WormMine: Gene WBGene00001968

• WormBase Gene ID: WBGene00001968
• Gene Name: hlh-29
• Sequence Name: F31A3.4
• Brief Description: hlh-29 encodes a REF-1-like protein with two bHLH domains that represses lag-2 transcription in ABa descendants (in response to a Notch signal, redundantly with REF-1, HLH-26, and HLH-27) and tbx-37 transcription in EMS descendants (independently of Notch, redundantly with REF-1, HLH-26, HLH-27, and perhaps HLH-28); HLH-29 is identical to residues 24-262 of HLH-28, shares near-identical promoter regions in a inverted duplex, and is likely to be highly redundant with HLH-28; HLH-29 (with HLH-28) is also required for late embryonic viability, and for normal fat metabolism, yolk protein transport, gonadal and vulval development, bordering behavior, and chemosensory responses, and repression of tax-4 and osm-9 transcription; lag-2 repression by HLH-29 may require UNC-37; HLH-29's paralogs include HLH-25 through HLH-28 and (more distantly) REF-1; hlh-29 is transcribed in the early MS and E lineages, probably due to MED-1/2 binding of clustered sites in the hlh-28/hlh-29 shared promoter region; HLH-29 is expressed in ABp granddaughters ~25 minutes after ABp first contacts an APX-1-expressing cell, and in ABa descendants after a second Notch interaction; HLH-29 is also expressed in all EMS granddaughters beginning at the 24-cell stage, in a SKN-1-dependent manner; furthermore, HLH-29 is expressed in amphid and phasmid neurons, ALA and PVT neurons, chemosensory and mechanosensory neurons, ASI, ASK, PHA, PQR, and neurons of the anterior pharynx, as well as in vulva, somatic gonad, rectal glands, intestine, and larval pharyngeal muscle PM1, ventral posterior coelomocytes, spermatheca, and vulval muscles; hlh-28/29 mRNA is present throughout development, but varies roughly 30-fold in quantity, with 3.5-fold more mRNA in L1 larvae than in adults; ectopic HLH-29 can rescue the intestinal defect of ref-1(RNAi) embryos; hlh-28/29 transcription is inhibited by LIN-12 and MED-1.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Expressed in several structures, including amphid sheath cell; coelomocyte; ganglia; non-striated muscle; and rectal gland cell.
• Biotype: SO:0001217
• Genetic Position: X :24.2565 ±0.040092
• Length (nt): 1148

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001968

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F31A3.4.1	F31A3.4.1	1047	X: 17547492-17548639

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F31A3.4	F31A3.4	720	X: 17547817-17548141

20 RNAi Result

• WBRNAi00045978
• WBRNAi00045979
• WBRNAi00070039
• WBRNAi00070036
• WBRNAi00070035
• WBRNAi00014127
• WBRNAi00014129
• WBRNAi00070038
• WBRNAi00031604
• WBRNAi00115873
• WBRNAi00070034
• WBRNAi00070033
• WBRNAi00070042
• WBRNAi00070043
• WBRNAi00070044
• WBRNAi00070037
• WBRNAi00084010
• WBRNAi00070041
• WBRNAi00092719
• WBRNAi00070040

8 Allele

• gk964260
• gk963810
• gk963581
• gk964446
• tm284
• gk367881
• tm11111
• gk308225

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001968
• Start: 17547492
• End: 17548639
• 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_chrX_17534882..17547491
• Length (nt): 12610
• Chromosome Location: X: 17534882-17547491
• Organism: Caenorhabditis elegans

