WormMine: Gene WBGene00012458

• WormBase Gene ID: WBGene00012458
• Gene Name: ash-2
• Sequence Name: Y17G7B.2
• Brief Description: ash-2 encodes the C. elegans ortholog of Drosophila Ash2, a trithorax group protein that is a member of the conserved H3K4 trimethylation (H3K4me3) complex; in C. elegans, loss of ash-2 via RNAi results in reduced levels of H3K4me3 at L3 larval stages indicating that ASH-2 functions in H3K4 trimethylation; ASH-2 also functions in the C. elegans germline to negatively regulate lifespan; in addition, loss of ash-2 activity via RNAi results in embryonic lethality characterized by defects in cortical activity and spindle rocking; loss of ash-2 activity in a lin-35 mutant background results in reduced brood size and lethality; two ash-2 deletion mutations, tm1903 and tm1905, also result in lethality and sterility; ASH-2 is highly expressed in the germ line and in early embryos; ASH-2 localizes to the nucleus.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable transcription cis-regulatory region binding activity. Involved in determination of adult lifespan; programmed cell death; and transdifferentiation. Located in nucleus. Part of MLL3/4 complex. Expressed in germ line. Is an ortholog of human ASH2L (ASH2 like, histone lysine methyltransferase complex subunit).
• Biotype: SO:0001217
• Genetic Position: II :5.53877 ±0.083198
• Length (nt): 9213

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00012458

Genomics

5 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
NcPrimaryTranscript	Transcript:Y17G7B.2c	Y17G7B.2c	2930	II: 11979838-11988972
MRNA	Transcript:Y17G7B.2b.1	Y17G7B.2b.1	2296	II: 11980426-11988978
MRNA	Transcript:Y17G7B.2a.1	Y17G7B.2a.1	2325	II: 11980463-11989050
MRNA	Transcript:Y17G7B.2e.1	Y17G7B.2e.1	2325	II: 11980464-11989042
MRNA	Transcript:Y17G7B.2d.1	Y17G7B.2d.1	2305	II: 11980465-11989017

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y17G7B.2e	Y17G7B.2e	1722	II: 11980475-11980545
CDS:Y17G7B.2a	Y17G7B.2a	1713	II: 11980475-11980545
CDS:Y17G7B.2b	Y17G7B.2b	1719	II: 11980475-11980545
CDS:Y17G7B.2d	Y17G7B.2d	1728	II: 11980475-11980545

18 RNAi Result

• WBRNAi00090741
• WBRNAi00072717
• WBRNAi00089506
• WBRNAi00087830
• WBRNAi00073473
• WBRNAi00087824
• WBRNAi00036671
• WBRNAi00091318
• WBRNAi00073475
• WBRNAi00073476
• WBRNAi00055581
• WBRNAi00073472
• WBRNAi00073474
• WBRNAi00073477
• WBRNAi00087848
• WBRNAi00108485
• WBRNAi00108480
• WBRNAi00110286

344 Allele

• gk963801
• gk963053
• gk962684
• gk963539
• WBVar01692062
• WBVar01605214
• WBVar01605215
• WBVar01820704
• WBVar01377630
• WBVar01547289
• WBVar01547292
• WBVar01547291
• WBVar01547294
• WBVar01547293
• WBVar01547296
• WBVar01547295
• h12574
• WBVar02029306
• WBVar02029305
• WBVar02029303
• WBVar02029309
• WBVar02029308
• WBVar02029307
• WBVar01826650
• otn14267
• otn14268
• otn14266
• otn14270
• otn14271
• otn14272

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00012458
• Start: 11979838
• End: 11989050
• 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

