WormMine: Gene WBGene00004737

• WormBase Gene ID: WBGene00004737
• Gene Name: scc-1
• Sequence Name: F10G7.4
• Brief Description: scc-1 encodes a member of the Rad21/Rec8-like family of cohesion proteins that affects embryonic viability, fertility, the rate of embryonic cell divisions and the incidence of male progeny; interacts with ATL-1, F56D12.5, and F11E6.1 based on yeast two-hybrid assays, and is expressed in nondividing embryonic and germline nuclei.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable chromatin binding activity and damaged DNA binding activity. Involved in meiotic cell cycle. Located in nucleus. Part of cohesin complex. Expressed in several structures, including SDQ; germ line; seam cell; touch receptor neurons; and ventral nerve cord. Human ortholog(s) of this gene implicated in Cornelia de Lange syndrome 4; carcinoma (multiple); and endometrial cancer. Is an ortholog of human RAD21 (RAD21 cohesin complex component) and RAD21L1 (RAD21 cohesin complex component like 1).
• Biotype: SO:0001217
• Genetic Position: II :-3.59162 ±0.111344
• Length (nt): 2274

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004737

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F10G7.4.1	F10G7.4.1	2135	II: 4698721-4700994

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F10G7.4	F10G7.4	1938	II: 4698721-4698972

17 RNAi Result

• WBRNAi00081503
• WBRNAi00044316
• WBRNAi00025068
• WBRNAi00027271
• WBRNAi00030793
• WBRNAi00088416
• WBRNAi00000880
• WBRNAi00013089
• WBRNAi00088922
• WBRNAi00088418
• WBRNAi00088420
• WBRNAi00088421
• WBRNAi00088919
• WBRNAi00005006
• WBRNAi00061556
• WBRNAi00081528
• WBRNAi00103264

26 Allele

• gk963801
• gk963053
• gk963140
• gk963141
• WBVar01437561
• gk405005
• ok1017
• gk601103
• gk385721
• gk629497
• gk431887
• gk141344
• gk862465
• gk890993
• gk838612
• gk141346
• gk725357
• gk141345
• gk369359
• gk659683
• gk141352
• gk141351
• gk141348
• gk141347
• gk141350
• gk141349

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004737
• Start: 4698721
• End: 4700994
• 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_chrII_4700995..4702068
• Length (nt): 1074
• Chromosome Location: II: 4700995-4702068
• Organism: Caenorhabditis elegans

154 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:all-neurons_L1-larva_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
	Genes that showed significantly increased expression in wrn-1(gk99) comparing to in N2, according to RNAseq.	DESeq was used to calculate the fold changes, log fold changes, and significance of the changes for each comparison.	WBPaper00045934:wrn-1(gk99)_upregulated
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_developing
	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: 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
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
	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 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 depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
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
	Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	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
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) 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_elt-2(RNAi)
	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 altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated

