IC4R015-RNA-Seq-2010-20086188 - Revision history

Liman: /* Research Findings */

2016-07-15T06:39:31Z

‎Research Findings

Liman: /* Research Findings */

2016-07-15T06:17:04Z

‎Research Findings

Liman: /* Research Findings */

2016-07-15T05:59:36Z

‎Research Findings

Liman: /* Research Findings */

2016-07-14T16:04:27Z

‎Research Findings

Liman: /* Research Findings */

2016-07-14T13:27:50Z

‎Research Findings

Liman: /* Illumina Sequencing */

2016-07-14T08:02:53Z

‎Illumina Sequencing

Liman: /* Plant Culture & Treatment */

2016-07-14T08:00:30Z

‎Plant Culture & Treatment

Liman: Created page with "==Project Title== * '''Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids''' ==The Background of This Project== * The behavio..."

2016-07-14T07:56:17Z

Created page with "==Project Title== * '''Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids''' ==The Background of This Project== * The behavio..."

New page

==Project Title==
* '''Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids'''

==The Background of This Project==
* The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. In this project, the researchers reported highly integrated maps of the epigenome, mRNA, and small RNA transcriptomes of two rice (Oryza sativa) subspecies and their reciprocal hybrids.

==Plant Culture & Treatment==

==Illumina Sequencing==

==Research Findings==

==Labs working on this Project==
* Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, National Laboratory of Protein Engineering and
Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
* National Institute of Biological Sciences, Beijing 102206, China
* Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
* Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
* Department of Botany, College of Life Sciences, Hunan Normal University, Changsha 410081, China

==Corresponding Author==
* xingwang.deng@yale.edu

@@ Line 17: / Line 17: @@
 [[File:IC4R015-RNA-Seq-2010-20086188-f1.png |center |thumb |800px |'''Figure 1. Correlations between Epigenetic Natural Variations and Changes in Transcript Abundance between Two Parental Lines.''']]
+<br>
 * From 20,638 genes analyzed, 5044 (24.4%, FDR = 0.0041) and 4951 (24.0%, FDR = 0.0042) were identified with differential expression in reciprocal hybrids, most of which showed a nonadditive expression pattern (Figure 2). These data indicate that variations in DNA methylation occur more often than histone modifications in hybrids.
 [[File:IC4R015-RNA-Seq-2010-20086188-f2.png |center |thumb |800px |'''Figure 2. Additive and nonadditive variation in gene expression and epigenetic modifications in hybrids.''']]
-* The researchers found that the small RNA transcriptome differed in composition and expression between hybrid offspring and their inbred parents.
+[[File:IC4R015-RNA-Seq-2010-20086188-f4.png |center |thumb |800px |'''Figure 4. Expression patterns of siRNA clusters in Nip/93-11 hybrid.''']]
 ==Labs working on this Project==

← Older revision		Revision as of 06:17, 15 July 2016
Line 17:		Line 17:

	[[File:IC4R015-RNA-Seq-2010-20086188-f1.png \|center \|thumb \|800px \|'''Figure 1. Correlations between Epigenetic Natural Variations and Changes in Transcript Abundance between Two Parental Lines.''']]		[[File:IC4R015-RNA-Seq-2010-20086188-f1.png \|center \|thumb \|800px \|'''Figure 1. Correlations between Epigenetic Natural Variations and Changes in Transcript Abundance between Two Parental Lines.''']]
		+
		+	* From 20,638 genes analyzed, 5044 (24.4%, FDR = 0.0041) and 4951 (24.0%, FDR = 0.0042) were identified with differential expression in reciprocal hybrids, most of which showed a nonadditive expression pattern (Figure 2). These data indicate that variations in DNA methylation occur more often than histone modifications in hybrids.
		+
		+	[[File:IC4R015-RNA-Seq-2010-20086188-f2.png \|center \|thumb \|800px \|'''Figure 2. Additive and nonadditive variation in gene expression and epigenetic modifications in hybrids.''']]

	* The researchers found that the small RNA transcriptome differed in composition and expression between hybrid offspring and their inbred parents.		* The researchers found that the small RNA transcriptome differed in composition and expression between hybrid offspring and their inbred parents.