94 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 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
	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
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
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 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
	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 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
	Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:Cisplatin_downregulated_WT
	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
	Genes that showed increased expression after germline ablation comparing to un-ablated animals.	The differential expression between germline-ablated versus gonad-ablated animals was computed via the functions makeContrasts and contrasts.fit in the limma package in R/Bioconductor.	WBPaper00045571:germline-ablation_upregulated
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Transcripts that showed significantly increased 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)_upregulated
	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
	Transcripts unqiuely expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_enriched
24 hours of AgNPs exposure.	Genes downregulated more than 2 fold after 24 hours of AgNPs exposure.	Statistical differences between the control and exposed worms were determined by a parametric t test, and a Pearson correlation test was performed for correlation analysis, using the Statistical Package for the Social Sciences (SPSS, Chicago, IL).	WBPaper00034661:AgNPs_downregulated
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 20C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_20C_upregulated
	Embryonic class (E): genes that significantly increase in abundance at some point during embryogenesis.	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_E
	Genes depleted in muscle cells (24hr muscle dataset). Dissociated myo-3::GFP embryos were cultured for 24 hours before FACS sorting.	A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets.	WBPaper00031003:24hr_muscle_depleted
	Total muscle depleted genes (complete list of non-overlapping genes from the 0hr and 24hr muscle depleted datasets).	A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets.	WBPaper00031003:total_muscle_depleted
	Transcripts enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector.	Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples.	WBPaper00051039:germline_enriched
Bacteria infection: Xenorhabdus nematophila	Caenorhabditis elegans Genes with expression levels changed significantly after treatment of Xenorhabdus nematophila.	Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets.	WBPaper00041606:CE_X.nematophila_regulated
control(maintained under normal lab light (mostly dark, in incubators).) vs EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h).	Genes differentially expressed in control vs under EtBr treatment without UVC exposure, at the -1h timepoint.	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_EtBr-exposed_48h
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 just prior to the third UVC dose (48h).	Genes differentially expressed in control vs after UVC exposure and EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)).	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_48h
	Significantly downregulated genes from cyc-1(RNAi) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips.	SAM algorithm with an FDR < 0.1.	WBPaper00033065:cyc-1(RNAi)_downregulated
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).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at just prior to the third UVC dose (48h).	Genes differentially expressed under EtBr treatment and UVC exposure vs under UVC exposure but without EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)).	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:UVC-EtBr-exposed_vs_UVC-exposed_48h

7 Expression Patterns

• Primary Identifier: Expr2009451
• 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: Expr9083
• Remark: Picture: Fig 3a, Fig S4a.
• Subcellular Localization: ASH-2 is expressed in the nuclei of cells from many tissues, and is highly expressed in the germline.

• Primary Identifier: Expr9084
• Remark: Picture: Fig S4b, S4c.
• Pattern: ASH-2 is highly expressed in the germline and in newly formed eggs.

• Primary Identifier: Expr1035511
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1012339
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1159083
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2027688
• 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).

13 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00012458
• Start: 11979838
• End: 11989050
• Strand: 1

13 Ontology Annotations

8 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly decreased expression in ash-2(RNAi) comparing to in wild type animals injected with vector.	Differential mRNA expression using DESeq2. mRNAs with a FDR < 0.05 and fold change > 2 considered differentially expressed.	WBPaper00066232:ash-2(RNAi)_downregulated_WT
	Genes that change expression level at day 8 adult stage after ash-2 RNAi.	One-class analysis in significance analysis of microarrays (SAM)38 was performed comparing empty vector to ash-2 RNAi using a 5% false discovery rate (FDR). Resulting SAM lists of genes regulated by ASH-2 were compared for genes that were specifically changed in N2, but not in glp-1(e2141ts) mutant worms. A complete linkage hierarchical clustering was performed using Gene Cluster 3.0. Clustering results were analysed further with Java Treeview40. GOstat41 was used to identify overrepresented gene ontology categories in the list of ASH-2 regulated genes that were dependent on the presence of the germline.	WBPaper00036383:ash-2_Day8_regulated
	Transcripts that showed significantly increased expression in ash-2(RNAi) comparing to in wild type animals injected with vector.	Differential mRNA expression using DESeq2. mRNAs with a FDR < 0.05 and fold change > 2 considered differentially expressed.	WBPaper00066232:ash-2(RNAi)_upregulated_WT
	Genes that showed decreased expression in ash-2(tm1095) comparing with in N2.	Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated.	WBPaper00045861:ash-2(tm1095)_downregulated
	Transcripts that showed significantly altered expression in dissected intestine tissue by comparing ash-2(RNAi) with empty vector control injected to N2.	Benjamini-Hochberg, FDR = 0.05	WBPaper00051039:ash-2(RNAi)_regulated_intestine
	Transcripts that showed significantly altered expression in dissected germline tissue by comparing ash-2(RNAi) with empty vector control injected to N2.	Benjamini-Hochberg, FDR = 0.05	WBPaper00051039:ash-2(RNAi)_regulated_germline
	Genes that showed increased expression in ash-2(tm1095) comparing with in N2.	Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated.	WBPaper00045861:ash-2(tm1095)_upregulated
	Genes that change expression level at L3 larva stage after ash-2 RNAi.	One-class analysis in significance analysis of microarrays (SAM)38 was performed comparing empty vector to ash-2 RNAi using a 5% false discovery rate (FDR). Resulting SAM lists of genes regulated by ASH-2 were compared for genes that were specifically changed in N2, but not in glp-1(e2141ts) mutant worms. A complete linkage hierarchical clustering was performed using Gene Cluster 3.0. Clustering results were analysed further with Java Treeview40. GOstat41 was used to identify overrepresented gene ontology categories in the list of ASH-2 regulated genes that were dependent on the presence of the germline.	WBPaper00036383:ash-2_L3_regulated

1 Sequence

• Length: 9213

1 Sequence Ontology Term