk389848

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003656
• Start: 8226331
• End: 8236602
• Strand: -1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

0 Downstream Intergenic Region

133 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	Transcripts of coding genes that showed significantly decreased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_depleted_coding-RNA
	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
	Genes that were upregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_upregulated
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	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 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
	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
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 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_developing
	Genes with expression level regulated by genotype (N2 vs CB4856) 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_regulated_aging
	Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 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_regulated_developing
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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_SM
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
Bacteria infection: Serratia marcescens	Genes with increased expression after 24 hours of infection by S.marcescens Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:S.marcescens_24hr_upregulated_TilingArray
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_downregulated

12 Expression Patterns

• Primary Identifier: Expr1031697
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr15543
• Pattern: In adult C. elegans, nhr-66 is broadly expressed, including hypodermis, gut, muscle, and neuronal cells of the ventral nerve chord, head, and tail ganglia. In the head ganglion, several sensory and interneurons, including AVA, express NHR-66. Interestingly, global nhr-66 expression was not altered with age.

• Primary Identifier: Expr9804
• Pattern: GFP was observed in a few nuclei in the posterior pharyngeal bulb and a few neuronal nuclei to both sides of the posterior pharyngeal bulb. GFP expression in the head does not look as extensive as in other nhr-66 reporter gene fusions constructed in this series (see UL3507, UL3411 and UL3531). Occasionally, GFP was seen in an unidentified cell in the tail and in intestinal nuclei. However, the expression was extremely faint, much weaker than for the reporter gene fusions made specifically for the other 2 transcripts, nhr-66a and nhr-66b.

• Primary Identifier: Expr438
• Remark: Other strains-- No expression observed in UL748, UL751, UL758
• Pattern: Faint expression is seen in intestinal cells, and some cells of the head and tail hypodermis and pharynx. This expression is seen from the three fold embryo stage through to adulthood.

• Primary Identifier: Expr9750
• Pattern: GFP was seen throughout all stages, in intestinal nuclei and many unidentified cells in the head and tail. No expression in the body wall was seen, in contrast to reporter fusions for nhr-66a (see UL3531).

• Primary Identifier: Expr1182
• Pattern: Neurons in anterior, lateral, retrovesicular ganglia; seam cells.

• Primary Identifier: Expr9771
• Pattern: GFP expression was observed from L1 to adult, in hypodermis and sometimes bodywall muscle. The expression pattern looks similar to that observed with gfp fused to the end of the nhr-66 protein coding region (see UL3507), except that there was no expression in spermathecae or intestine. This is in contrast to the reporter expression pattern observed for a fusion to nhr-66.b (see UL3411) which includes intestinal nuclei but not the body wall.

• Primary Identifier: Expr9766
• Pattern: GFP expression was seen in all stages with many components. GFP was observed in nuclei of hypodermis, intestine, sometimes spermathecae and maybe bodywall muscle. Compared to other transcription factors, signal intensity is high and of about same intensity in the different components.

• Primary Identifier: Expr1156514
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1026429
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2032458
• Pattern: 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).

• Primary Identifier: Expr2014217
• Pattern: 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).

12 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003656
• Start: 8226331
• End: 8236602
• Strand: -1

12 Ontology Annotations

1 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Differentially expressed genes in nhr-66(ok940) compared to wild-type animals using microarray analysis.	Pair-wise significance testing (mutant vs. wild-type) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Criteria for differential expression was set by employing log2(ratio) >= 0.848 and p-value < 0.001.	WBPaper00040998:nhr-66_regulated

1 Sequence

• Length: 10272

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00031724
• WBStrain00034508
• WBStrain00034505

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_8236603..8241544
• Length (nt): 4942
• Chromosome Location: IV: 8236603-8241544
• Organism: Caenorhabditis elegans