WormMine: Gene WBGene00002016

• WormBase Gene ID: WBGene00002016
• Gene Name: hsp-16.2
• Sequence Name: Y46H3A.3
• Brief Description: hsp-16.2 encodes a 16-kD heat shock protein (HSP) that is a member of the hsp16/hsp20/alphaB-crystallin (HSP16) family of heat shock proteins; hsp-16.2 expression, strongest in intestine and pharynx, is induced in response to heat shock or other environmental stresses; HSP-16.2 has been shown to interact with intracellular human beta amyloid peptide, a primary component of the extracellular plaques found in Alzheimer's disease; HSP-16.2 is likely to function as a passive ligand temporarily preventing unfolded proteins from aggregating.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable unfolded protein binding activity. Involved in response to heat. Located in cytoplasm. Expressed in several structures, including coelomocyte; enteric muscle; gonad; somatic nervous system; and spermatid.
• Biotype: SO:0001217
• Genetic Position: V :-17.5804 ±0.043798
• Length (nt): 624

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002016

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y46H3A.3a.1	Y46H3A.3a.1	578	V: 1804334-1804957
Transcript:Y46H3A.3b.1	Y46H3A.3b.1	384	V: 1804441-1804870

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y46H3A.3b	Y46H3A.3b	384	V: 1804441-1804752
CDS:Y46H3A.3a	Y46H3A.3a	438	V: 1804441-1804752

11 RNAi Result

• WBRNAi00056700
• WBRNAi00106382
• WBRNAi00113926
• WBRNAi00020672
• WBRNAi00113923
• WBRNAi00076795
• WBRNAi00027604
• WBRNAi00063652
• WBRNAi00063187
• WBRNAi00070128
• WBRNAi00117978

16 Allele

• gk963301
• gk963591
• gk963553
• gk964259
• gk963850
• gk963027
• WBVar01971241
• WBVar02052002
• WBVar01737738
• gk567833
• gk403186
• gk595683
• gk682258
• gk249
• gk227615
• gk227616

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002016
• Start: 1804334
• End: 1804957
• 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_1803144..1804333
• Length (nt): 1190
• Chromosome Location: V: 1803144-1804333
• Organism: Caenorhabditis elegans

406 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
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
	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
	Genes that were upregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_upregulated
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
Heat shock: 35C for 1 hour.	Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite endu-2(tm4977) animals were exposed to 35C for 1 hour.	The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01.	WBPaper00065749:Heat-Shock_upregulated_endu-2(tm4977)
Heat shock: 35C for 1 hour.	Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite N2 animals were exposed to 35C for 1 hour.	The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01.	WBPaper00065749:Heat-Shock_upregulated_N2
	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 body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_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 that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	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 rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	Transcripts expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
	Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
	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
	mRNAs that showed increased expression in P-granule RNAi animales (simultaneously targeting pgl-1, pgl-3, glh-1 and glh-4) comparing to in control RNAi animals. Set 1 transcripts were defined as P-value < 0.05 and fold change > 2.	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:P-granule-RNAi_upregulated_Set1
	Transcripts that showed significantly increased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_upregulated
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
	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
	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
	Transcripts that showed significantly increased expression in cco-1(RNAi) comparing to in vector control animals.	The limma package47 was used for differential expression. Genes with a Benjamini-Hochberg adjusted P-value <0.05 and an absolute log fold change of 2 were considered differentially expressed.	WBPaper00053402:cco-1(RNAi)_upregulated

12 Expression Patterns

• Primary Identifier: Expr1031176
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2757
• Pattern: Upon induction by thermal stress, the GFP fluorescence is visible at the head of the worm, including the pharynx and the anterior nerve ring in the transgenic worm but not in the wild-type controls.

