WormMine: Gene WBGene00000479

• WormBase Gene ID: WBGene00000479
• Gene Name: cgh-1
• Sequence Name: C07H6.5
• Brief Description: cgh-1 encodes a putative DEAD-box RNA helicase, orthologous tobudding yeast Dhh1p, fission yeast Ste13p, Drosophila ME31B, andhuman DDX6 (OMIM:600326); CGH-1 inhibits physiological apoptosis inoocytes, keeping it down to a normal level of ~50% in hermaphroditegonads; independently of apoptosis, CGH-1 is also required for spermfunction, oocyte fertilization, and early embryonic cytokinesis; byorthology with budding yeast, CGH-1 is expected to enabledecapping-dependent mRNA degradation; CGH-1 is expressed in meioticgerm cells, oocytes, sperm, early embryonic P granules, otherunidentified cytoplasmic foci of the gonad core and early embryos,and the germline precursors Z2 and Z3; cgh-1(RNAi) hermaphroditeslose ~100% of their oocytes to physiological apoptosis; gonadal CGH-1accumulation is suppressed by either glh-1/4 RNAi orgld-1(q485);gld-2(q497) mutations, yet physiological apoptosis (whichwould normally be elevated by loss of CGH-1) is also abnormally lowin these genotypes; cgh-1(RNAi) males have sterile sperm withabnormally short pseudopods; CGH-1 associates with CAR-1, DCAP-2, andCEY-2/3/4 in P granules and cytoplasmic particles of the earlyembryo; CGH-1 is required for normal CAR-1 localization in earlyembyros, and binds CAR-1 in an RNA-dependent manner.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable RNA helicase activity and mRNA binding activity. Involved in several processes, including P-body assembly; determination of adult lifespan; and negative regulation of translation. Located in P granule; P-body; and cytoplasmic stress granule. Part of ribonucleoprotein complex. Expressed in several structures, including Z2; Z3; germ line; gonad; and neurons. Is an ortholog of human DDX6 (DEAD-box helicase 6).
• Biotype: SO:0001217
• Genetic Position: III :-0.727171 ±0.000843
• Length (nt): 2513

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000479

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C07H6.5.1	C07H6.5.1	2273	III: 7495320-7497832

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C07H6.5	C07H6.5	1293	III: 7496262-7496527

49 RNAi Result

• WBRNAi00082168
• WBRNAi00065800
• WBRNAi00067223
• WBRNAi00067258
• WBRNAi00067295
• WBRNAi00067349
• WBRNAi00067373
• WBRNAi00008365
• WBRNAi00075471
• WBRNAi00080666
• WBRNAi00085439
• WBRNAi00094025
• WBRNAi00082167
• WBRNAi00083335
• WBRNAi00083338
• WBRNAi00022560
• WBRNAi00022687
• WBRNAi00001162
• WBRNAi00007857
• WBRNAi00097879
• WBRNAi00065805
• WBRNAi00065807
• WBRNAi00081977
• WBRNAi00028653
• WBRNAi00065801
• WBRNAi00071316
• WBRNAi00002498
• WBRNAi00002797
• WBRNAi00040044
• WBRNAi00040045

37 Allele

• gk964518
• gk963887
• ok492
• gk603411
• gk868885
• gk461892
• WBVar01990177
• gk899909
• gk402845
• gk655824
• gk498934
• gk597382
• gk485058
• gk376111
• gk323269
• gk351059
• WBVar01657042
• gk933056
• gk778609
• gk607736
• tn691
• gk958878
• ttTi55428
• ttTi13956
• gk178400
• gk178399
• gk178402
• gk178401
• ttTi13961
• dz407

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000479
• Start: 7495320
• End: 7497832
• 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_chrIII_7495232..7495319
• Length (nt): 88
• Chromosome Location: III: 7495232-7495319
• Organism: Caenorhabditis elegans

250 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
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
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
	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
	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
	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
	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
	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
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	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
	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)
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	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 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 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
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
	Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_downregulated
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_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
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	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

15 Expression Patterns

• Primary Identifier: Expr2009943
• 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: Expr8554
• Remark: New Symbol: tia-1. Picture: Fig. 1, Fig S1.
• Subcellular Localization: All P-body and stress granule GFP fusions localized to cytoplasmic foci. Some fusions appeared almost exclusively in foci (DCAP-1 and PATR-1), whereas others were also detected diffusely in the cytoplasm (CGH-1, LSM-1/-3, CCF-1, PAB-1, and TIA-1). DCAP-1, CGH-1, PATR-1, and CCF-1 fusions formed foci in both somatic and germline blastomeres. In contrast, LSM-1 and LSM-3 fusions only localized to foci in somatic blastomeres, and PAB-1 and TIA-1 fusions only localized to foci in germline blastomeres. In contrast, exosome GFP fusions were diffusely distributed in the cytoplasm and nuclei in all blastomeres and did not form distinct foci.

