WormMine: Gene WBGene00000414

• WormBase Gene ID: WBGene00000414
• Gene Name: cec-1
• Sequence Name: ZK1236.2
• Brief Description: cec-1 encodes a nuclear protein with a chromodomain that is ubiquitously expressed in somatic cells, but is dispensable for embryonic survival or gross adult morphology.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable chromatin binding activity and methylated histone binding activity. Predicted to be involved in heterochromatin formation. Predicted to be located in chromosome and nucleus. Predicted to be part of pericentric heterochromatin. Expressed in several structures, including germ line; oocyte; and somatic cell.
• Biotype: SO:0001217
• Genetic Position: III :-0.26203 ±0.000311
• Length (nt): 2251

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000414

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:ZK1236.2.1	ZK1236.2.1	1240	III: 8426333-8428583

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:ZK1236.2	ZK1236.2	915	III: 8426340-8426399

5 RNAi Result

• WBRNAi00059164
• WBRNAi00021834
• WBRNAi00113465
• WBRNAi00005191
• WBRNAi00038177

21 Allele

• gk964518
• gk963887
• gk524660
• gk578278
• gk348108
• gk368839
• gk838143
• gk797572
• gk545762
• gk381487
• WBVar01266201
• h13407
• gk958287
• WBVar01999744
• WBVar00065344
• pk80
• WBVar00068083
• ok1005
• WBVar00065334
• gk180124
• gk180125

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000414
• Start: 8426333
• End: 8428583
• 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_chrIII_8428584..8429296
• Length (nt): 713
• Chromosome Location: III: 8428584-8429296
• Organism: Caenorhabditis elegans

128 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
	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_upregulated
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	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 that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	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 expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	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 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 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
	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
	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
	Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with heat killed E. coli OP50.	Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2.	WBPaper00059824:rnp-6(dh1127)_regulated_OP50
	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
	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 altered expression after 24 hour exposure to nitroguanidine (NQ).	Multivariate permutation tests with random variance model implemented in BRB-Array Tools version 4.5 were performed to infer differentially expressed genes (DEGs). One thousand random permutations were computed per chemical class (i.e., a group of 16 arrays or samples). The confidence level of false discovery rate assessment was set at 80%, and the maximum allowed portion of false-positive genes was 10%.	WBPaper00055899:nitroguanidine_regulated
	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
	Germline-enriched and sex-biased expression profile cluster A.	hierarchical clustering	[cgc6390]:Cluster_A

10 Expression Patterns

• Primary Identifier: Expr1162584
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2009832
• 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: Expr1030230
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1200184
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr13920
• Pattern: Using immunofluorescence, we found that CEC-1 was nuclear and broadly expressed in the embryo, larval and adult animals. Although CEC-1 was suggested to be soma-specific (AGOSTONI et al. 1996), its transcript was detected in the oogenic germline by RNA-Seq (ORTIZ et al. 2014; BOECK et al. 2016). Consistent with these findings, while we do not observe CEC-1 in the distal germline, it is detected in proximal germ cells and oocytes, albeit at a lower level than somatic cells.

• Primary Identifier: Expr1599
• Pattern: No CEC-1 could be detected in zygotes and early embryos. The protein was first detected in embryos at about the 50- to 80-cell stage. At this stage, weak immunostaining appeared in all somatic nuclei. Again, the specificity of the antibodies was confirmed by preincubating the serum with the purified cec-1-antigen which abolished all observed signals. Later in development, nuclear staining becomes stronger and persists in all somatic cells of wild-type and transgenic embryos and larvae. In adult wild-type worms, CEC-1 is present in all somatic nuclei. The intensity of the signals varied with the size of the nuclei; the large polyploid nuclei of the hypodermis and intestine showed intense immunofluorescence, while the smaller diploid nuclei had weaker signals. Neither in wild-type nor in transgenic animals were detected any nuclear staining in the germ line cells, in the germ precursor cells Z2 and Z3, and in early blastomeres. Furthermore, the presence of CEC-1 in the cytoplasm of these cells was excluded by comparison with control animals treated with the preimmune serum.
• Subcellular Localization: CEC-1 staining in interphase nuclei was homogeneous and no speckles or foci could be detected, suggesting a uniform distribution of the protein. High-resolution imaging of the anti-CEC-1 antibody staining also revealed uniform staining of interphase nuclei. Interestingly, when the chromosomes started to condense during early mitosis, the protein appeared to dissociate from them, as shown in prometaphase nuclei. In fully condensed metaphase chromosomes, the protein was no longer associated with them.

• Primary Identifier: Expr1020453
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2028072
• 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: Expr1600
• Remark: Hybridization of the embryos with the sense probe as control gave no signal.
• Pattern: Large amounts of cec-1 mRNA are localized in the cytoplasm of all blastomeres from early embryos. Indeed, cytoplasmic staining in the gonads of the hermaphrodites confirmed that maternal cec-1 mRNA is packaged into the oocytes. The signals were very strong in the early embryos prior to the onset of protein production at the 50- to 80-cell stage and weakened as development proceeded. Staining of the cytoplasm appeared uniform and no distribution gradient of cec-1 mRNA could be observed at any stage.
• Subcellular Localization: cytoplasm

• Primary Identifier: Expr13918
• Pattern: Western blots of tagged proteins from staged worm populations indicated that both CEC-1 and CEC-6 are present in embryos. While CEC-1 is also expressed throughout development, CEC-6 levels were low until the L4 and adult stages, when the number of germ cells dramatically increases and gametes are produced.

10 GO Annotation

12 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000414
• Start: 8426333
• End: 8428583
• Strand: 1

10 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2251

1 Sequence Ontology Term