WormMine: Gene WBGene00001867

• WormBase Gene ID: WBGene00001867
• Gene Name: him-8
• Sequence Name: T07G12.12
• Brief Description: him-8 encodes a protein with two C-terminal noncanonical C2H2zinc-fingers whose paralogs include ZIM-1/-3 and C02F5.12; HIM-8 isrequired by X chromosomes for normal homolog pairing, synapsis,recombination, and segregation during meiosis; him-8 mutants have anincreased frequency of genotypically XO males in self-fertilehermaphrodite populations; HIM-8 is expressed during meiosis, and isassociated with the X chromosome's meiotic pairing center (PC), whichassociates with the nuclear envelope during meiotic prophase; him-8mutations are enhanced by rearrangements that inactivate theX-chromosomal PC; HIM-8 functions are genetically separable, since thehim-8(me4) point mutation (which alters a domain N-terminal to HIM-8'szinc fingers) permits normal chromosome binding and nuclearlocalization, but causes abnormal pairing and synapsis; while theC-terminal region of HIM-8 most closely resembles those of its orthologsin other Caenorhabditis species, its N-terminal region is highlydivergent, suggesting species-specific functions; unlike other himmutations, him-8 solely affects X chromosomes, and does not produceembryonic lethality via autosomal nondisjunction or aneuploidy; however,failure of X-chromosomal synapsis in him-8 mutants blocks the pachytenetransistion from polarized to nonpolarized meiotic nuclei, by blockingthe resolution of recombination intermediates on other chromosomes;him-8-blocked meiotic autosomes show persistent RAD-51 foci and haveexcess crossovers, both of which may be symptoms of a HUS-1-independentcheckpoint induced by X-chromosomal nonsynapsis rather than DNA damage;HIM-8 also acts outside of meiosis, by inhibiting EGL-13 expression oractivity; mutations of the HIM-8 zinc-finger domain semidominantlysuppress missense (but not null) egl-13 mutations, due to him-8haploinsufficiency; mutant HIM-8 fails to suppress mutant egl-13 on afree transgenic array, and also fails to suppress native mutant egl-13if transgenic excess copies of the egl-13 promoter are present.
• Organism: Caenorhabditis elegans
• Automated Description: Involved in meiotic chromosome segregation. Located in X chromosome; condensed nuclear chromosome; and nuclear envelope.
• Biotype: SO:0001217
• Genetic Position: IV :4.63925±
• Length (nt): 2070

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001867

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T07G12.12a.1	T07G12.12a.1	1254	IV: 10561905-10563974
Transcript:T07G12.12b.1	T07G12.12b.1	120	IV: 10563487-10563815

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T07G12.12b	T07G12.12b	120	IV: 10563487-10563505
CDS:T07G12.12a	T07G12.12a	1086	IV: 10561914-10562006

8 RNAi Result

• WBRNAi00052787
• WBRNAi00018391
• WBRNAi00097679
• WBRNAi00089582
• WBRNAi00089654
• WBRNAi00089656
• WBRNAi00089657
• WBRNAi00097689

36 Allele

• gk964278
• gk964078
• gk964500
• gk962765
• tm11441
• tm611
• WBVar02021167
• WBVar00602788
• h4715
• h6831
• WBVar00191814
• ec56
• WBVar01730773
• WBVar01730774
• WBVar01730771
• WBVar01730772
• WBVar01730775
• e14890
• gk211049
• gk796110
• gk404398
• gk211047
• gk211048
• gk211045
• me4
• gk211046
• mn253
• e1489
• sy599
• gk681048

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001867
• Start: 10561905
• End: 10563974
• Strand: 1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_10563975..10566276
• Length (nt): 2302
• Chromosome Location: IV: 10563975-10566276
• Organism: Caenorhabditis elegans

87 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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
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 intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_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)
	Transcripts expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
	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
	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
	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 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 increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
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
	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 decreased expression in hpl-2(tm1489) comparing to in N2 animals.	DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2.	WBPaper00054493:hpl-2(tm1489)_downregulated
	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
	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 unqiuely expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_enriched
	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
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
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 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: Expr1031099
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2012432
• 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: Expr13056

• Primary Identifier: Expr3800
• Subcellular Localization: Dissected gonads were costained with antibodies to HIM-8 and to the NE proteins LMN-1/lamin or SUN-1/matefin. Close association between HIM-8 foci and nuclear-envelope staining is clearly evident, particularly in individual optical sections from these data sets. Fluorescence-intensity profiles confirm that HIM-8 foci are peripheral with respect to the mass of DAPI-stained chromatin and lie very close to or embedded within the nuclear lamina. Frequently, HIM-8 foci have a crescent-shaped appearance, especially in the transition zone, as if the protein localizes to a patch along the nuclear surface. In him-8(me4), the only mutant allele in which HIM-8 foci remain associated with the X PC, the protein also retains its localization at the NE.

• Primary Identifier: Expr1156392
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr16168
• Subcellular Localization: HIM-8 localizes to chromosome sites outside the X Pairing Center. In addition to the major focus of HIM-8 at the X-PC, we detected lower levels of HIM-8 at a number of additional chromosome site. Additional HIM-8 signals were most prominent on the X chromosomes, but were also detected on autosomes.

• Primary Identifier: Expr1023130
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2030668
• 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).

7 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001867
• Start: 10561905
• End: 10563974
• Strand: 1

7 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2070

1 Sequence Ontology Term

• Name: gene

122 Strains

• WBStrain00022554
• WBStrain00022735
• WBStrain00022497
• WBStrain00022498
• WBStrain00023443
• WBStrain00024103
• WBStrain00024106
• WBStrain00024121
• WBStrain00004698
• WBStrain00028625
• WBStrain00028626
• WBStrain00029248
• WBStrain00029247
• WBStrain00029468
• WBStrain00029647
• WBStrain00029511
• WBStrain00029553
• WBStrain00029576
• WBStrain00029592
• WBStrain00029591
• WBStrain00029935
• WBStrain00030689
• WBStrain00030692
• WBStrain00034112
• WBStrain00034470
• WBStrain00034354
• WBStrain00034391
• WBStrain00034922
• WBStrain00035115
• WBStrain00035128

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_10561430..10561904
• Length (nt): 475
• Chromosome Location: IV: 10561430-10561904
• Organism: Caenorhabditis elegans