• Primary Identifier: Expr1030281
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr14946
• Pattern: We examined functional transgenes of full-length DCAP-1 or CGH-1 expressed under their respective promoters and observed expression in many neurons including TRNs and motor neurons, localizing to cytoplasmic puncta in neuronal cell bodies.

• Primary Identifier: Expr3516
• Subcellular Localization: During postembryonic stages CGH-1 is expressed specifically in the germline. At the distal tip of each hermaphrodite gonad arm, in proliferating germ cells that have not entered meiosis, CGH-1 is present at low levels and is associated with P granules. As germ cells enter meiosis CGH-1 staining levels increase dramatically and CGH-1 appears within the central gonad core, where it is detected in a predominantly punctate pattern. In oocytes at the proximal gonad end CGH-1 continues to be readily detectable in association with P granules and in these additional cytoplasmic particles. CGH-1 is later detected in each of these types of foci during early embryonic stages.

• Primary Identifier: Expr3741
• Pattern: In adult hermaphrodites, the CGH-1 protein was detectable by western blotting exclusively in the germline.

• Primary Identifier: Expr1640
• Pattern: The cgh-1 mRNA is expressed in the germline during larval and adult stages.

• Primary Identifier: Expr1642
• Pattern: CGH-1 remained present in somatic and P granules in the early embryo. Embryonic P granules can be detected by PGL-1 staining, and are initially segregated by four cell divisions to a single germline precursor (P4), which forms the two germline precursors Z2 and Z3 at around the 100 cell stage. In the germline, these PGL-1 particles were associated with co-localized CGH-1 staining through the 100 cell stage. CGH-1 staining then disappeared from Z2 and Z3 by the 200 cell stage. CGH-1 was also readily detectable in somatic granules throughout the embryo through the four-cell stage. The latter CGH-1 staining then began to diminish, and was barely detectable at the 28 cell stage and absent in 50-100 cell embryos. No CGH-1 staining was detected at later stages. In intact hermaphrodite larvae and adults, CGH-1 was detectable specifically in the gonad in germline but not somatic cells. Paralleling its mRNA expression, CGH-1 levels were barely detectable in L1 and L2 animals, higher during the L3 stage, and significantly increased in L4 and adult gonads. CGH-1 levels remained modest in proliferating cells at the distal gonad end, where it co-localized with the P granule components PGL-1 and the GLH helicases. In the transition zone, where cells enter meiosis, CGH-1 appeared in additional cytoplasmic granules within the central gonad core. These were referred as CGH-1 somatic granules because they appeared to be maintained in the cytoplasm throughout oogenesis and into early embryogenesis, during which they were not segregated to the germline. CGH-1 remained at high levels in association with each granule type in later stage meiotic cells and oocytes. In contrast, in the male gonad, CGH-1 was readily detectable only in cells that were entering meiosis, in which it was also co-localized with P granules.
• Subcellular Localization: CGH-1 is co-localized with the P granule.

• Primary Identifier: Expr1641
• Pattern: cgh-1 mRNA appeared to be restricted to the two germline precursors Z2 and Z3 in wild-type L1 stage hermaphrodites, and was detectable specifically in the gonad at low levels into the L3 stage. cgh-1 expression was significantly higher during the early L4 stage, however, when numerous meiotic cells are present. In adults it remained gonad-specific and was not apparent in the somatically derived uterus.

• Primary Identifier: Expr12213
• Pattern: cgh-1 is expressed in the PVD and broadly throughout development excluding the germ line, which often silences repetitive DNA such as the extrachromosomal arrays generated by DNA microinjection in worms.

• Primary Identifier: Expr12232
• Subcellular Localization: CGH-1 translational fusion to GFP is localized to the cytoplasm. More specifically, CGH-1::GFP is enriched in the perinuclear region and small puncta are present throughout the cytoplasm including particles in dendrites.

• Primary Identifier: Expr2028183
• 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: Expr1144112
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1014922
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr3743
• Subcellular Localization: Throughout the gonad CGH-1 associates with P granules, as revealed by its overlapping localization with the constitutive P granule component PGL-1. CGH-1 staining levels increase dramatically in response to meiosis entry, and CGH-1 particles that are independent of P granules then accumulate within the core.

38 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000479
• Start: 7495320
• End: 7497832
• Strand: -1

38 Ontology Annotations

1 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	mRNAs associated with germ line CGH-1 complex, with > 3-fold increase in expression level in microrarray analysis of RNA IPs with CGH-1 relative to IgG controls.	At least 3 fold enrichment of CGH-1 vs IgG control.	WBPaper00032097:CGH-1-associated-mRNA

1 Sequence

• Length: 2513

1 Sequence Ontology Term