WormMine: Gene WBGene00003406

• WormBase Gene ID: WBGene00003406
• Gene Name: mrg-1
• Sequence Name: Y37D8A.9
• Brief Description: mrg-1 encodes a chromodomain-containing protein orthologous to mammalian MRG15, an essential mortality factor-related protein that promotes cell proliferation;during development, maternal MRG-1 is required for embryonic viability and for proliferation and survival of primordial germs cells (PGCs); in embryonic and PGC development MRG-1 likely functions as a transcriptional regulator, as loss of mrg-1 activity results in aberrant patterns of gene expression in wild-type and mutant backgrounds in germline and somatic tissues, respectively; MRG-1 is a nuclear protein that localizes to autosomes in a MES-2- and MES-4-independent manner; MRG-1 is present at all stages of development, with expression in embryos and young larvae seen in both germ and somatic cells and expression in older larvae and adults seen primarily in germ cells.
• Organism: Caenorhabditis elegans
• Automated Description: Involved in several processes, including protein localization to euchromatin; regulation of gene expression; and sexual reproduction. Located in autosome. Part of euchromatin. Expressed in several structures, including Caa; Cpa; Ea; Psub4; and somatic cell. Is an ortholog of human MORF4L2 (mortality factor 4 like 2).
• Biotype: SO:0001217
• Genetic Position: III :19.1041 ±0.026236
• Length (nt): 3628

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003406

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y37D8A.9a.1	Y37D8A.9a.1	1499	III: 12871029-12874656
Transcript:Y37D8A.9b.1	Y37D8A.9b.1	1258	III: 12871274-12874654

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y37D8A.9a	Y37D8A.9a	1008	III: 12871518-12871667
CDS:Y37D8A.9b	Y37D8A.9b	1014	III: 12871518-12871667

66 RNAi Result

• WBRNAi00086521
• WBRNAi00061139
• WBRNAi00061141
• WBRNAi00055891
• WBRNAi00055892
• WBRNAi00062996
• WBRNAi00098277
• WBRNAi00022944
• WBRNAi00022945
• WBRNAi00085768
• WBRNAi00086519
• WBRNAi00113478
• WBRNAi00069471
• WBRNAi00006369
• WBRNAi00007165
• WBRNAi00081772
• WBRNAi00081808
• WBRNAi00081837
• WBRNAi00108031
• WBRNAi00022946
• WBRNAi00036793
• WBRNAi00112061
• WBRNAi00112062
• WBRNAi00086523
• WBRNAi00086525
• WBRNAi00086527
• WBRNAi00086531
• WBRNAi00081866
• WBRNAi00086529
• WBRNAi00086532

66 Allele

• gk963887
• gk963904
• gk963552
• gk189261
• gk189263
• gk189262
• gk189265
• gk189264
• gk189266
• gk189268
• gk189267
• qa6200
• gk963763
• gk963762
• WBVar00182258
• h8144
• WBVar02078362
• WBVar01793686
• WBVar01793685
• WBVar00237579
• gk802223
• WBVar01449631
• WBVar01338822
• WBVar01338823
• WBVar01449630
• WBVar01338824
• WBVar01449628
• gk831472
• gk745836
• gk725935

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003406
• Start: 12871029
• End: 12874656
• 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_chrIII_12870298..12871028
• Length (nt): 731
• Chromosome Location: III: 12870298-12871028
• Organism: Caenorhabditis elegans

139 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
	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 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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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_L1-larva_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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:AVE-neuron_L1-larva_expressed
	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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	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
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
	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
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
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 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 altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	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:A-class-motor-neurons_L2-larva_expressed
	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

11 Expression Patterns

• Primary Identifier: Expr4504
• Pattern: MRG-1 is highly enriched in nuclei and concentrated on chromatin. In early embryos, MRG-1 is present in the nuclei of all blastomeres. In late embryos and young larvae, MRG-1 staining is higher in the nuclei of the two primordial germ cells, Z2 and Z3, than in somatic blastomeres. In larvae and adults, MRG-1 staining is seen primarily in the nuclei of germ cells, although it is also faintly visible in the nuclei of several somatic cell types, including intestinal cells. In the adult germ line, all germ nuclei in the mitotic and meiotic regions are stained. These results demonstrate that MRG-1 is present in the germ line at all stages of development and is maternally loaded into embryos. In addition, zygotically expressed MRG-1 is produced in all cells by at least the 100-cell stage; it accumulates to higher levels in the primordial germ cells than in somatic tissues.
• Subcellular Localization: Expressed in nuclei.

• Primary Identifier: Expr1031575
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2013685
• 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: Expr16146
• Pattern: The reporter protein was detected only in somatic cells, beginning around the 50-cell stage, but not in the germline blastomeres. This result strongly suggests that mrg-1 can be transcribed zygotically in somatic cells, but not in the germline, during embryogenesis. mrg-1 3'UTR is responsible for MRG-1 distribution.

• Primary Identifier: Expr1981
• Pattern: The anti-MRG-1 antibody used in this article strongly stained mitotic and meiotic germ cells in adult hermaphrodites. However, since the anti-MRG-1 antibody cross-reacts with an unknown protein of 55 kDa, it is not sure whether MRG-1 is a germline-specific protein. Therefore, the levels of MRG-1 was examined by Western blot analysis in three temperature-sensitive mutants with distinct deficiencies in germline development. These mutant animals show the following phenotypes at the restrictive temperature: in glp-4(bn2) animals, mitosis of PGCs is very slow because of the reduced function of glp-4, resulting in only ten to 20 mitotic germ cells and no meiotic cells in the gonad at the young adult stage. In fem-3(e2006) animals, the male sex-determination pathway is abolished because of the reduced function of fem-3, and only oocytes are produced. In fem-3(q20) animals, the male sex-determination pathway is constitutively activated because of the gain-of-function of fem-3, and only sperms are produced. MRG-1 was detected in all of the mutant adult hermaphrodites at the permissive temperature and also in fem-3(e2006) mutant hermaphrodites at the restrictive temperature at similar levels as in wild-type hermaphrodites. At the restrictive temperature, MRG-1 could not be detected in glp-4(bn2) mutant animals. In fem-3(q20) mutant animals at the restrictive temperature, the level of MRG-1 was significantly reduced. These results demonstrate that MRG-1 is expressed predominantly in oocytes.

• Primary Identifier: Expr14575
• Subcellular Localization: MRG-1 proteins only partially colocalize with LIN-53 in germ cell nuclei

• Primary Identifier: Expr1159415
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1980
• Pattern: MRG-1 was clearly detected in embryos, L1 larvae and adult hermaphrodites, whereas it decreased drastically between the L2 and L4 larval stages. It was suggested that the decrease of MRG-1 in the L2L4 stages is regulated at the level of protein stability because a few smaller antibody-reactive proteins (31 and 28 kDa) appeared as the level of MRG-1 decreased.

• Primary Identifier: Expr16147
• Pattern: MRG-1 protein detected in the PGCs consists essentially of maternally supplied gene product.

• Primary Identifier: Expr1016650
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2031920
• 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).

24 GO Annotation

9 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003406
• Start: 12871029
• End: 12874656
• Strand: -1

24 Ontology Annotations

3 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 decreased 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)_downregulated_PGCs
	Proteins interacting with MRG-1-3xHA according to co-IP mass spectrometry.	N.A.	WBPaper00064159:MRG-1_interacting

1 Sequence

• Length: 3628

1 Sequence Ontology Term