33 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis 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:E.faecalis_24hr_upregulated_TilingArray
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_downregulated
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
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
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly increased 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_upregulated
	Genes that showed significant differential expressed between control and 150 mg\/L Atrazine treatment.	t-test, p < 0.05.	WBPaper00036123:Atrazine_regulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 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:Rapamycin-Rifampicin-Allantoin_downregulated
Bacteria infection: Photorhabdus luminescens	Genes with increased expression after 24 hours of infection by P.lumniescens 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:P.lumniescens_24hr_upregulated_TilingArray
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Psora_downregulated
	Transcripts that showed significantly decreased 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)_downregulated
	Transcripts that showed significantly decreased expression in mex-1(or286) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	RPKM fold change > 2.	WBPaper00058598:mex-1(or286)_downregulated
	Transcripts that interact with both BAZ-2 and SET-6 in Chip-Seq analysis.	N.A.	WBPaper00059356:BAZ-2_SET-6_interacting
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Rifampicin-Psora_downregulated
	Potental DAF-12 target genes identified by ChIP-chip analysis performed on strain ALF4 [daf-12	Affymetrix TAS software that computed for each probe estimates of fold enrichment (in linear scale) over hybridization with input DNA. At the same time, TAS calculated for each probe a p-value by applying a Wilcoxon signed rank test. A threshold of 2.5 was selected, which corresponds to probe intensities approximately 2.5 times stronger on the ChIP array than on the Input array. Additional TAS threshold parameters were MinRun=180 bp, MaxGap=300 bp. TAS analysis showed that the selected threshold of 2.5 corresponds approximately to a p-value of 0.01.	WBPaper00040221:DAF-12_target_ALF4
	Genes that showed significantly decreased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control.	Fold change > 1.2 or < 0.8.	WBPaper00042477:rsr-2(RNAi)_downregulated_TilingArray
Bacteria diet: Comamonas sp. 12022 MYb131	Transcripts that showed significantly increased expression after animals were fed by Comamonas sp. 12022 MYb131, comparing to animals fed by OP50.	edgeR FDR <= 0.05, fold change >= 4.	WBPaper00061424:Diet_MYb131_upregulated
	Transcripts that showed significantly decreased expression in mrps-5(RNAi) comparing to in control animals.	Fold change > 4, p-value < 0.01	WBPaper00056330:mrps-5(RNAi)_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Psora-Allantoin_downregulated
	Transcripts that showed significantly decreased expression in mex-3(eu149) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	RPKM fold change > 2.	WBPaper00058598:mex-3(eu149)_downregulated
control(maintained under normal lab light (mostly dark, in incubators).) vs UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) at 3 h after the first UVC dose (3h).	Genes differentially expressed in control vs after UVC exposure and EtBr treatment at the -45h timepoint (3 hours after the first UVC dose).	Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first.	WBPaper00041939:control_vs_UVC-EtBr-exposed_3h
	Transcripts that showed significantly decreased expression in swsn-1(os22ts) comparing to in N2 animals at young adult worms.	DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.)	WBPaper00060764:swsn-1(os22ts)_downregulated
	Transcripts that showed significantly increased expression in DA116[eat-2(ad1116)] comparing to in N2.	The DESeq2 package (v1.24.0) was used to identify differentially expressed genes (DEGs). Fold change > 2, FDR < 0.05.	WBPaper00061040:eat-2(ad1116)_upregulated
	Genes with expression level up regulated in mir-35 mutants comparing with N2.	The raw data was normalized and t-statics were computed using R and Bioconductor with the affy package and Benjamini-Hoch-berg (BH) correction method for multiple comparisons. RNA levels that changed at least 1.5-fold with a probability of p < 0.005 after BH correction were considered significantly different in mir-35(gk262) mutants relative to wild-type.	WBPaper00040876:mir-35_upregulated
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_downregulated
	Transcripts that showed significantly decreased expression in spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_downregulated
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_upregulated
	Genes that showed significant differential expressed between control and 1000 mg\/L Fluoranthene treatment.	t-test, p < 0.05.	WBPaper00036123:Fluoranthene_regulated
Bacteria: C.neoformans strain H99	Transcripts that showed significantly increased expression after infection by C. neoformans H99.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:C.neoformans_H99_upregulated
	Genes with differential expression under 0.5mg/l Chlorpyrifos (CPF) and 1.0mg/l Diazinon (DZN) treatment at 16 centigrade.	To identify the differentially expressed genes in each treatment authors used linear models per toxicant and temperature (gene expression = Toxicant (effect) + error). The lm function in R stats package was used to implement the linear models analysis with recommended default options. For threshold determination authors used a permutation approach. For each of the 23,232 permutations used authors randomly picked a transcript (array spot), which could only be picked once. Authors combined all the expression values of this transcript and randomly distributed them over the replicates and used them in the linear model. In this way authors obtained a threshold for each of the toxicants. Authors used a -log10 p-value 2 as common threshold for the analysis, which resembles to the following FDR per toxicant: 0.0155 for CPF at 24 centigrade, 0.0148 for DZN at 24 centigrade, 0.0168 for CPF+DZN at 24 centigrade, 0.0142 for CPF at 16 centigrade, 0.0151 for DZN at 16 centigrade, and 0.0148 for CPF+DZN, at 16 centigrade.	WBPaper00037113:Chlorpyrifos_Diazinon_16C_regulated

