WormMine: Gene WBGene00017990

• WormBase Gene ID: WBGene00017990
• Gene Name: cec-4
• Sequence Name: F32E10.2
• Brief Description: cec-4 is an ortholog of human CBX1 (chromobox 1), CBX5 (chromobox 5) and CBX3 (chromobox 3); CEC-4 is required for the perinuclear anchoring of chromatin methylated on histone H3 Lysine 9 (H3K9) in embryos; the CEC-4 chromodomain is 42% identical to human CBX1 (chromobox 1) chromodomain and CBX5 (chromobox 5) chromodomain; CEC-4 has a large C-terminal domain that does not have homology to other known proteins; it has no chromoshadow domain, and no hinge domain and is therefore not a homolog of HP1; CEC-4-tagged version is expressed in all developmental stages of the worm life cycle, and it is localized to the inner nuclear membrane, positioned between nuclear pores; CEC-4 binds all methylated forms of H3K9 with similar affinities in in vitro assays; cec-4(ok3124) allele supports normal development and does not affect fertility.
• Organism: Caenorhabditis elegans
• Automated Description: Enables methylated histone binding activity. Involved in chromosome attachment to the nuclear envelope; regulation of cell differentiation; and regulation of gene expression. Located in nuclear inner membrane. Expressed in germ cell and somatic cell.
• Biotype: SO:0001217
• Genetic Position: IV :3.35786 ±0.000254
• Length (nt): 1609

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00017990

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F32E10.2.2	F32E10.2.2	1119	IV: 7575718-7577326
Transcript:F32E10.2.1	F32E10.2.1	977	IV: 7576181-7577325

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F32E10.2	F32E10.2	813	IV: 7576187-7576375

12 RNAi Result

• WBRNAi00046143
• WBRNAi00046144
• WBRNAi00046147
• WBRNAi00014224
• WBRNAi00113468
• WBRNAi00077835
• WBRNAi00031688
• WBRNAi00031689
• WBRNAi00007743
• WBRNAi00112218
• WBRNAi00112219
• WBRNAi00117739

26 Allele

• gk964278
• gk964500
• gk963722
• gk963417
• gk963416
• gk946329
• h15609
• WBVar00190746
• gk205748
• gk205749
• gk205747
• gk205750
• gk623726
• gk535170
• gk439632
• gk543196
• gk774574
• gk597449
• gk748984
• gk684493
• WBVar01966615
• WBVar01581636
• WBVar01794839
• WBVar00270636
• WBVar01913431
• ok3124

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00017990
• Start: 7575718
• End: 7577326
• Strand: 1

3 Data Sets

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

0 Downstream Intergenic Region

131 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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	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
	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)
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
	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
	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
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
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure at 25C.	Transcripts that showed significantly increased expression in N2 animals with 24 hours of exposure to P. aeruginosa PA14 for 24 hrs at 25C, comparing to N2 animals without exposure to PA14.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00058948:PA14_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
Growth temperature	Transcripts that are significantly downregulated at 15C compared to both 25C and 20C, with no statistical difference between 25C and 20C, in worms feeding B. subtilis PY79.	DESeq2 and EdgeR, adjusted p-value < 0.05.	WBPaper00053814:15C_downregulated_PY79
Fungi infection: Haptoglossa zoospora.	Transcripts that showed significantly altered expression after L4 N2 animals were exposed to omycete Haptoglossa zoospora for 6 hours.	Kalisto abundance files were converted and analysed using Sleuth in a R pipeline. Standard Sleuth protocols were used to calculate differential expression. P value < 0.01 and FDR < 0.01.	WBPaper00062354:H.zoospora_6h_regulated
	Proteins interacting with HA-PPM-1.D.	N.A.	WBPaper00062498:PPM-1.D_interacting
Bacteria: B.thuringiensis	Transcripts in N2 animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_N2
	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
	Transcripts that showed significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	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
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
20C vs 25C	Transcripts that showed differential expression in 20C vs 25C in mir-34(OverExpression) animals at adult stage.	N.A.	WBPaper00050488:20C_vs_25C_regulated_mir-34(OverExpression)_adult
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_downregulated
	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
	Expression Pattern Group D, enriched for genes involved in catabolic processes.	The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05.	WBPaper00036286:Pattern_D
20C vs 25C	Transcripts that showed differential expression in 20C vs 25C in mir-34(gk437) animals at adult stage.	N.A.	WBPaper00050488:20C_vs_25C_regulated_mir-34(gk437)_adult