• Primary Identifier: Expr1381
• Pattern: Expression of both the 48.1C and 41.2C transgenes was consistently observed in embryos from gastrulation onward, in all larval stages and in adults. In postembryonic stages, both transgenes were expressed in most tissues. Although 41.2C is expressed in numerous tissues, especially the pharynx and gut, it is not expressed in the gonad. 41.8C express in a tissue general fashion and expression s in every cell type has been observed in strains carrying this transgene, including neurons, muscle, intestine, and hypodermis. Only the germ-line failed to express this fusion gene. Tissues expressing the hsp-16::lacZ fusion in these strains include nerve ganglia in the head and ventral cord; hypodermal nuclei of the lateral hypodermis, vulva, head and tail, body wall and pharyngeal muscle, somatic gonad, mesodermal tissue such as coelomocytes, and muscles involved in defecation. On the other hand, subtle differences in the expression pattern of these two transgenes were identified. 41.2C stain most intensely throughout the pharynx whereas 48.1C demonstrated conspicuous expression in body wall muscle.

• Primary Identifier: Expr10722

• Primary Identifier: Expr1117
• Remark: Reporter gene fusion type not specified. Similar patterns of HSP16 distribution were observed with two other polyclonal antibodies, one with greater specificity for HSP16-41 and another which cross-reacts with all four stress-inducible HSP16s. Thus the staining pattern described here reflects the distribution of the HSP16 family in general. Non-stressed animals showed little or no detectable signal.
• Pattern: HSP16-2 is ubiquitously expressed throughout most somatic tissues of larvae after heat-shock, and the intensity gradually decreased with age. HSP16 labelling is prominent in spermathecae and in the vulval region in L4 and adult hermaphrodites. The spermathecal labelling seems to consist of cytoplasmic localization of HSP16-2 in sperm, and perhaps also in the spermathecal cage cells. The prominent localization of HSP16 to intestinal cells was previously noted in transgenic animals expressing a lacZHSP16 gene fusion. Vulval expression of HSP16 was also seen in transgenic reporter experiments. In males, HSP16-2 was distributed more generally, though it was slightly concentrated in the lower testis in the region corresponding to spermatids, and in tail structures. The latter expression pattern was also seen with transgenic reporter constructs.
• Subcellular Localization: Counterstaining with DAPI revealed HSP16 localized in discrete regions within the cytoplasm of intestinal cells, characterized by their large nuclei. Concentrations of HSP16-2 occur along the luminal border of these cells.

• Primary Identifier: Expr2012618
• 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: Expr15517
• Pattern: Most of the small heat shock protein transgenes did not exhibit detectable signals in the epidermis.

• Primary Identifier: Expr1384
• Remark: Express condition: after heat shock.
• Pattern: RNA prepared from non-heat-shocked developmental stages did not contain detectable levels of hsp16 mRNA by Northern ananlysis. After heat shock, hsp16 mRNA was at its highest level in the egg and L1 stages, and lowest in adults. At each stage, mRNA for hsp16-2 gene was more abundant than that for hsp16-1 gene, but the difference was greatest in the egg and L1 stages.

• Primary Identifier: Expr1160170
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2030854
• 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: Expr1200268
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr1018763
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

9 GO Annotation

29 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002016
• Start: 1804334
• End: 1804957
• Strand: -1

9 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 624

1 Sequence Ontology Term

• Name: gene

36 Strains

• WBStrain00022677
• WBStrain00022744
• WBStrain00022745
• WBStrain00022746
• WBStrain00022175
• WBStrain00022174
• WBStrain00023474
• WBStrain00028984
• WBStrain00028982
• WBStrain00028983
• WBStrain00028980
• WBStrain00028981
• WBStrain00028906
• WBStrain00028904
• WBStrain00028909
• WBStrain00028910
• WBStrain00028912
• WBStrain00028952
• WBStrain00029008
• WBStrain00029014
• WBStrain00029013
• WBStrain00029946
• WBStrain00029945
• WBStrain00030548
• WBStrain00030838
• WBStrain00030852
• WBStrain00030720
• WBStrain00034895
• WBStrain00034899
• WBStrain00034984

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_1804958..1805177
• Length (nt): 220
• Chromosome Location: V: 1804958-1805177
• Organism: Caenorhabditis elegans