WormMine: Gene WBGene00008400

• WormBase Gene ID: WBGene00008400
• Gene Name: drh-3
• Sequence Name: D2005.5
• Brief Description: drh-3 encodes a DEAH/D-box helicase; drh-3 is required for germline RNAi and for production of several types of endogenous small RNA molecules; in addition, drh-3 plays an essential role in germ cell proliferation, gamete formation, and chromosome segregation; drh-3 is also involved in resistance to X-ray irradiation and genetic studies suggest that drh-3 may also control expression of small RNAs that regulate cell fate specification via Ras-ERK signaling; DRH-3 interacts with the DCR-1 endoribonuclease essential for several distinct small-RNA-mediated silencing pathways and with the RRF-1 RNA-directed RNA polymerase.
• Organism: Caenorhabditis elegans
• Automated Description: Enables several functions, including ATP hydrolysis activity; ATP-dependent activity, acting on RNA; and RNA binding activity. Involved in P granule assembly; regulatory ncRNA-mediated post-transcriptional gene silencing; and siRNA processing. Located in P granule; condensed nuclear chromosome; and metaphase plate. Expressed widely. Is an ortholog of human RIGI (RNA sensor RIG-I).
• Biotype: SO:0001217
• Genetic Position: I :2.36836 ±0.002116
• Length (nt): 5548

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00008400

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:D2005.5.1	D2005.5.1	3510	I: 7820831-7826378

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:D2005.5	D2005.5	3360	I: 7820843-7820940

30 RNAi Result

• WBRNAi00082036
• WBRNAi00082040
• WBRNAi00043430
• WBRNAi00082032
• WBRNAi00077377
• WBRNAi00003280
• WBRNAi00113527
• WBRNAi00076020
• WBRNAi00076018
• WBRNAi00076015
• WBRNAi00097178
• WBRNAi00097367
• WBRNAi00030372
• WBRNAi00082512
• WBRNAi00077378
• WBRNAi00082593
• WBRNAi00116684
• WBRNAi00075588
• WBRNAi00076009
• WBRNAi00061509
• WBRNAi00076012
• WBRNAi00075533
• WBRNAi00076011
• WBRNAi00076010
• WBRNAi00076014
• WBRNAi00075531
• WBRNAi00076017
• WBRNAi00097223
• WBRNAi00097268
• WBRNAi00097313

85 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• WBVar01432185
• gk962720
• gk962721
• fj52
• WBVar02072885
• tm1217
• WBVar00154625
• WBVar00154626
• WBVar00154629
• WBVar00154630
• WBVar00154627
• WBVar00154628
• ne4253
• gk816711
• gk625025
• WBVar00154631
• gk488501
• gk936507
• gk897592
• gk650881
• ttTi9318
• sam2
• WBVar01909873
• sam27
• WBVar01909874
• ne3197

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00008400
• Start: 7820831
• End: 7826378
• Strand: 1

4 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrI_7826379..7826441
• Length (nt): 63
• Chromosome Location: I: 7826379-7826441
• Organism: Caenorhabditis elegans

135 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_upregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 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_N2
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	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 increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
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
	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 that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_downregulated
	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 were regulated by both set-6(ok2195) and baz-2(tm0235) at 2-day post L4 adult hermaphrodite stage.	N.A.	WBPaper00059356:set-6(ok2195)_baz-2(tm0235)_regulated
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
	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
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated
	Transcripts that showed significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	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)
	Germline-intrinsic transcripts.	Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization.	[cgc6390]:intrinsic
	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
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes

9 Expression Patterns

• Primary Identifier: Expr4899
• Remark: Picture: Figure 2.
• Pattern: Levels of the drh-3 transcripts in animals at adult stages were approximately threefold higher than that in larval nematodes.

• Primary Identifier: Expr7853
• Remark: Picture: Figure S5.
• Pattern: Expressed in somatice cells.

• Primary Identifier: Expr1033638
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8818
• Remark: Picture: Fig 3A.
• Pattern: Western blot analyses revealed that DRH-3 is present at all developmental stages. DRH-3 was detected in glp-4(bn2) adults, which fail to develop a germline and are thus greatly enriched in post-mitotic cells.

• Primary Identifier: Expr2011089
• 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: Expr9631
• Subcellular Localization: Finally, all aspects of the localization patterns were absent in each respective mutant background. In the mitotic cells of embryos, each factor became enriched in prophase nuclei. As chromosomes condensed, DRH-3, EGO-1, and EKL-1 became enriched along the length of each chromosome, while CSR-1 remained nuclear. All four proteins exhibited robust localization around the metaphase plate. CSR-1 and DRH-3 displayed a pattern similar to cohesins, whereas EKL-1 (and to a lesser degree, EGO-1) appeared to be more closely associated with chromosomes in a pattern similar to kinetochore proteins. In fact, EKL-1 retained a robust association with chromosomes during anaphase, whereas the other RNAi factors became more difficult to detect. Cytoplasmic localization was also detected for each protein. The larger CSR-1 isoform was expressed throughout larval development and was also present at low levels in post-mitotic populations lacking a germline. Quantitative real-time RT-PCR analysis of both csr-1 transcripts indicated that their expression recapitulates the protein expression pattern. DRH-3, EGO-1, and CSR-1 colocalize in the germline with PGL-1, a previously characterized component of the germline nuage structures called P granules. EKL-1 was not detected in P granules. While many developmentally important factors transiently localize to P granules, DRH-3 and CSR-1 maintained their P granule localization in germ cells throughout the life cycle. As oocytes matured, EGO-1 was lost from the P granules, while DRH-3 and CSR-1 maintained P granule association. In mature oocytes, CSR-1 and EGO-1 both became enriched in nuclei, where CSR-1 was enriched on the diakinetic chromosomes.

• Primary Identifier: Expr2029325
• 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: Expr1027221
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1147425
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

22 GO Annotation

27 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00008400
• Start: 7820831
• End: 7826378
• Strand: 1

22 Ontology Annotations

4 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly decreased expression in drh-3(rrr2) comparing to in N2.	edgeR, log2 fold change > 2 or < -2.	WBPaper00053888:drh-3(rrr2)_downregulated
	Transcripts that showed significantly increased expression in drh-3(rrr2) comparing to in N2.	edgeR, log2 fold change > 2 or < -2.	WBPaper00053888:drh-3(rrr2)_upregulated
	Genes significantely Down-regulated by GRO-seq in drh-3 (ne4253) vs. N2 using DESeq p<0.05	DESeq package with an FDR of < 0.05.	WBPaper00045050:drh-3 (ne4253)_downregulated
	Genes significantely Up-regulated by GRO-seq in drh-3 (ne4253) vs. N2 using DESeq p<0.05	DESeq package with an FDR of < 0.05.	WBPaper00045050:drh-3 (ne4253)_upregulated

1 Sequence

• Length: 5548

1 Sequence Ontology Term

• Name: gene

9 Strains

• WBStrain00040442
• WBStrain00040467
• WBStrain00040474
• WBStrain00040473
• WBStrain00040472
• WBStrain00040878
• WBStrain00006431
• WBStrain00006414
• WBStrain00006429

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_7820479..7820830
• Length (nt): 352
• Chromosome Location: I: 7820479-7820830
• Organism: Caenorhabditis elegans