WormMine: Gene WBGene00001170

• WormBase Gene ID: WBGene00001170
• Gene Name: egl-1
• Sequence Name: F23B12.9
• Brief Description: egl-1 encodes a novel protein that contains a region similar to the BH3 (Bcl-2 homology region 3) domain of mammalian cell death activators; EGL-1 functions as an upstream activator in the general programmed cell death pathway and positively regulates programmed cell death by interacting directly with CED-9 to induce CED-4 release from CED-4/CED-9 complexes and ultimately activate the CED-3 caspase; EGL-1 also induces WAH-1/apoptosis-inducing factor release from the mitochondria; in hermaphrodites, egl-1 is transcriptionally repressed by TRA-1, permitting survival of the HSN neurons required for egg laying; egl-1 message is detected at low abundance in embryonic and L1 larval mRNA preparations, but not in mRNA preparations from later larval stages or young adults.
• Organism: Caenorhabditis elegans
• Automated Description: Involved in several processes, including actin filament depolymerization; apoptotic process; and positive regulation of cellular component organization. Located in cytosol; mitochondrion; and presynapse. Expressed in several structures, including ABalappaapp; ABaraapapaad; HSN; URX; and proctodeal cell.
• Biotype: SO:0001217
• Genetic Position: V :6.30737 ±0.004622
• Length (nt): 1052

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001170

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F23B12.9.1	F23B12.9.1	559	V: 14431308-14432359

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F23B12.9	F23B12.9	321	V: 14431482-14431630

10 RNAi Result

• WBRNAi00089860
• WBRNAi00045385
• WBRNAi00027801
• WBRNAi00077439
• WBRNAi00077438
• WBRNAi00077440
• WBRNAi00089904
• WBRNAi00090064
• WBRNAi00090222
• WBRNAi00115692

48 Allele

• gk963271
• gk962657
• gk963706
• gk962658
• gk963301
• gk964458
• gk964459
• gk963796
• WBVar02062301
• WBVar02062302
• sm157
• n5334
• n2164
• n1796
• n487
• n987
• n986
• a487
• gk521926
• gk581541
• gk571019
• gk253656
• gk918646
• gk253655
• gk420353
• WBVar01871942
• WBVar01871943
• n497
• WBVar01871944
• WBVar01871945

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001170
• Start: 14431308
• End: 14432359
• Strand: -1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_14430411..14431307
• Length (nt): 897
• Chromosome Location: V: 14430411-14431307
• Organism: Caenorhabditis elegans

172 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
	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 increased 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_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
	Transcripts that showed significantly increased expression after animals were treated with 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:Psora-Allantoin_upregulated
	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
	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
	Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
	Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_upregulated
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	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 altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Transcripts that showed significantly decreased 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)_downregulated
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
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite npr-8(ok1439) animals grown at 25C, comparing to in N2 animals.	CuffDiff, fold change > 2.	WBPaper00065096:npr-8(ok1439)_upregulated_Day10_25C
Gamma irradiation 100 mGY per hour for 72 hours since L1 larva.	Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage.	DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3.	WBPaper00058958:100mGy-irradiation-72h_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:A-class-motor-neurons_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:all-neurons_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:coelomocytes_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:GABAergic-motor-neurons_L2-larva_expressed
	Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	Transcripts that showed significantly increased expression in BAT525 [hmg-3 (tm2539) / dpy-5(e61) unc-13(e1091) I.] comparing to in N2 at 1-day post L4 adult hermaphrodite stage.	DESeq 2, fold change > 4, adjusted p-value < 0.05.	WBPaper00055013:hmg-3(bar24)_upregulated
	Transcripts that showed significantly increased expression in hmg-4(RNAi) comparing to in vector control worm at L4 larva stage.	DESeq 2, fold change > 4, adjusted p-value < 0.05.	WBPaper00055013:hmg-4(RNAi)_upregulated
	Transcripts that showed significantly increased expression in spt-16(RNAi) comparing to in vector control worm at L4 larva stage.	DESeq 2, fold change > 4, adjusted p-value < 0.05.	WBPaper00055013:spt-16(RNAi)_upregulated
	Transcripts that showed significantly increased expression in mut-16(pk710), comparing to in N2 animals.	DESeq2 v. 1.22.2, adjusted p-value <= 0.05.	WBPaper00059605:mut-16(pk710)_upregulated
	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

16 Expression Patterns

• Primary Identifier: Expr4229
• Remark: Reporter gene fusion type not specified.
• Pattern: Pegl-1gfp is expressed in 0% of the HSNs in wild-type XX animals (n = 27).

