WormMine: Gene WBGene00001852

• WormBase Gene ID: WBGene00001852
• Gene Name: hil-1
• Sequence Name: C30G7.1
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable double-stranded DNA binding activity and nucleosomal DNA binding activity. Involved in several processes, including body morphogenesis; egg-laying behavior; and pharynx development. Located in intermediate filament cytoskeleton and nucleolus. Expressed in several structures, including body wall musculature; excretory system; head neurons; marginal cell; and vulval muscle.
• Biotype: SO:0001217
• Genetic Position: V :7.02109 ±0.009647
• Length (nt): 3023

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001852

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C30G7.1.1	C30G7.1.1	910	V: 14949777-14952799

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C30G7.1	C30G7.1	699	V: 14949804-14949938

4 RNAi Result

• WBRNAi00041573
• WBRNAi00022789
• WBRNAi00011403
• WBRNAi00064087

45 Allele

• gk963271
• gk963301
• gk964458
• gk964459
• gk963796
• gk963805
• WBVar00243400
• WBVar01975581
• WBVar01549210
• tm1442
• WBVar02112609
• WBVar00017855
• WBVar00017860
• gk567450
• WBVar01800157
• gk229
• gk254769
• gk254768
• WBVar01744636
• gk254767
• gk254766
• gk254765
• gk254764
• gk254763
• gk832384
• gk380036
• WBVar01775604
• gk749139
• gk450176
• gk865018

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001852
• Start: 14949777
• End: 14952799
• 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_chrV_14952800..14953106
• Length (nt): 307
• Chromosome Location: V: 14952800-14953106
• Organism: Caenorhabditis elegans

282 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	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
	Transcripts that showed significantly decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	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
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_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
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	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
	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 that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	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 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_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)
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	Transcripts that showed significantly increased 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)_upregulated
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	Transcripts that showed significantly increased expression at the intestine cells of daf-2(e1370) comparing to the intestine cells of N2 animals at L2 larva stage.	DESeq2 (version 1.24.0), fold change >= 2, FDR < 0.05	WBPaper00064632:daf-2(e1370)_upregulated_intestine
	Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2.	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_N2-background
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in control animals.	NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%.	WBPaper00064727:daf-2(e1370)_upregulated
	Significantly upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips.	SAM algorithm with an FDR < 0.1.	WBPaper00033065:clk-1(qm30)_upregulated
	Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage.	DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed.	WBPaper00048971:daf-16(mgDf50)_downregulated_L1
	Transcripts that showed significantly increased expression in glna-3(syb1403); glna-2(syb1406)glna-1(syb1405) triple knockout mutant comparing to in N2 animals at L1 larva stage.	DESeq2, fold change > 2.	WBPaper00065074:glna(-)_upregulated

