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Enrichment of H3K9me2 on Unsynapsed Chromatin in Caenorhabditis elegans Does Not Target de Novo Sites.

Guo Y, Yang B, Li Y, Xu X, Maine EM - G3 (Bethesda) (2015)

Bottom Line: Loss of the SET domain protein, MET-2, greatly reduces H3K9me2 abundance and results in germline mortality.These results suggest that MET-2 activity is elevated in him-8 mutants generally as well as targeted preferentially to the unsynapsed X.We hypothesize H3K9me2 may have a structural function critical for germline immortality, and a greater abundance of these marks may be required when a chromosome does not synapse.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Syracuse University, Syracuse, New York 13244.

No MeSH data available.


Related in: MedlinePlus

The effect of histone H3 lysine 9 dimethylation (H3K9me2) loss on the adult hermaphrodite gonad transcriptome. (A) Scatter plot represents the transcriptome data from him-8 gonads vs.met-2;him-8 gonads. Transcripts present at a statistically different level are highlighted in red if more highly expressed in met-2;him-8 and blue if more highly expressed in him-8. X- and Y-axis scale is expressed in RPKM (see text). (B) The table lists the number of genes on each chromosome with transcripts that are differentially abundant in met-2; him-8vs.him-8 gonads. These represent the highlighted transcripts in (A). (C) Screen shots of representative differential transcripts: clec-85 transcripts are elevated in met-2;him-8 and egl-30 transcripts are reduced in met-2;him-8. Transcripts from adjacent genes, Y54G2A.16 and emr-1, are statistically unchanged. (D) Chromosomal distribution of genes whose transcripts are differentially abundant in met-2;him-8vs.him-8. Lines extending upward indicate transcripts that are more abundant in met-2; him-8, and lines extending downward indicate transcripts that are less abundant in met-2;him-8. Longer lines represent “genotype-specific” genes whose transcripts are detected in one genotype and not the other. Shorter lines represent genotype-regulated genes whose transcripts are more abundant in one genotype than the other; their length is proportional to the log2 value of the fold-change.
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fig7: The effect of histone H3 lysine 9 dimethylation (H3K9me2) loss on the adult hermaphrodite gonad transcriptome. (A) Scatter plot represents the transcriptome data from him-8 gonads vs.met-2;him-8 gonads. Transcripts present at a statistically different level are highlighted in red if more highly expressed in met-2;him-8 and blue if more highly expressed in him-8. X- and Y-axis scale is expressed in RPKM (see text). (B) The table lists the number of genes on each chromosome with transcripts that are differentially abundant in met-2; him-8vs.him-8 gonads. These represent the highlighted transcripts in (A). (C) Screen shots of representative differential transcripts: clec-85 transcripts are elevated in met-2;him-8 and egl-30 transcripts are reduced in met-2;him-8. Transcripts from adjacent genes, Y54G2A.16 and emr-1, are statistically unchanged. (D) Chromosomal distribution of genes whose transcripts are differentially abundant in met-2;him-8vs.him-8. Lines extending upward indicate transcripts that are more abundant in met-2; him-8, and lines extending downward indicate transcripts that are less abundant in met-2;him-8. Longer lines represent “genotype-specific” genes whose transcripts are detected in one genotype and not the other. Shorter lines represent genotype-regulated genes whose transcripts are more abundant in one genotype than the other; their length is proportional to the log2 value of the fold-change.

Mentions: We compared the him-8 and met-2;him-8 gonad transcriptomes to each other. We calculated the RPKM (Reads Per Kilobase of transcript per Million mapped reads) for each transcript in our mRNA-seq datasets. For purposes of comparing the him-8 and met-2;him-8 transcriptomes, we considered transcripts present at a relatively permissive cut-off value of >0.5 RPKM. A transcript was defined as present at a significantly different level in him-8vs.met-2;him-8 if the Cuffdiff q-value was <0.05 (see the section Materials and Methods). The vast majority of transcripts were present at statistically similar levels in both datasets; however we did identify a set of 181 differentially expressed transcripts (Figure 7) that fall into two classes. Transcripts from 108 genes were detected in only one genotype (RPKM = 0 in the other genotype); we refer to these as genotype-specific transcripts. Transcripts from 73 genes were detected in both genotypes, but at significantly different levels; we refer to these as genotype-regulated transcripts. The log2 fold-change of genotype-regulated transcripts ranged from 5.3 (40-fold) to 0.96 (1.9-fold). These 181 differentially regulated genes are distributed across the genome (Figure 7D).