6 Expression Patterns

• Primary Identifier: Expr2009835
• 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: Expr1150031
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2028075
• 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: Expr12611
• Pattern: Confocal fluorescence microscopy of CEC-4-mCherry showed that the protein forms a ring at the nuclear periphery at all embryonic stages. This distribution persisted in larval and adult differentiated tissues and in the germline of adult worms.Quantification of fluorescence intensity of CEC-4-mCh in L1 larval stage showed protein level variation in a tissue-specific fashion. CEC-4 is weakly expressed in intestine, highly expressed in muscle, and is found at intermediate levels in almost every other tissue.
• Subcellular Localization: CEC-4 localizes on the inner nuclear membrane.

• Primary Identifier: Expr1037745
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1018597
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

14 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00017990
• Start: 7575718
• End: 7577326
• Strand: 1

14 Ontology Annotations

6 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly decreased expression (fold change > 2, adjusted p-value < 0.05) in RB2301[cec-4(ok3124)] injected with vector RNAi, comparing to control animals (N2 injected with vector RNAi).	Differential expression analysis was performed using DESeq2 v1.6.3 in R version 3.2.3. All analyses were performed with genes that had average expression level above 1 RPKM (fragments per kilobase per million, as calculated by Cufflinks).	WBPaper00050193:cec-4(ok3124)_downregulated_L1
	Transcripts that showed significantly increased expression (fold change > 2, adjusted p-value < 0.05) in RB2301[cec-4(ok3124)] injected with vector RNAi, comparing to in control animals (N2 injected with vector RNAi).	Differential expression analysis was performed using DESeq2 v1.6.3 in R version 3.2.3. All analyses were performed with genes that had average expression level above 1 RPKM (fragments per kilobase per million, as calculated by Cufflinks).	WBPaper00050193:cec-4(ok3124)_upregulated_L1
	Transcripts that showed significantly decreased expression in cec-4(ok3124); ygIs2[baf-1p-GFP-lmn-1(Y59C)] comparing to in ygIs2[baf-1p-GFP-lmn-1(Y59C)] control.	edgeR v3.24, FDR < 0.01, fold change >= 1.5.	WBPaper00059378:cec-4(ok3124);lmn-1(Y59C)_vs_lmn-1(Y59C)_downregulated
	Transcripts that showed significantly increased expression in cec-4(ok3124); ygIs2[baf-1p-GFP-lmn-1(Y59C)] comparing to in ygIs2[baf-1p-GFP-lmn-1(Y59C)] control.	edgeR v3.24, FDR < 0.01, fold change >= 1.5.	WBPaper00059378:cec-4(ok3124);lmn-1(Y59C)_vs_lmn-1(Y59C)_upregulated
	Transcripts that showed significantly decreased expression in cec-4(ok3124); ygIs1[baf-1p-GFP-lmn-1 wt] comparing to in ygIs1[baf-1p-GFP-lmn-1 wt] control.	edgeR v3.24, FDR < 0.01, fold change >= 1.5.	WBPaper00059378:cec-4(ok3124);lmn-1(WT)_vs_lmn-1(WT)_downregulated
	Transcripts that showed significantly increased expression in cec-4(ok3124); ygIs1[baf-1p-GFP-lmn-1 wt] comparing to in ygIs1[baf-1p-GFP-lmn-1 wt] control.	edgeR v3.24, FDR < 0.01, fold change >= 1.5.	WBPaper00059378:cec-4(ok3124);lmn-1(WT)_vs_lmn-1(WT)_upregulated

1 Sequence

• Length: 1609

1 Sequence Ontology Term