7 Expression Patterns

• Primary Identifier: Expr1926
• Remark: hil-1 = C30G7.1 = H1.X
• Pattern: H1.X::GFP is expressed in body-wall muscles, as well as in the vulva sex muscles. In both cases the general appearance of the cells corresponds to the situation already described for the marginal cells of the pharynx: the fluorescence signal fills the cytoplasm, and the cells' nuclei appear as the brightest fluorescent structure. H1.X presence in muscle cells was not detected with the two different antibodies. H1.X::GFP was also expressed in a limited number of head neurons, in which the fluorescence signal filled the total cytoplasm, including the neuronal projections. The presence of H1.X in these cells was confirmed with the H1.X-101 antibody. Furthermore, H1.X::GFP was detected in the cytoplasm of excretory cells. In C. elegans embryos, H1.X::GFP expression starts with the 30-cell stage. The most prominent structures labeled with both antibodies as well as with H1.X::GFP in transgenic animals are the marginal cells and the tonofilaments therein. The signal appears in all larval stages and in adult C. elegans. No further nuclear or cytoplasmic signal appears besides the labeling of all nuclear lamina caused by the anti-lamin crossreactivity of H1.X-11. This result is confirmed by independent antibody labeling with H1.X-101. In these preparations no nuclear signal appeared in the nuclei of the marginal cells, although the cytoplasm of some head neurons was stained.
• Subcellular Localization: A double labeling experiment was performed with H1.X-11 and the monoclonal antibody IFA, which stains the intermediate filament proteins of the tonofilaments. Both antibodies label identical structures - the tonofilaments in the marginal cells. Antibody labeling with H1.X-101 revealed a prominent labeling of the nucleoli in the polyploid gut nuclei of adult C. elegans hermaphrodites, which colocalized with fibrillarin, a structural component of small nucleolar RNPs (snoRNPs). H1.X was never detected in condensed mitotic or meiotic chromosomes or as a structural component of the interphase chromatin, as revealed by antibody labeling ( H1.X-11) of embryos and meiotic oocytes. H1.X::GFP was never found localized to condensed chromosomes. H1.1-GFP fluorescence is readily observed in condensed mitotic chromosomes in C. elegans embryos, and it is detected as a structural component of interphase chromatin in antibody labeling of embryonic blastomeres and all other cell types of C. elegans. H1.X-101 did not label the nuclear lamina. In H1.X::gfp transgenic animals, the cytoplasm of the marginal cells appeared brightly fluorescent, and the nuclei therein became visible as the brightest fluorescent structures of the cells. The GFP fluorescence was almost homogeneously distributed throughout the whole cytoplasm, but the tonofilaments therein became clearly visible as bright green dots when visualized in axial orientation.

• Primary Identifier: Expr881
• Remark: According to cgc5366, this antibody is not reactive with H1.X. M163.3, Y73B6BL.U, F22F1.1, C18G1.5, B0414.3, F59A7.4, C01B10.5 and C30G7.1 encodes H1.1-H1.6, H1.Q and H1.x. Sequence: C01B10.5 not available in WS59, but there are C01B10.5a, b and c. Sequence: Y73B6BL.U not available in WS42.
• Pattern: All nuclei of the soma of all life stages as well as all nuclei of the germline were detected. In the male gonad, the germline-nuclei of mitotic and of meiotic regions were reactive with the antibody, as were spermatids and mature spermatozoa.
• Subcellular Localization: nuclei

• Primary Identifier: Expr1145591
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1024212
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2030650
• 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: Expr2012414
• 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: Expr1927
• Remark: C30G7.1 = H1.X Type: mammalian cell transfection. For the expression of H1.X::GFP in human HeLa cells, the H1.X cDNA was amplified with the primers ESMG73 5 -GGGGTACCACCATGGTGACCACTTCGCTCATCCACATGG-3 and MJ12 5 -CGGGATCCCGACAATAGCTCTTTCTGGTTCCGG-3 from the cDNA clone yk480h7 and cloned with KpnI and BamHI into the vector pEGFP-N1 (Clontech). The resulting plasmid expresses H1.X as an unfused protein from the CMV promotor and was used for the transfection of HeLa cells with lipofectamine (GibcoBRL).
• Subcellular Localization: In HeLa cells, H1.X::GFP does not appear in the cytoplasm but is a strictly nuclear protein. When H1.X::GFP-expressing HeLa cells were fixed and Triton X-100 extracted, the GFP fluorescence of the nucleoplasm was strongly reduced and the nucleoli appeared brightly fluorescent. These results show that H1.X::GFP is a highly soluble protein in the nucleoplasm of HeLa cells and that it specifically binds to the nucleolus, like it does in C. elegans. In fixed as well as living HeLa cells H1.X::GFP is additionally localized in small spot-like structures, which may represent further nuclear bodies.

22 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001852
• Start: 14949777
• End: 14952799
• Strand: 1

22 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3023

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00035761

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_14947423..14949776
• Length (nt): 2354
• Chromosome Location: V: 14947423-14949776
• Organism: Caenorhabditis elegans