Enrichment of H3K9me2 on Unsynapsed Chromatin in Caenorhabditis elegans Does Not Target de Novo Sites.

Guo Y, Yang B, Li Y, Xu X, Maine EM - G3 (Bethesda) (2015)

The effect of histone H3 lysine 9 dimethylation (H3K9me2) loss on the adult hermaphrodite gonad transcriptome. (A) Scatter plot represents the transcriptome data from him-8 gonads vs.met-2;him-8 gonads. Transcripts present at a statistically different level are highlighted in red if more highly expressed in met-2;him-8 and blue if more highly expressed in him-8. X- and Y-axis scale is expressed in RPKM (see text). (B) The table lists the number of genes on each chromosome with transcripts that are differentially abundant in met-2; him-8vs.him-8 gonads. These represent the highlighted transcripts in (A). (C) Screen shots of representative differential transcripts: clec-85 transcripts are elevated in met-2;him-8 and egl-30 transcripts are reduced in met-2;him-8. Transcripts from adjacent genes, Y54G2A.16 and emr-1, are statistically unchanged. (D) Chromosomal distribution of genes whose transcripts are differentially abundant in met-2;him-8vs.him-8. Lines extending upward indicate transcripts that are more abundant in met-2; him-8, and lines extending downward indicate transcripts that are less abundant in met-2;him-8. Longer lines represent “genotype-specific” genes whose transcripts are detected in one genotype and not the other. Shorter lines represent genotype-regulated genes whose transcripts are more abundant in one genotype than the other; their length is proportional to the log2 value of the fold-change.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4555223&req=5

fig7: The effect of histone H3 lysine 9 dimethylation (H3K9me2) loss on the adult hermaphrodite gonad transcriptome. (A) Scatter plot represents the transcriptome data from him-8 gonads vs.met-2;him-8 gonads. Transcripts present at a statistically different level are highlighted in red if more highly expressed in met-2;him-8 and blue if more highly expressed in him-8. X- and Y-axis scale is expressed in RPKM (see text). (B) The table lists the number of genes on each chromosome with transcripts that are differentially abundant in met-2; him-8vs.him-8 gonads. These represent the highlighted transcripts in (A). (C) Screen shots of representative differential transcripts: clec-85 transcripts are elevated in met-2;him-8 and egl-30 transcripts are reduced in met-2;him-8. Transcripts from adjacent genes, Y54G2A.16 and emr-1, are statistically unchanged. (D) Chromosomal distribution of genes whose transcripts are differentially abundant in met-2;him-8vs.him-8. Lines extending upward indicate transcripts that are more abundant in met-2; him-8, and lines extending downward indicate transcripts that are less abundant in met-2;him-8. Longer lines represent “genotype-specific” genes whose transcripts are detected in one genotype and not the other. Shorter lines represent genotype-regulated genes whose transcripts are more abundant in one genotype than the other; their length is proportional to the log2 value of the fold-change.
Mentions: We compared the him-8 and met-2;him-8 gonad transcriptomes to each other. We calculated the RPKM (Reads Per Kilobase of transcript per Million mapped reads) for each transcript in our mRNA-seq datasets. For purposes of comparing the him-8 and met-2;him-8 transcriptomes, we considered transcripts present at a relatively permissive cut-off value of >0.5 RPKM. A transcript was defined as present at a significantly different level in him-8vs.met-2;him-8 if the Cuffdiff q-value was <0.05 (see the section Materials and Methods). The vast majority of transcripts were present at statistically similar levels in both datasets; however we did identify a set of 181 differentially expressed transcripts (Figure 7) that fall into two classes. Transcripts from 108 genes were detected in only one genotype (RPKM = 0 in the other genotype); we refer to these as genotype-specific transcripts. Transcripts from 73 genes were detected in both genotypes, but at significantly different levels; we refer to these as genotype-regulated transcripts. The log2 fold-change of genotype-regulated transcripts ranged from 5.3 (40-fold) to 0.96 (1.9-fold). These 181 differentially regulated genes are distributed across the genome (Figure 7D).

Bottom Line: Loss of the SET domain protein, MET-2, greatly reduces H3K9me2 abundance and results in germline mortality.These results suggest that MET-2 activity is elevated in him-8 mutants generally as well as targeted preferentially to the unsynapsed X.We hypothesize H3K9me2 may have a structural function critical for germline immortality, and a greater abundance of these marks may be required when a chromosome does not synapse.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Syracuse University, Syracuse, New York 13244.

No MeSH data available.


Related in: MedlinePlus