• Primary Identifier: Expr1030747
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr14875
• Pattern: To our surprise, we also found that the egl-1 reporter was expressed in adult animals in a very small subset of neurons, and in one pair especially strongly in all individuals. This expression persisted throughout the entire life of the worm. We used cell-specific reporters and morphological characterization to identify the neurons most brightly expressing the reporter as the bilaterally symmetric neuron pair URX (YU et al. 1997). By examining eggs, we found that egl-1 reporter expression was detectable in URX by at least the 3-fold stage, albeit at extremely faint levels compared to later expression. In addition to URX, we also found that AQR, PQR and one of the AWCon/off neuron pair expressed the reporter less often. Of these neurons, the expression in the URX neuron pair was the most consistent and robust.

• Primary Identifier: Expr12256
• Pattern: In 30 out of 32 wild-type embryos examined, a Pegl-1::GFP reporter was expressed in the RID sister cell shortly after the division of its precursor, which coincided with its apoptosis.

• Primary Identifier: Expr2011211
• 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: Expr11092
• Pattern: The egl-1 gene appears to be expressed in the HSNs in males, in which the HSNs normally undergo programmed cell death, but not in hermaphrodites, in which the HSNs normally survive.

• Primary Identifier: Expr14876
• Pattern: We used single molecule fluorescence in-situ hybridization (smFISH) to confirm whether endogenous egl-1 mRNA transcripts could be found in URX (JOHNSEN AND HORVITZ 2016). To test the co-localization of the egl-1 fluorescent reporter and endogenous egl-1 mRNA, we used animals that carry the egl-1 reporter transgene nIs343, which expresses nuclear-localized GFP using 6.5 kb of the upstream promoter region of egl-1 (HIROSE AND HORVITZ 2013). These animals showed the same expression pattern as our egl-1 reporter described in Expr14875 (vxIs601), including expression of GFP in a small number of neurons persisting past development, and especially strongly in URX. We found that the GFP expression always (8/8 worms) co-localized with the smFISH signal from probes targeted to the egl-1 transcript. Notably, this expression continued past the L2 larval stage, which is when the last somatic cell deaths in the hermaphrodite occur (SULSTON AND HORVITZ 1977).

• Primary Identifier: Expr1016862
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr13314
• Pattern: The egl-1 reporter was expressed strongly in the B.al/rapaav cell fated to die and not at all or only weakly in the B.al/rapaav homolog, which is fated to live. All B.al/rapaav corpses in fourth larval stage wild-type animals were GFP- positive (n = 53), confirming that the GFP expression is associated with the secondary fate of cell death.

• Primary Identifier: Expr13315
• Pattern: We used single-molecule fluorescent in situ hybridization (smFISH) to determine whether, like the Pegl-1::4xNLS::gfp reporter (Expr13314), endogenous cell-death genes are transcribed in the dying B.al/rapaav. We usually detected egl-1 mRNA expression in B.al/rapaav and only rarely in the B.al/rapaav homolog, consistent with the expression pattern of Pegl-1::4xNLS::gfp.

• Primary Identifier: Expr2029447
• 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: Expr11093
• Pattern: egl-1 appears to be specifically expressed in cells destined to die during embryogenesis, including the NSM sister cells. The NSM sister cells normally die during a stage called the 1.5-fold stage of embryogenesis. At this stage of development it is difficult to identify cells on the basis of their position within the embryo. The authors therefore analysed the expression of Pegl-1his24-gfp in the background of the ced-3 lf mutation n717. ced-3(n717) blocks programmed cell death, including the death of the NSM sister cells. They found that the activity of EGL-1 is regulated at the transcriptional level in the NSMs and NSM sister cells and, hence, that the cell-death fate of these cells is specified by egl- 1 expression.

• Primary Identifier: Expr13272
• Pattern: egl-1 mRNA is already transcribed in the mothers of dying cells (smRNA FISH).

• Primary Identifier: Expr1149308
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr3857
• Pattern: In wild-type transgenic hermaphrodites, expression of the reporter in the posterior ventral nerve cord matches the wild-type pattern of programmed cell deaths, with expression of gfp in one nucleus each generated by the P9 and P10 lineages, two nuclei generated by the P11 lineage, and three nuclei generated by the P12 lineage.

• Primary Identifier: Chronogram599
• Remark: Original chronogram file: chronogram.1628.xml
• Reporter Gene: [F23B12.9:gfp] transcriptional fusion.

28 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001170
• Start: 14431308
• End: 14432359
• Strand: -1

28 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1052

1 Sequence Ontology Term

• Name: gene

17 Strains

• WBStrain00026925
• WBStrain00026947
• WBStrain00026954
• WBStrain00026979
• WBStrain00026625
• WBStrain00026787
• WBStrain00027341
• WBStrain00027000
• WBStrain00027011
• WBStrain00027054
• WBStrain00029449
• WBStrain00032004
• WBStrain00051757
• WBStrain00051758
• WBStrain00051756
• WBStrain00051687
• WBStrain00054867

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_14432360..14434562
• Length (nt): 2203
• Chromosome Location: V: 14432360-14434562
• Organism: Caenorhabditis elegans