WormMine: Gene WBGene00001207

• WormBase Gene ID: WBGene00001207
• Gene Name: egl-43
• Sequence Name: R53.3
• Brief Description: egl-43 encodes a zinc finger protein that affects HSN cell migration and development of the phasmid neurons; expressed in the HSN and phasmid neurons.
• Organism: Caenorhabditis elegans
• Automated Description: Enables DNA-binding transcription factor activity. Involved in several processes, including regulation of developmental process; regulation of mitotic cell cycle; and regulation of transcription by RNA polymerase II. Located in nucleus. Expressed in several structures, including MSaaap; MSpaap; gonad; neurons; and somatic gonad precursor. Human ortholog(s) of this gene implicated in dilated cardiomyopathy 1LL and myeloid neoplasm. Is an ortholog of human MECOM (MDS1 and EVI1 complex locus) and PRDM16 (PR/SET domain 16).
• Biotype: SO:0001217
• Genetic Position: II :1.81525 ±0.002697
• Length (nt): 7836

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001207

Genomics

4 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:R53.3a.1	R53.3a.1	2475	II: 9955185-9962995
NcPrimaryTranscript	Transcript:R53.3c	R53.3c	1791	II: 9955186-9962153
MRNA	Transcript:R53.3b.1	R53.3b.1	2339	II: 9957011-9962978
MRNA	Transcript:R53.3b.2	R53.3b.2	1938	II: 9960231-9963020

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:R53.3a	R53.3a	1632	II: 9955186-9955305
CDS:R53.3b	R53.3b	969	II: 9960333-9960485

44 RNAi Result

• WBRNAi00107800
• WBRNAi00107697
• WBRNAi00107699
• WBRNAi00107698
• WBRNAi00107799
• WBRNAi00107798
• WBRNAi00089842
• WBRNAi00052038
• WBRNAi00009084
• WBRNAi00078882
• WBRNAi00070945
• WBRNAi00070944
• WBRNAi00026131
• WBRNAi00099861
• WBRNAi00100460
• WBRNAi00027692
• WBRNAi00070216
• WBRNAi00100834
• WBRNAi00071200
• WBRNAi00099255
• WBRNAi00099659
• WBRNAi00099457
• WBRNAi00100086
• WBRNAi00100273
• WBRNAi00070950
• WBRNAi00070209
• WBRNAi00070210
• WBRNAi00070949
• WBRNAi00070211
• WBRNAi00070212

146 Allele

• gk963801
• gk963053
• gk962682
• WBVar01604540
• WBVar01377856
• h17914
• h12410
• gk151880
• WBVar01998881
• WBVar01627115
• gk151882
• WBVar01627116
• gk151881
• WBVar01627117
• gk151888
• gk151887
• gk151890
• gk151889
• WBVar00602461
• gk151884
• cxTi8210
• gk151883
• gk151886
• gk151885
• gk151896
• WBVar00174865
• gk151895
• WBVar00174866
• gk151898
• gk151897

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001207
• Start: 9955185
• End: 9963020
• Strand: 1

4 Data Sets

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

0 Downstream Intergenic Region

147 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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	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
	Coexpression clique No. 60, 176662_at-Y53F4B.16, on the genome-wide coexpression clique map for the nematode GPL200 platform.	All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.	WBPaper00061527:176662_at-Y53F4B.16
	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 intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	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 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 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
	Transcripts depleted in purified oocyte P bodies comparing to in the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	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
	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 increased expression in mep-1(ne4629[MEP-1-GFP-Degron]) 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:mep-1(ne4629)_upregulated
	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-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_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
	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
	Transcripts that showed significantly increased expression in pgl-1(ct131) animals (isolated from SS0002[pgl-1(ct131)him-3(e1147)], comparing to in control animals SS1174, at 1-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_pgl-1(ct131)_vs_control_day1-adult
Starvation 48 hours at L1 arrest	Transcripts that showed significantly increased expression in starved N2 animals (48 hours at L1 arrest)	Fold change > 2.	WBPaper00064005:starvation_upregulated_N2_mRNA
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to tiling array analysis towards total RNA.	A linear model and moderated t-statistic were used to determine differentially expressed genes as implemented by the limma package (v3.21.4). Enriched list contains only genes significantly enriched in the NSM neurons versus the reference <=1.5X and <= 5% FDR.	WBPaper00045974:NSM_enriched_totalRNA_tiling

10 Expression Patterns

• Primary Identifier: Expr4761
• Pattern: A transcriptional reporter consisting of 1.7 kb of 5' regulatory sequences upstream of the egl-43L start codon showed GFP expression first in the ventral uterine (VU) cells of mid L2 larvae (Pn.p stage) and then in the AC beginning in mid L3 larvae, after the first round of vulval cell divisions had occurred. AC expression increased during AC invasion in late L3 larvae, but remained constant in the VU descendants. gfp expression was also observed in the gut and a set of neurons in the head region. However, no expression could be detected in the vulval cells during vulval cell fate specification and AC invasion.

• Primary Identifier: Expr4501
• Pattern: egl-43::YFP expression in the gonad was first detected in the pre-AC/pre-VU cells at early L2, and was maintained in their 37 descendants at early L4. egl-43::YFP was also expressed in the AC and VU cells when their cell fates become specified at mid-L2. Expression in the two dorsal uterine precursor (DU) cells (Z1.pap and Z4.apa) was first detected at late L2 and was maintained in their descendants. Thus, egl-43 is expressed in the AC, VU and DU lineages in the somatic gonad.

• Primary Identifier: Expr1030766
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr11260
• Pattern: In addition to neuronal expression described previously, EGL-43::GFP was expressed at about 150 minutes in four descendants of a blastomere called MS; these descendants are pharyngeal/ valve precursors.

• Primary Identifier: Expr669
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: EGL-43 is nuclear localized and is expressed in HSN before and during the cells migration from tail to the gonad primordium of the embryo. EGL-43 expression is down regulated after HSN migration. In embryo ~400 min after cleavage, expression observed in HSN/PHB precursor, PHA sensory neuron in the tail. ~430 min after first cleavage, expression observed in HSN nucleus which has migrated out of the tail, as well as a phasmid neuron nucleus. During its migration, HSN expresses EGL-43 as well as phasmid neuron nuclei.
• Subcellular Localization: Expressed in the nuclei.

• Primary Identifier: Expr2011222
• 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: Expr15011
• Pattern: Both reporters, gfp::egl-43L and egl-43::gfp, were expressed in the invading AC and in the surrounding ventral and dorsal uterine (VU and DU) cells. We found no obvious difference in the expression pattern of the two egl-43 reporters, suggesting that the long egl-43L isoform accounts for most of the expression observed.

• Primary Identifier: Expr1016323
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1155673
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2029458
• 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).

17 GO Annotation

10 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001207
• Start: 9955185
• End: 9963020
• Strand: 1

17 Ontology Annotations

1 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that interact with endogenous EGL-43-GFP at L3 larva stage according to CHIP-Seq analysis.	N.A.	WBPaper00059471:EGL-43_interacting

1 Sequence

• Length: 7836

1 Sequence Ontology Term