WormMine: Gene WBGene00006997

• WormBase Gene ID: WBGene00006997
• Gene Name: zyg-12
• Sequence Name: ZK546.1
• Brief Description: zyg-12 encodes three coiled-coil domain-containing proteins that belong to the Hook protein family, members of which likely act as linker proteins that connect membrane compartments with the microtubule cytoskeleton; during embryonic development, zyg-12 activity is essential and is required continuously for nuclear-centrosome attachment and proper nuclear positioning within cells; in addition, zyg-12 is required after fertilization for proper pronuclear migration; two predicted transmembrane isoforms of ZYG-12 localize to the nuclear envelope and to centrosomes, while a third ZYG-12 isoform lacking a transmembrane domain localizes only to centrosomes; ZYG-12 nuclear envelope localization is seen in the syncytial gonad, oocytes, and early embryonic nuclei and requires SUN-1 function; in turn, ZYG-12 is required for nuclear envelope localization of DHC-1/dynein heavy chain, LIS-1, and ARP-1; ZYG-12 localization to centrosomes requires microtubules; in yeast two-hybrid assays, ZYG-12 interacts with itself and with the DLI-1/dynein light intermediate chain.
• Organism: Caenorhabditis elegans
• Automated Description: Enables dynein light intermediate chain binding activity. Involved in several processes, including centrosome localization; chromosome segregation; and pronuclear migration. Located in centrosome and nuclear envelope. Expressed in gonad and oocyte. Used to study Emery-Dreifuss muscular dystrophy. Is an ortholog of human HOOK1 (hook microtubule tethering protein 1) and HOOK2 (hook microtubule tethering protein 2).
• Biotype: SO:0001217
• Genetic Position: II :-2.65±
• Length (nt): 3593

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006997

Genomics

8 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:ZK546.1d.3	ZK546.1d.3	3197	II: 4949900-4953483
Transcript:ZK546.1b.1	ZK546.1b.1	2909	II: 4949900-4953488
Transcript:ZK546.1d.1	ZK546.1d.1	2891	II: 4949900-4953485
Transcript:ZK546.1c.1	ZK546.1c.1	2861	II: 4949900-4953488
Transcript:ZK546.1d.2	ZK546.1d.2	2577	II: 4949900-4953492
Transcript:ZK546.1a.3	ZK546.1a.3	2939	II: 4949902-4953478
Transcript:ZK546.1a.1	ZK546.1a.1	2905	II: 4949902-4953492
Transcript:ZK546.1a.2	ZK546.1a.2	2584	II: 4949902-4953492

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:ZK546.1c	ZK546.1c	2286	II: 4949911-4950069
CDS:ZK546.1d	ZK546.1d	2202	II: 4949911-4950069
CDS:ZK546.1a	ZK546.1a	2211	II: 4949911-4950069
CDS:ZK546.1b	ZK546.1b	2334	II: 4949911-4950069

4 RNAi Result

• WBRNAi00009474
• WBRNAi00059501
• WBRNAi00038328
• WBRNAi00027075

39 Allele

• gk963801
• gk963053
• h18057
• gk964277
• WBVar01719687
• ie14
• WBVar00223105
• WBVar00223108
• gk713625
• gk932489
• gk469191
• gk696101
• gk911628
• gk321743
• gk141912
• gk141911
• gk141914
• gk141913
• gk141910
• or577
• gk141916
• gk141915
• gk141917
• WBVar01413427
• bw54
• WBVar01783292
• gk909604
• gk521591
• gk849888
• gk848264

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006997
• Start: 4949900
• End: 4953492
• 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_4953493..4953588
• Length (nt): 96
• Chromosome Location: II: 4953493-4953588
• Organism: Caenorhabditis elegans

102 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
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
	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 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 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
	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 increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_downregulated
	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
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:all-neurons_L2-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
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 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
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
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)
	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 decreased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_downregulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (FLT) starting at L1 lava stage.	DESeq	WBPaper00053302:alovudine_24h_regulated
	Transcripts that showed significantly increased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:jmjd-3.1(+)_upregulated
	Transcripts that showed significantly increased expression in rgef-1p::jmjd-1.2 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:rgef-1p-jmjd-1.2(+)_upregulated
	Transcripts that showed significantly increased expression in sur-5p::jmjd-1.2 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:sur-5p-jmjd-1.2(+)_upregulated
20C vs 25C	Transcripts that showed differential expression in 20C vs 25C in N2 animals at adult stage.	N.A.	WBPaper00050488:20C_vs_25C_regulated_N2_adult
	Transcripts that showed significantly depleted expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm.	Fold change > 2, p-value < 0.05.	WBPaper00060661:sensory-neuron_depleted
	Transcripts that showed significantly decreased expression in pals-22(jy3) comparing to in N2 at L4 larva stage.	Differential expression analysis was performed in RStudio (v1.1.453) using R (v3.50) and Bioconductor (v3.7) packages. As outlined in the RNAseq123 vignette, data was imported, filtered and normalized using edgeR, and linear modeling and differential expression analysis was performed using limma. An FDR cutoff of <0.01 was used to define differentially expressed genes; no fold-change criteria was used.	WBPaper00056034:pals-22(jy3)_downregulated

8 Expression Patterns

• Primary Identifier: Expr1162915
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2036348
• 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: Expr1032993
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2828
• Remark: When microtubules were depleted via tba-2 RNAi, centrosomal localization of ZYG-12A,B,C::GFP was lost although the nuclear envelope localization was completely normal. These data are consistent with localization of ZYG-12 to the centrosome arising by direct or indirect binding of ZYG-12 to microtubules.
• Pattern: Expressed in oocytes, gonad and all cells during in early embryo.
• Subcellular Localization: ZYG-12A,B,C::GFP localized to the nuclear envelope in the syncytial gonad, oocytes, and all nuclei during the development of the early embryo. The tagged ZYG-12 isoforms also localized to the region around the centrosome. This hollow sphere of localization appeared similar to that of the proximal ends of microtubules organized by the centrosome. Labeled microtubules extended in a linear fashion to the cortex, whereas the ZYG-12 labeling was concentrated at the centrosome and did not extend more than a few m away from the centrosome. ZYG-12A::GFP alone localized to only the centrosome and was not detected at the nuclear envelope. Expression of ZYG-12B,C::GFP resulted in localization to both the nuclear envelope and centrosomes. Expression of either ZYG-12B::GFP or ZYG-12C::GFP alone resulted in identical localization as ZYG-12B,C::GFP.

• Primary Identifier: Expr1012697
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2018210
• 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: Expr12819
• Subcellular Localization: ZYG-12 localizes to the outer membrane of the nuclear envelope.

• Primary Identifier: Expr2829
• Subcellular Localization: ZYG-12 localized to both the centrosome and nuclear envelope in a pattern identical to that seen with ZYG-12A,B,C::GFP (see Expr2828).

27 GO Annotation

11 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006997
• Start: 4949900
• End: 4953492
• Strand: 1

27 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3593

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00040374
• WBStrain00007377

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_4949528..4949899
• Length (nt): 372
• Chromosome Location: II: 4949528-4949899
• Organism: Caenorhabditis elegans