WormMine: Gene WBGene00003312

• WormBase Gene ID: WBGene00003312
• Gene Name: mir-84
• Sequence Name: B0395.4
• Brief Description: mir-84 encodes a microRNA, a small non-protein coding RNA that appears to be conserved in Drosophila and humans; mir-84 is similar in sequence to the let-7 stRNA suggesting they may have the same target sites; mir-84 seems to act redundantly with other members of the let-7 family, mir-48 and mir-241 to control the L2 larval to L3 larval stage transition and larval to adult transition; an overexpression of mir-84 results in abnormal vulval and uterine morphologies; a mir-84-gfp fusion construct is expressed temporally in cells that give rise to the vulva and uterus; mir-84 is expressed starting from the L2 larval stage; mir-84 expression is promoted by lin-4.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable translation repressor activity. Involved in several processes, including miRNA-mediated gene silencing by inhibition of translation; negative regulation of Ras protein signal transduction; and positive regulation of development, heterochronic. Expressed in several structures, including P5.ppp; gonad; somatic gonad precursor; touch receptor neurons; and vulval precursor cell. Used to study Parkinson's disease.
• Biotype: SO:0001265
• Genetic Position: X :23.6761 ±0.082927
• Length (nt): 75

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003312

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:B0395.4b	B0395.4b	23	X: 16022410-16022432
Transcript:B0395.4a	B0395.4a	24	X: 16022447-16022470

Other

0 CDSs

0 RNAi Result

11 Allele

• gk964260
• gk962707
• gk963810
• gk963581
• gk963633
• gk962525
• gk962524
• gk473
• tm1304
• zen194
• n4037

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003312
• Start: 16022404
• End: 16022478
• Strand: -1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_16021756..16022403
• Length (nt): 648
• Chromosome Location: X: 16021756-16022403
• Organism: Caenorhabditis elegans