8 Expression Patterns

• Primary Identifier: Expr2579
• Pattern: SCC-1/COH-2 was expressed in germ cells throughout the development, including the adult stage. SCC-1/COH-2 was detected in virtually all mitotic germ nuclei. Similarly to somatic cells in embryos, SCC-1/COH-2 was dispersed in the cytoplasm at mitotic prometaphase and was absent from the condensed anaphase chromosomes in germ cells. In female germ cells that entered meiotic prophase in adult hermaphrodites, SCC-1/COH-2 was observed uniformly in the nuclei. It was unclear whether SCC-1/COH-2 localized to the condensed meiotic chromosomes, because of the strong SCC-1/COH-2 signal emitted from the nucleoplasm. SCC-1/COH-2 was detected also in male germ cells at mitosis and meiosis, but it was not detectable in mature sperm. SCC-1/COH-2 was strongly expressed in virtually all cells in early embryos, but its expression was gradually weakened, and the signal could hardly be detected in late embryos, in which cell division was ceased almost completely. Strong nuclear signals of SCC-1/COH-2 reappeared in larvae, though they were limited to a subset of cells. SCC-1/COH-2 was detectable only in cells that were going to divide. For example, in an L1 larva, intense SCC-1/COH-2 signals were detected in the 14 hypodermal V lineage cells, which divide synchronously. The SCC-1/COH-2 signal was dispersed and not detectable on condensed chromosomes, as observed in embryos of an intermediate stage. In a slightly older L1 larva, expression of SCC-1/COH-2 was seen in 22 P lineage cells to constitute the ventral nerve cord and in four Q lineage cells to produce posterior neuronal cells, all of which divide at the same time. In this L1 larva, no signal was detected in the V lineage cells, suggesting that the SCC-1/COH-2 protein is present only for a short time in the cell cycle, and likely to be degraded quickly after cell division. Larvae of later stages also expressed SCC-1/COH-2 in dividing cells: in an L3 larva, SCC-1/COH-2 was detected in four M lineage cells to produce the uterine and vulval muscle cells and in 10 P lineage vulval precursor cells, which divide concurrently. The embryos were stained with both anti-SCC-1/COH-2 antibodies and an antibody against a component of the nuclear pore complexes. The SCC-1/COH-2 signal was evenly distributed within the nuclear envelope except for the chromosomal region, suggesting that SCC-1/COH-2 molecules dissociated from the chromosomes at metaphase were trapped by the nuclear envelope. Consistently with this interpretation, the SCC-1/COH-2 staining around the metaphase plate was no longer seen at later stages of embryogenesis involving >30 cells, where nuclear envelope is known to break down before metaphase. SCC-1/COH-2 was dispersed into the whole cytoplasm of metaphase cells at these stages.
• Subcellular Localization: SCC-1/COH-2 seemed to localize to the chromosomes in a cell cycle-dependent manner. In interphase, SCC-1/COH-2 was seen throughout the nucleus, overlapping largely with DNA. At mitotic prophase, SCC-1/COH-2 started to separate from condensing chromosomes, and it was not detected on the chromosomes at prometaphase and metaphase. At metaphase, the SCC-1/COH-2 signal seemed as if surrounding the metaphase plate, although it was possible that a small amount of SCC-1/COH-2 was remaining on the metaphase chromosomes but escaped detection, because cohesin is reported to become detectable on metaphase chromosomes only after detergent extraction of soluble background in other metazoans. The SCC-1/COH-2 signal was then dispersed in the cytoplasm at anaphase. At telophase, the SCC-1/COH-2 protein began to reaccumulate on the chromosomes.

• Primary Identifier: Expr1032337
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1350
• Pattern: coh-2 was expressed primarily in germline cells as seen by immunofluorescence. Its product was present as dots, mainly at the periphery but also inside nuclei of the mitotic zone. In later stages, COH-2 assumed an exclusively peripheral distribution. In pachytene nuclei, 10 (10.1 1.5 [n = 25 nuclei]) distinct spots were counted but by diplotene and later COH-2 was not detectable. COH-2 was present in the nuclei of embryos but was not associated with condensed mitotic chromosomes.
• Subcellular Localization: nuclei

• Primary Identifier: Expr2015621
• 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: Expr2033856
• 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: Expr11962
• Subcellular Localization: The C. elegans mitotic kleisin SCC-1, previously thought to function only during mitosis, contributes to cohesion in pachytene nuclei. SCC-1 associates with axial structures of transition zone and pachytene nuclei of wild-type animals. SCC-1 staining was detected between homologs, suggesting that SCC-1 cohesin associates with the meiotic chromosomal axis, similar to REC-8 and COH-3/4 cohesins. Diffuse nuclear staining obscured any chromosomal signal in diplotene/diakinesis nuclei; however, SCC-1 was undetectable on chromosomes following nuclear envelope breakdown, when the nucleoplasmic signal dissipated. Thus, any role played by SCC-1 in meiotic SCC of wild-type animals or kleisin triple mutants is likely to occur during pachytene, but not prometaphase I.

• Primary Identifier: Expr1015315
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1148255
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

18 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004737
• Start: 4698721
• End: 4700994
• Strand: 1

18 Ontology Annotations

4 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in scc-1(ubs19);coh-1(ubs26) comparing to in control animals.	DESeq2 v.1.34, fold change > 2, FDR < 0.05.	WBPaper00067078:scc-1(ubs19);coh-1(ubs26)_upregulated
	Transcripts that showed significantly increased expression in scc-1(ubs19) comparing to in control animals.	DESeq2 v.1.34, fold change > 2, FDR < 0.05.	WBPaper00067078:scc-1(ubs19)_upregulated
	Transcripts that showed significantly decreased expression in scc-1(ubs19) comparing to in control animals.	DESeq2 v.1.34, fold change > 2, FDR < 0.05.	WBPaper00067078:scc-1(ubs19)_downregulated
	Transcripts that showed significantly decreased expression in scc-1(ubs19);coh-1(ubs26) comparing to in control animals.	DESeq2 v.1.34, fold change > 2, FDR < 0.05.	WBPaper00067078:scc-1(ubs19);coh-1(ubs26)_downregulated

1 Sequence

• Length: 2274

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00035987

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_4698428..4698720
• Length (nt): 293
• Chromosome Location: II: 4698428-4698720
• Organism: Caenorhabditis elegans