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Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq.

Tran NT, Huang CH - Gene Regul Syst Bio (2014)

Bottom Line: Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer.We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions.These genes are not currently in the Ensemble gene database at NCBI.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.

ABSTRACT
Recent study has identified the cis-regulatory elements in the mouse genome as well as their genomic localizations. Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer. In this work, we further identified highly expressed genes by H3K4me3 mark or by both H3K4me3 and H3K4me1 marks in mouse liver using ChIP-Seq and RNA-Seq. We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions. We also identified novel genes in RNA-Seq experiments for mouse liver and for mouse embryonic stem cells. These genes are not currently in the Ensemble gene database at NCBI.

No MeSH data available.


Overlapping and non-overlapping genes from co-localization between ChIP-Seq for H3K4me3 and ChIP-Seq for H3K4me1 in Experiment 4.
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Related In: Results  -  Collection


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f4-grsb-8-2014-033: Overlapping and non-overlapping genes from co-localization between ChIP-Seq for H3K4me3 and ChIP-Seq for H3K4me1 in Experiment 4.

Mentions: As in Experiment 2, we obtained the matched genes between H3K4me3 and H3K4me1 in ChIP-Seq. These matched genes were compared with the genes found in RNA-Seq for obtaining overlapping and non-overlapping genes. Again, all overlapping genes and non-overlapping genes in ChIP-Seq were confirmed in the reference. However, a number of non-overlapping genes in RNA-Seq were not found in the reference. We also verified a number of genes that were not located in the reference using the Entrez Gene website and the results are shown as reported in Experiment 1. All comparison results are in Table 1 and Figure 4. All novel genes found are included in Additional file 3.xls.


Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq.

Tran NT, Huang CH - Gene Regul Syst Bio (2014)

Overlapping and non-overlapping genes from co-localization between ChIP-Seq for H3K4me3 and ChIP-Seq for H3K4me1 in Experiment 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3921077&req=5

f4-grsb-8-2014-033: Overlapping and non-overlapping genes from co-localization between ChIP-Seq for H3K4me3 and ChIP-Seq for H3K4me1 in Experiment 4.
Mentions: As in Experiment 2, we obtained the matched genes between H3K4me3 and H3K4me1 in ChIP-Seq. These matched genes were compared with the genes found in RNA-Seq for obtaining overlapping and non-overlapping genes. Again, all overlapping genes and non-overlapping genes in ChIP-Seq were confirmed in the reference. However, a number of non-overlapping genes in RNA-Seq were not found in the reference. We also verified a number of genes that were not located in the reference using the Entrez Gene website and the results are shown as reported in Experiment 1. All comparison results are in Table 1 and Figure 4. All novel genes found are included in Additional file 3.xls.

Bottom Line: Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer.We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions.These genes are not currently in the Ensemble gene database at NCBI.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.

ABSTRACT
Recent study has identified the cis-regulatory elements in the mouse genome as well as their genomic localizations. Recent discoveries have shown the enrichment of H3 lysine 4 trimethylation (H3K4me3) binding as an active promoter and the presence of H3 lysine 4 monomethylation (H3K4me1) outside promoter regions as a mark for an enhancer. In this work, we further identified highly expressed genes by H3K4me3 mark or by both H3K4me3 and H3K4me1 marks in mouse liver using ChIP-Seq and RNA-Seq. We found that in mice, the liver carries embryonic stem cell-related functions while the embryonic stem cell also carries liver-related functions. We also identified novel genes in RNA-Seq experiments for mouse liver and for mouse embryonic stem cells. These genes are not currently in the Ensemble gene database at NCBI.

No MeSH data available.