WormMine: Gene WBGene00017641

• WormBase Gene ID: WBGene00017641
• Gene Name: csr-1
• Sequence Name: F20D12.1
• Brief Description: csr-1 encodes, by alternative splicing, two isoforms of an Argonaute protein required for chromosome segregation, embryonic viability, Slicer activity induced by secondary siRNAs, and (partially) for germline RNAi; csr-1(RNAi) embryos are generally inviable, with disordered metaphase chromosomes and anaphase DNA bridges; CSR-1 is found in secondary-type siRNA/Slicer complexes, and isolated recombinant CSR-1 itself shows Slicer activity with secondary-type siRNAs; csr-1(fj54) mutant cell-free extracts have only 10% the normal level of secondary siRNA-induced Slicer activity; csr-1 mutants are partially defective in germline RNAi; CSR-1 belongs to a nematode-specific group of Argonaute homologs, and is most closely related to C04F12.1; like ALG-1/2 and RDE-1, but unlike some other Argonaute homologs, CSR-1 retains key catalytic residues in an RNAse H domain.
• Organism: Caenorhabditis elegans
• Automated Description: Enables endoribonuclease activity, cleaving siRNA-paired mRNA. Involved in P granule assembly; mitotic sister chromatid segregation; and siRNA-mediated gene silencing by mRNA destabilization. Located in P granule; condensed nuclear chromosome; and metaphase plate. Expressed in several structures, including germ line; intestine; somatic cell; spermatocyte; and in male.
• Biotype: SO:0001217
• Genetic Position: IV :3.5093 ±0.00096
• Length (nt): 4891

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00017641

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F20D12.1a.1	F20D12.1a.1	3662	IV: 7957267-7962157
Transcript:F20D12.1a.2	F20D12.1a.2	3599	IV: 7957568-7962157
Transcript:F20D12.1b.1	F20D12.1b.1	2604	IV: 7958613-7961663

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F20D12.1a	F20D12.1a	3093	IV: 7957580-7958054
CDS:F20D12.1b	F20D12.1b	2604	IV: 7958613-7958758

11 RNAi Result

• WBRNAi00081765
• WBRNAi00082037
• WBRNAi00082041
• WBRNAi00045101
• WBRNAi00082033
• WBRNAi00069462
• WBRNAi00103295
• WBRNAi00094995
• WBRNAi00025149
• WBRNAi00008667
• WBRNAi00031170

90 Allele

• gk964278
• gk964500
• gk963722
• gk963417
• gk963416
• tm892
• tm11488
• WBVar02124417
• WBVar02124418
• fj54
• gk206387
• gk206390
• gk206391
• gk206388
• gk206389
• gk206394
• gk206395
• gk206392
• gk206393
• gk206397
• gk206398
• gk206399
• gk206396
• WBVar01729975
• gk790839
• gk391164
• gk920897
• gk839520
• gk382926
• gk377459

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00017641
• Start: 7957267
• End: 7962157
• 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

167 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
	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
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
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 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_N2
	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 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 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 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 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)
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	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_SM
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 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
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
	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 depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	Transcripts depleted in purified oocyte P bodies comparing to in the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	Transcripts that showed significantly increased expression in daf-2(e1370;mes-1(bn84ts) comparing to in mes-1(bn84ts).	DESeq2 was used for differential expression analysis. A BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a significance cutoff.	WBPaper00049368:daf-2(e1370)_upregulated
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_downregulated
	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:dopaminergic-neurons_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

13 Expression Patterns

• Primary Identifier: Expr1019334
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr7852
• Remark: Picture: Figure S5.
• Pattern: Expressed in somatice cells.

• Primary Identifier: Expr8820
• Remark: Picture: Fig 3A.
• Pattern: Western blot analyses revealed that two isoforms of CSR-1 are present at all developmental stages, and that CSR-1 are most enriched in young adults, gravid adults, and embryos.

• Primary Identifier: Expr8822
• Subcellular Localization: Finally, all aspects of the localization patterns were absent in each respective mutant background. In the mitotic cells of embryos, each factor became enriched in prophase nuclei. As chromosomes condensed, DRH-3, EGO-1, and EKL-1 became enriched along the length of each chromosome, while CSR-1 remained nuclear. All four proteins exhibited robust localization around the metaphase plate. CSR-1 and DRH-3 displayed a pattern similar to cohesins, whereas EKL-1 (and to a lesser degree, EGO-1) appeared to be more closely associated with chromosomes in a pattern similar to kinetochore proteins. In fact, EKL-1 retained a robust association with chromosomes during anaphase, whereas the other RNAi factors became more difficult to detect. Cytoplasmic localization was also detected for each protein. The larger CSR-1 isoform was expressed throughout larval development and was also present at low levels in post-mitotic populations lacking a germline. Quantitative real-time RT-PCR analysis of both csr-1 transcripts indicated that their expression recapitulates the protein expression pattern. DRH-3, EGO-1, and CSR-1 colocalize in the germline with PGL-1, a previously characterized component of the germline nuage structures called P granules. EKL-1 was not detected in P granules. While many developmentally important factors transiently localize to P granules, DRH-3 and CSR-1 maintained their P granule localization in germ cells throughout the life cycle. As oocytes matured, EGO-1 was lost from the P granules, while DRH-3 and CSR-1 maintained P granule association. In mature oocytes, CSR-1 and EGO-1 both became enriched in nuclei, where CSR-1 was enriched on the diakinetic chromosomes.