24 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure.	Small RNAs (21-26nt) that showed significantly increased expression after L4 animals were exposed to P .aeruginosa strain PA14 for 24 hours.	DESeq2, FDR < 0.05	WBPaper00056868:P.aeruginosa_upregulated_smallRNA
	Potental DAF-12 target genes identified by ChIP-chip analysis performed on strain ALF4 [daf-12	Affymetrix TAS software that computed for each probe estimates of fold enrichment (in linear scale) over hybridization with input DNA. At the same time, TAS calculated for each probe a p-value by applying a Wilcoxon signed rank test. A threshold of 2.5 was selected, which corresponds to probe intensities approximately 2.5 times stronger on the ChIP array than on the Input array. Additional TAS threshold parameters were MinRun=180 bp, MaxGap=300 bp. TAS analysis showed that the selected threshold of 2.5 corresponds approximately to a p-value of 0.01.	WBPaper00040221:DAF-12_target_ALF4
	Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in intestine.	Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2.	WBPaper00066447:Day8_vs_Day1_downregulated_intestine
	Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in coelomocyte.	Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2.	WBPaper00066447:Day8_vs_Day1_downregulated_coelomocyte
	miRNAs that showed significantly increased expression in pry-1(mu38) comparing to in N2.	Fold change > 2, FDR < 0.05	WBPaper00057033:pry-1(mu38)_upregulated
	Micro RNAs that showed significantly increased expression in hrpk-1(tm5522) comparing to in N2 at L4 larva stage.	DESeq, fold change > 2, p-value <= 0.05.	WBPaper00058673:hrpk-1(tm5522)_upregulated_miRNA_L4
	MicroRNAs that showed significantly decreased expression in alg-5(ram2), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(ram2)_downregulated_miRNA
	miRNAs that showed increased expression in 1 day post L4 adult hermaphrodite eat-2(ad1116) comparing to in N2.	A fold change >= 1.5 with a minimum read count of >= 10 were used to filter the differentially expressed miRNA. The p-value cutoff was set at p <= 0.05 based on Kals Z test statistical.	WBPaper00046156:eat-2(ad1116)_Day1_upregulated
	MicroRNAs that showed significantly decreased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_downregulated_miRNA
	MicroRNAs that showed significantly decreased expression in alg-2(ok304), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-2(ok304)_downregulated_miRNA
	MicroRNAs that showed significantly increased expression in alg-2(ok304), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-2(ok304)_upregulated_miRNA
	MicroRNAs that showed significantly decreased expression in alg-5(tm1163), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(tm1163)_downregulated_miRNA
Heat Shock: 35C 4 hours at L4 larva stage.	Micro RNAs that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_miRNA
	MicroRNAs that showed significantly increased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite.	Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method.	WBPaper00053318:mir-71(n4115)_upregulated_miRNA
Bacteria infection: Pseudomonas aeruginosa PA14	miRNAs up regulated by Pseudomonas aeruginosa infection.	N.A.	WBPaper00046303:P.aeruginosa_upregulated_miRNA
	Micro RNAs that showed significantly increased expression in hrpk-1(zen17) comparing to in N2 at embryo stage.	DESeq, fold change > 2, p-value <= 0.05.	WBPaper00058673:hrpk-1(zen17)_upregulated_miRNA_embryo
	MicroRNAs that showed significantly increased expression in alg-5(tm1163), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(tm1163)_upregulated_miRNA
	MicroRNAs that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated_miRNA
	Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in neuron.	Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2.	WBPaper00066447:Day8_vs_Day1_downregulated_neuron
Temperature Shift: 35 centigrade for 4 hours.	miRNAs down regulated after 4 hours of exposure to 35C.	miRNAs with > 1.9 fold change in expression were considered differentially expressed.	WBPaper00046567:HeatStress_downregulated
	miRNAs that showed decreased expression after 100ug\/L microcystin-LR exposure.	Differentially expressed miRNA-genes were identified using the Student t-test. Changes in miRNA gene expression were considered statistically significant if the p-value was less than 0.1 and the fold-change compared to the control was at least <= 0.83 or >= 1.2.	WBPaper00045807:microcystin-LR_downregulated_miRNA
space radition and microgravity	Micro RNAs that showed decreased expression in space flight N2 samples comparing to in ground control, affected by space radition and microgravity.	Differentially expressed miRNAs (>1.5-fold change and <0.67) and mRNAs (>2-fold change and <0.5) were identified through fold-change filtering.	WBPaper00048474:SpaceRadiation-Microgravity_downregulated_N2
space radition	Micro RNAs that showed decreased expression in space flight N2 samples (animals were put in a centrifugal device in space) comparing to in ground control, affected by space radition but not microgravity.	Differentially expressed miRNAs (>1.5-fold change and <0.67) and mRNAs (>2-fold change and <0.5) were identified through fold-change filtering.	WBPaper00048474:SpaceRadiation_downregulated_N2

13 Expression Patterns

• Primary Identifier: Expr4327
• Remark: No obvious difference in expression was observed between this particular mir-84::gfp fusion gene and one in which 8.1 kb of sequence upstream of mir-84 was fused to yellow fluorescent protein, kindly provided by A. Yoo and I. Greenwald.
• Pattern: Transgenic mgEx674[mir-84::gfp] animals expressed GFP in the lateral hypodermal seam cells and other cells. The mir-84::gfp reporter was expressed in seam cells during early larval stages in some transgenic animals, although expression was more prevalent in L3-stage and older animals.

• Primary Identifier: Expr8479
• Pattern: Expression seen from L1 to adult stages. Strong expression seen is pharynx, vulva and rectal glands. Weak expression seen in hypodermis and seam cells. Also seen in canal nerves, spermatheca/uterine valve and head neuron. Posterior intestine expression also detected.

• Primary Identifier: Expr10880
• Pattern: mir-84 is expressed in AVM and ALM touch neurons.

• Primary Identifier: Expr8405
• Remark: Picture: Fig 2A.
• Pattern: Northern blot temporal expression: L1 to adult.

