WormMine: Gene WBGene00003222

• WormBase Gene ID: WBGene00003222
• Gene Name: mes-4
• Sequence Name: Y2H9A.1
• Brief Description: mes-4 encodes a SET domain-containing protein that also contains three plant homeodomain (PHD) fingers; MES-4 is required maternally for normal germline development, but in contrast to MES-2, -3, and -6, does not appear to be required for somatic anteroposterior patterning; in germline development, MES-4 activity is essential for regulating active chromatin states and for excluding the MES-2/MES-3/MES-6 chromatin repression complex from the autosomes; MES-4 is also required for germline silencing of repetitive transgene arrays; MES-4 localizes to autosomes, and is detectable in the distal, mitotic region of the germline, in meiotic germ cells during late pachytene, and in oocytes; MES-4 is detected in all somatic and germline nuclei of the early embryo, but by the 100-cell stage, its expression becomes restricted to the primordial germ cells, Z2 and Z3; exclusion of MES-4 from X chromosomes requires the activity of the MES-2, -3, -6 complex.
• Organism: Caenorhabditis elegans
• Automated Description: Enables histone H3K36 methyltransferase activity. Involved in germ-line sex determination and heterochromatin formation. Acts upstream of or within with a positive effect on dosage compensation by hypoactivation of X chromosome. Located in X chromosome; autosome; and nuclear chromosome. Part of chromatin. Expressed in Z2; Z3; and germ line. Human ortholog(s) of this gene implicated in several diseases, including Sotos syndrome 1; lung non-small cell carcinoma; and neuroblastoma. Is an ortholog of human NSD1 (nuclear receptor binding SET domain protein 1); NSD2 (nuclear receptor binding SET domain protein 2); and NSD3 (nuclear receptor binding SET domain protein 3).
• Biotype: SO:0001217
• Genetic Position: V :5.34414 ±0.004146
• Length (nt): 4496

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003222

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y2H9A.1.1	Y2H9A.1.1	3121	V: 13433050-13437545

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y2H9A.1	Y2H9A.1	2697	V: 13433442-13433681

41 RNAi Result

• WBRNAi00055763
• WBRNAi00020158
• WBRNAi00069474
• WBRNAi00081781
• WBRNAi00081804
• WBRNAi00081816
• WBRNAi00081834
• WBRNAi00081845
• WBRNAi00081864
• WBRNAi00085954
• WBRNAi00081892
• WBRNAi00085953
• WBRNAi00085956
• WBRNAi00081699
• WBRNAi00085955
• WBRNAi00026633
• WBRNAi00081902
• WBRNAi00089598
• WBRNAi00078967
• WBRNAi00078970
• WBRNAi00081914
• WBRNAi00081916
• WBRNAi00085984
• WBRNAi00084330
• WBRNAi00085985
• WBRNAi00111011
• WBRNAi00084338
• WBRNAi00081869
• WBRNAi00089628
• WBRNAi00091494

85 Allele

• gk963271
• gk963706
• gk963301
• gk964458
• gk964459
• WBVar02061823
• WBVar02061824
• WBVar02061825
• WBVar02061826
• WBVar02061827
• otn8958
• WBVar01869605
• WBVar01869606
• WBVar01869602
• WBVar01869603
• WBVar01869604
• WBVar01975248
• gk712837
• gk679311
• gk871095
• gk742338
• gk329176
• gk925506
• gk958444
• gk879898
• gk876324
• gk635859
• gk450169
• gk915895
• WBVar02115605

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003222
• Start: 13433050
• End: 13437545
• 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_chrV_13432715..13433049
• Length (nt): 335
• Chromosome Location: V: 13432715-13433049
• Organism: Caenorhabditis elegans

157 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 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
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
	Genes that were upregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_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 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
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	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)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	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: 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 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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
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
	Top 300 transcripts enriched in ABalppppppa, ABpraaapppa according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:ASE_parent
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_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
	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 in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment.	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:sek-1(km4)_downregulated_cisplatin
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:hypodermis_L3-L4-larva_expressed
	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 detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed

9 Expression Patterns

• Primary Identifier: Expr4222
• Pattern: In a wild-type germ line, the MES-4 pattern is dynamic. MES-4 levels are highest in the distal mitotic region, drop to nearly undetectable levels at the transition zone, rise modestly during late pachytene, and become markedly enhanced after fertilization. MES-4 is not detectable in gut nuclei.
• Subcellular Localization: Expressed in nuclei.

• Primary Identifier: Expr1031522
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr14367

• Primary Identifier: Expr1905
• Pattern: MES-4 is present in the distal, mitotic region of the germ line, barely detectable in the early- to mid-pachytene region, and up-regulated in later pachytene and in oocytes. In embryos, MES-4 is present in both somatic and germline nuclei until the 80- to 100-cell stage. Subsequently, MES-4 staining diminishes in somatic cells but persists in the primordial germ cells Z2 and Z3.
• Subcellular Localization: MES-4 is localized to nuclei and associated with chromosomes. Staining in one-cell embryos revealed that one chromosome of each parental set of six lacks MES-4. In four-cell embryos two chromosomes in each diploid nucleus lack MES-4. MES-4 is also restricted to the autosomes in the adult hermaphrodite germ line. After the near-disappearance and then reappearance of MES-4 during pachytene, it associates with five bivalents but is lacking from one, presumably the X. Thus, MES-4 is off the Xs when X-linked oocyte genes become detectably expressed in late pachytene. MES-4 staining in male germ lines resembles that in hermaphrodites.

• Primary Identifier: Expr2013532
• 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: Expr1200052
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr2031766
• 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: Expr1159295
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1027992
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

28 GO Annotation

3 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003222
• Start: 13433050
• End: 13437545
• Strand: -1

28 Ontology Annotations

8 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in mes-4(bn73) comparing to in control animals in early germ cells (EGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mes-4(bn73)_upregulated_EGCs
	Transcripts that showed significantly decreased expression in mes-4(bn73) comparing to in control animals in early germ cells (EGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mes-4(bn73)_downregulated_EGCs
	Transcripts that showed significantly decreased expression in mes-4(bn73) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mes-4(bn73)_downregulated_PGCs
	Transcripts that showed significantly increased expression in mes-4(bn73) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mes-4(bn73)_upregulated_PGCs
	Genes upregulated in mes-4 relative to wild type.	Confidence levels were determined using a two-tailed paired t-test.	WBPaper00028483:Up_mes-4_vs_WT
	Genes that showed decreased expression in mes-2; mes-4 comparing with in wild type background.	Statistical analysis for mis-expression was performed using a moderated t-test from the package limma. All genes with a false discovery rate of <= 5% (q <= 0.05) were selected for further analysis.	WBPaper00041688:mes-2_mes-4_downregulated
	Genes that showed increased expression in mes-2; mes-4 comparing with in wild type background.	Statistical analysis for mis-expression was performed using a moderated t-test from the package limma. All genes with a false discovery rate of <= 5% (q <= 0.05) were selected for further analysis.	WBPaper00041688:mes-2_mes-4_upregulated
	Genes downregulated in mes-4 relative to wild type.	Confidence levels were determined using a two-tailed paired t-test.	WBPaper00028483:Down_mes-4_vs_WT

1 Sequence

• Length: 4496

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00022581
• WBStrain00029957
• WBStrain00034440
• WBStrain00036937

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_13437546..13441960
• Length (nt): 4415
• Chromosome Location: V: 13437546-13441960
• Organism: Caenorhabditis elegans