• Primary Identifier: Expr16408

• Primary Identifier: Expr15939
• Pattern: CSR-1 is expressed mainly in the germline of adult worms and localizes in the cytoplasm and germ granules.

• Primary Identifier: Expr15940
• Pattern: In early embryos, CSR-1 localizes to both the germline and somatic blastomeres. CSR-1 in the somatic blastomeres is mainly cytoplasmic and persists for several cell divisions.

• Primary Identifier: Expr11465
• Remark: Temporal description
• Pattern: CSR-1 is abundant in mature sperm. CSR-1 was associated with P-granules throughout the syncytial male germline and into differentiating spermatocytes, where P-granules disperse and disappear. In developing gametes, CSR-1 localized to large cytoplasmic foci and in discrete chromatin domains of spermatocytes undergoing nuclear condensationas well as in haploid spermatids.

• Primary Identifier: Expr2010561
• 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: Expr1037573
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr12894
• Pattern: In strains in which the sole source of CSR-1 was GFP::CSR-1 encoded by a functional single-copy transgene, the authors observed the previously described P-granule localization but no detectable GFP signal on chromosomes in oocytes or early mitotic embryos.

• Primary Identifier: Expr1149051
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2028801
• 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).

18 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00017641
• Start: 7957267
• End: 7962157
• Strand: 1

18 Ontology Annotations

11 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_upregulated_25C
	Genes significantely Up-regulated by GRO-seq in csr-1 hypomorph vs. N2 using DESeq p < 0.05.	DESeq package with an FDR of < 0.05.	WBPaper00045050:csr-1(hypomorph)_upregulated
	Transcripts that showed significantly decreased expression in csr-1a(tor159) comparing to in N2 at 25C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_downregulated_25C
	mRNAs that showed increased expression in csr-1(RNAi) animales comparing to in control RNAi animals. Set 1 transcripts were defined as P-value < 0.05 and fold change > 1.9.	DESeq was used. Fold change between the average of the four control replicates and the average of the four test replicates was used to calculate the significance using a negative binomial distribution. An adjusted P-value was calculated using the Benjamini-Hochberg method for multiple testing correction.	WBPaper00046805:csr-1(RNAi)_upregulated_Set1
	Transcripts that showed significantly decreased expression in csr-1a(tor159) comparing to in N2 at 20C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_downregulated_20C
	mRNAs that showed increased expression in csr-1(RNAi) animales comparing to in control RNAi animals. Set 2 transcripts were defined as adjusted p-value < 0.05 and fold change > 2.6.	DESeq was used. Fold change between the average of the four control replicates and the average of the four test replicates was used to calculate the significance using a negative binomial distribution. An adjusted P-value was calculated using the Benjamini-Hochberg method for multiple testing correction.	WBPaper00046805:csr-1(RNAi)_upregulated_Set2
	Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 20C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_upregulated_20C
	Proteins that bind CSR-1 according to immunoprecipitation and mass spectrometry.	To estimate the significance of the change in protein abundance, a linear model (adjusted for peptides and biological replicates) was performed, and P values were FDR-adjusted using the BenjaminiHochberg procedure with a control threshold set to 0.05.	WBPaper00059254:CSR-1_interacting
	Genes significantely Down-regulated by GRO-seq in csr-1 hypomorph vs. N2 using DESeq p < 0.05.	DESeq package with an FDR of < 0.05.	WBPaper00045050:csr-1(hypomorph)_downregulated
	mRNAs that showed decreased expression in csr-1(RNAi) animales comparing to in control RNAi animals. Set 1 transcripts were defined as P-value < 0.05 and fold change > 1.9.	DESeq was used. Fold change between the average of the four control replicates and the average of the four test replicates was used to calculate the significance using a negative binomial distribution. An adjusted P-value was calculated using the Benjamini-Hochberg method for multiple testing correction.	WBPaper00046805:csr-1(RNAi)_downregulated_Set1
	mRNAs that showed decreased expression in csr-1(RNAi) animales comparing to in control RNAi animals. Set 1 transcripts were defined as adjusted p-value < 0.05 and fold change > 2.6.	DESeq was used. Fold change between the average of the four control replicates and the average of the four test replicates was used to calculate the significance using a negative binomial distribution. An adjusted P-value was calculated using the Benjamini-Hochberg method for multiple testing correction.	WBPaper00046805:csr-1(RNAi)_downregulated_Set2

1 Sequence

• Length: 4891

1 Sequence Ontology Term