8 Expression Patterns

• Primary Identifier: Expr4683
• Pattern: hlh-29/hlh-28 mRNA is present at all developmental stages and does not vary significantly during later larval stages. Embryos and early L1-stage larvae produce significantly more hlh-29/hlh-28 RNA than later larvae. In separate assays from three independent cDNA samples, L1-stage larvae produced an average of 3 1/2 times more hlh-29 RNA than did L4 stage larvae and adults.

• Primary Identifier: Expr4684
• Pattern: GFP expression was detected at most developmental stages, with the spatial expression depending on the developmental stage of the animal. Neuronal expression of hlh-29 was detected in larvae and adults in both amphid and phasmid sockets, in the ALA and PVT neurons, in the chemosensory and mechanosensory neurons, ASI, ASK, PHA, and PQR, and in neurons of the anterior pharyngeal bulb. Weaker expression was also detected in the ASG chemosensory neurons in some transgenic lines. L1 animals show strong expression of hlh-29 in intestinal cells, and weaker expression in the rectal glands and the pharyngeal muscle cell PM1. By L3 stage, intestinal expression of the hlh-29::GFP is limited to the posterior intestinal cells, and PM1 expression is no longer detected. Expression is also detected in the ventral posterior coelomocytes in the later L3-stage larvae, and in the spermatheca and vulval muscles of L4 and adult animals.

• Primary Identifier: Expr8065
• Remark: Picture: Figure 4D.
• Pattern: hlh-29 was expressed in all EMS granddaughters beginning at the 24-cell stage. Approximately 25 min after ABp first contacts a ligand-expressing cell at the four-cell stage, all ref-1 family members were expressed in the ABp granddaughters. No expression was detected in ABa descendants or descendants of other early blastomeres such as EMS or P3. The second Notch interaction begins at the 12-cell stage, when two of the four ABa descendants contact a ligand-expressing cell. The ref-1 family was expressed about 25 min later in the daughters of the two Notch-activated ABa descendants, but not in other ABa descendants; these same embryos continued to show expression in the ABp descendants activated by the first interaction.

• Primary Identifier: Expr16143
• Pattern: hlh-29 is expressed in most cells of the spermatheca of L4 and adult animals, and in the vulva muscles, but not in the spermatheca or vulval precursor cells of younger animals.

• Primary Identifier: Expr3505
• Pattern: Expressed in: early MS, E lineage.

• Primary Identifier: Expr1149879
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2030742
• 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: Expr2012503
• 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).

5 GO Annotation

3 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001968
• Start: 17547492
• End: 17548639
• Strand: -1

5 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes up regulated by 2.0 fold or greater in hlh-29(tm284) mutants.	The T-test was performed to find the candidates for differential expression, and genes with significant signal level between different conditions (p < 0.05) were collected. In addition, fold change analysis were performed on the genes with significant expression, and all genes showing greater than two-fold change were considered putative targets.	WBPaper00042178:hlh-29(tm284)_upregulated
	Genes down regulated by 2.0 fold or greater in hlh-29(tm284) mutants.	The T-test was performed to find the candidates for differential expression, and genes with significant signal level between different conditions (p < 0.05) were collected. In addition, fold change analysis were performed on the genes with significant expression, and all genes showing greater than two-fold change were considered putative targets.	WBPaper00042178:hlh-29(tm284)_downregulated

1 Sequence

• Length: 1148

1 Sequence Ontology Term