@@ Line 11: / Line 11: @@
 * Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions and was treated with RNase-free DNase I (New England Biolabs) to remove any contaminating genomic DNA. mRNA was extracted from total RNA using Dynabeads oligo(dT) (Invitrogen Dynal) following the manufacturer’s directions. First- and secondstrand cDNA were generated using Superscript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the standard Illumina protocol. Small RNAs were gel isolated from total RNA and were used to create libraries for Illumina sequencing as described previously. Genomic DNA extraction, methylated genomic DNA enrichment, and construction of Illumina sequencing libraries were performed as described previously. Chromatin from seedling shoots was immunoprecipitated with antibodies against H3K4me3 (Upstate), H3K9ac (Upstate), or H3K27me3 (Upstate) as described previously. The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer’s protocol.
 ==Research Findings==
-* The researchers found a high frequency of concurrence between gene expression and two activating histone modifications, H3K4me3 and H3K9ac. Interestingly, we also detected a significant frequency of concurrence between gene expression and the repressive mark H3K27me3. The researchers found that most genes with DNA methylation (84.3%) were transcriptionally silent, indicating a strong repressive effect of this epigenetic modification on gene activity. Further inspection revealed that gene expression levels were positively correlated with the ratio of H3K4me3/H3K27me3 and were negatively correlated with the ratio of H3K27me3/H3K4me3, thereby facilitating our understanding of the repressive role of H3K27me3 on gene activity. These analyses suggest that in rice, DNA methylation plays a role in dictating the transcriptional activity of genes and that the combinatorial interactions of histone modifications provide a finetuning of their expression levels.
+* The researchers found a hierarchical relationship of gene expression and epigenetic modifications in the rice genome. The researchers found a high frequency of concurrence between gene expression and two activating histone modifications, H3K4me3 and H3K9ac. Interestingly, we also detected a significant frequency of concurrence between gene expression and the repressive mark H3K27me3. The researchers found that most genes with DNA methylation (84.3%) were transcriptionally silent, indicating a strong repressive effect of this epigenetic modification on gene activity. Further inspection revealed that gene expression levels were positively correlated with the ratio of H3K4me3/H3K27me3 and were negatively correlated with the ratio of H3K27me3/H3K4me3, thereby facilitating our understanding of the repressive role of H3K27me3 on gene activity. These analyses suggest that in rice, DNA methylation plays a role in dictating the transcriptional activity of genes and that the combinatorial interactions of histone modifications provide a finetuning of their expression levels.
-* The researchers found a hierarchical relationship of gene expression and epigenetic modifications in the rice genome.
+* The researchers found that variations in DNA methylation occur more often than for histone modifications between Nipponbare and 93 -11.To investigate the relationship between natural epigenetic variation and changes in transcript abundance, we counted the frequencies of concurrence between differential gene expression and differential modifications (Figure 1). This might indicate that there are differences in combinatorial H3K4me3/H3K27me3 modifications and their effects on gene expression between the two parental inbred lines.
-* The researchers identified abundant epigenetic and transcriptional variations among hybrids and parental inbred lines and found that these two types of polymorphisms correlate.
+* The researchers found that H3K4me3 was strongly positively correlated with differential gene expression (Pearson correlation = 0.776) (Figures 1E and 1G), whereas DNA methylation was negatively correlated with differential gene expression, albeit only weakly (Pearson correlation = 20.314) (Figure 1D). We also observed a weak correlation between differential H3K27me3 modification and differential gene expression (Figure 1F). Furthermore,we detected the same overall correlation patterns between differential gene expression and differential epigenetic modifications when parental inbred lines and their hybrid offspring were compared.
 * The researchers found that the small RNA transcriptome differed in composition and expression between hybrid offspring and their inbred parents.

← Older revision		Revision as of 13:27, 14 July 2016
Line 12:		Line 12:

	==Research Findings==		==Research Findings==
		+	* The researchers found a high frequency of concurrence between gene expression and two activating histone modifications, H3K4me3 and H3K9ac. Interestingly, we also detected a significant frequency of concurrence between gene expression and the repressive mark H3K27me3. The researchers found that most genes with DNA methylation (84.3%) were transcriptionally silent, indicating a strong repressive effect of this epigenetic modification on gene activity. Further inspection revealed that gene expression levels were positively correlated with the ratio of H3K4me3/H3K27me3 and were negatively correlated with the ratio of H3K27me3/H3K4me3, thereby facilitating our understanding of the repressive role of H3K27me3 on gene activity. These analyses suggest that in rice, DNA methylation plays a role in dictating the transcriptional activity of genes and that the combinatorial interactions of histone modifications provide a finetuning of their expression levels.

	==Labs working on this Project==		==Labs working on this Project==

← Older revision		Revision as of 08:02, 14 July 2016
Line 9:		Line 9:

	==Illumina Sequencing==		==Illumina Sequencing==
		+	* Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions and was treated with RNase-free DNase I (New England Biolabs) to remove any contaminating genomic DNA. mRNA was extracted from total RNA using Dynabeads oligo(dT) (Invitrogen Dynal) following the manufacturer’s directions. First- and secondstrand cDNA were generated using Superscript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the standard Illumina protocol. Small RNAs were gel isolated from total RNA and were used to create libraries for Illumina sequencing as described previously. Genomic DNA extraction, methylated genomic DNA enrichment, and construction of Illumina sequencing libraries were performed as described previously. Chromatin from seedling shoots was immunoprecipitated with antibodies against H3K4me3 (Upstate), H3K9ac (Upstate), or H3K27me3 (Upstate) as described previously. The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer’s protocol.

	==Research Findings==		==Research Findings==

← Older revision		Revision as of 08:00, 14 July 2016
Line 6:		Line 6:

	==Plant Culture & Treatment==		==Plant Culture & Treatment==
		+	* Rice cultivar Nipponbare (Oryza sativa ssp japonica) and 93-11 (O. sativa ssp indica) and their reciprocal F1 hybrids (Nipponbare/93-11 and 93-11/ Nipponbare) were used for all experiments in this study. Seeds were grown in soil under 16-h-light/8-h-dark conditions at 288C in a greenhouse. After 4 weeks, seedling shoots at the four-leaf stage were harvested, frozen in liquid nitrogen, and stored at –808C for DNA and total RNA isolation or processed directly after harvesting for ChIP assay.

	==Illumina Sequencing==		==Illumina Sequencing==