• Primary Identifier: Expr3472
• Remark: mir-84::gfp expression was observed in all the VPCs except for P6.p at the stage when their fate in vulval development is determined by signaling from the AC, suggesting that mir-84 could play a role in vulval cell fate determination. A second let-7 family member, mir-48, was also expressed in non-P6.p VPCs, suggesting the potential for redundancy between mir-48 and mir-84 in the VPCs.
• Pattern: mir-84::gfp was first observed in the somatic gonad in larval stage 1 (L1). In L3 animals, strong expression was observed in uterine cells including the anchor cell (AC), and weak dynamic expression was observed in the vulval precursor cells (VPCs). mir-84::gfp expression was observed during the early to mid L3 stage in all the VPCs except for P6.p, in which expression was rarely observed. Subsequent VPC expression in the mid to late L3 stage was restricted to the daughters (Pn.px) of P5.p and P7.p with weaker GFP first appearing in the P6.p daughters just before their division into P6.pxx. Thereafter, equivalent expression was observed in the granddaughters (Pn.pxx) of P5.p, P6.p, and P7.p. In the L4 stage, GFP expression was maintained in the AC and other uterine cells, appeared weakly in hypodermal seam cells, and was upregulated to higher levels in many P5.p to P7.p descendants.

• Primary Identifier: Expr12247
• Pattern: mir-84 temporal expression was observed in the hypodermal seam cells at the early L4 stage, similar to let-7 seam cell expression. mir-84 was expressed at the L1 stage in the Z1 and Z4 cells of the gonad, and during the L3 stage in the distal tip cells and uterine cells of the somatic gonad. mir-84 expression was additionally observed in the sheath cells, the spermatheca, the uterine cells surrounding the eggs. In addition, the lin-4 family member, mir- 237, and the let-7 family member, mir- 84, were both expressed in the anchor cell and in the VPCs except P6.p at the mL3 stage. However, expression of mir-84 in the vulval precursor cells appeared dynamic in nature and was detected in the P5.p, P6.p, and P7.p descendants but down-regulated in the P3.p, P4.p, and P8.p descendants by the end of the L3 stage (Johnson et al., 2005). It is interesting to note that expression of mir-237, mir-84, and mir-48 was absent in the P6.p cell during the mid- to late L3 stage, and expression of mir-237 and mir-84 but not mir-48 was present in the anchor cell.

• Primary Identifier: Expr13544
• Pattern: Neurons in the head (close to pharynx) and in the tail.

• Primary Identifier: Expr12025
• Remark: Figure S4.
• Pattern: pri-mir-84 levels are highest near the molt and peak out of phase with the other pri-miRNAs analyzed, suggesting that mir-84 is controlled by a different regulatory regime than that of its paralogs.

• Primary Identifier: Expr3740
• Pattern: Previous study reported that the let-7 family members, miR-84, miR-48, and miR-241, were expressed in a similar manner as the let-7 RNA, which was first detected during the L3 stage. However, this paper reveal that miR-241 and miR-48 both appeared one stage earlier than let-7 at eL2 with robust expression by L3. miR-84 appeared at low levels in the early L1 stage, was upregulated to an intermediate level in mid-L2, and had a high level of expression in early L4.

• Primary Identifier: Expr3773
• Remark: Previous studies did not detect the four let-7 family members until the L3 stage, but earlier expression of all four microRNAs was detected by enhancing the sensitivity of detection.
• Pattern: When normalized to U6 expression, miR-84 reached half-maximal expression at about the L3 stage.

• Primary Identifier: Expr2523
• Pattern: No signal detected in embryos, L1 and L2 larva. Intense signals detected in L3, L4 larva, adults, and glp-4(bn2) adults.

• Primary Identifier: Expr12019

• Primary Identifier: Expr1668
• Pattern: Expressed in L3, L4 and adults.

5 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003312
• Start: 16022404
• End: 16022478
• Strand: -1

5 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 75

1 Sequence Ontology Term