Epigenomic Studies in Rice - Revision history

Zhennan at 02:16, 28 June 2016

2016-06-28T02:16:29Z

Zhennan at 09:52, 27 June 2016

2016-06-27T09:52:52Z

Xysj1990: /* Epigenetic changes in stress */

2016-06-22T07:37:31Z

‎Epigenetic changes in stress

Xysj1990: /* Projects List */

2016-06-22T04:40:35Z

‎Projects List

Xysj1987: Created page with "==What is Epigenome ? == * An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an org..."

2016-06-21T04:33:57Z

Created page with "==What is Epigenome ? == * An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an org..."

New page

==What is Epigenome ? ==
* An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism's offspring via transgenerational epigenetic inheritance. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome. The epigenome is involved in regulating gene expression, development, tissue differentiation, and suppression of transposable elements. Unlike the underlying genome which is largely static within an individual, the epigenome can be dynamically altered by environmental conditions<ref name="ref1"/>.
== Overview of Epigenomic Studies in Rice ==
* During recent years rice genome-wide epigenomic information such as DNA methylation and histone modifications, which are important for genome activity has been accumulated. The function of a number of rice epigenetic regulators has been studied, many of which are found to be involved in a diverse range of developmental and stress–responsive pathways. Analysis of epigenetic variations among different rice varieties indicates that epigenetic modification may lead to inheritable phenotypic variation. Characterizing phenotypic consequences of rice epigenomic variations and the underlining chromatin mechanism and identifying epialleles related to important agronomic traits may provide novel strategies to enhance agronomically favorable traits and grain productivity in rice.
* Rice epigenomic studies revealed both general and specific features, profiling additional chromatin modification patterns in a tissue-specific and cell-specific manner will help to largely refine the rice epigenomic architecture. Rice is rich in germplasm resources including large collections of cultivated rice and their wild relatives, in which variations in morphological and adaptive traits may be related to epimutations. Therefore, investigating rice and other Oryza epigenomes will be important to identify specific epigenetic marks and epialleles involved in the emergence of important agronomic traits. The identification of most of the epialleles was based on DNA methylation variation. It will be necessary to investigate whether histone modification is involved in transgenerational inheritance of adaptive traits. Functional characterization of the full set of rice chromatin modification regulators will be essential to understand the mechanism of establishment, maintenance, recognition and inheritance or erasure of rice epigenomes. This may unravel mechanisms on how epigenomic marks corresponding to specialized plant cell types or responding to specific environmental cues can be memorized during subsequent cell divisions and inherited in following generations.<br><br>
[[File: IC4R-Epigenomic-overview-1.png|center|thumb|870px|'''Figure 1. Models of epigenetic mark changes over genes induced by environmental signals (A), and transposons induced by stresses in rice (B).''']]

== Epigenetic changes in stress==
* Natural plant populations are constantly exposed to environmental changes. Because they are sessile organisms, they cannot move away from stressful environments. For this reason, plants have developed intricate mechanisms enabling them to respond and adapt to recurring biotic and abiotic stresses [6]. In nature, stresses do not generally arise in isolation but often cross-talk with each other. Plants can mitigate the effects of stresses by regulating various genes of diverse and shared pathways, which allows them to combat and tolerate stress conditions. The basic information that determines the biological behavior of a plant is contained in its genome. New gene combinations, arising from genetic recombination, can enhance the plant's tolerance or resistance to environmental stresses. However, the rate of environmental change is faster than the rate of new gene combinations [13].In this context, genetic changes in plant genomes have to cope with the different types of stress to which they are exposed.
[[File: IC4R-Epigenomic-overview-2.png|center|thumb|870px|'''Figure 2. Cross-talk between epigenetic changes to promote gene regulation for stress tolerance. Stress signals can activate or repress gene expression, which can also be modulated by epigenetic changes. DNA methylation, histone modifications and npcRNAs may work together or alone to target negative gene regulators of stress tolerance. They may also induce target positive gene regulators of stress tolerance, resulting in the accumulation of gene products. Both mechanisms will lead to stress tolerance of the plant.''']]
* Nuclear DNA has important levels of organization responsible for perpetuating genetic information across generations. This organization is provided by the chromatin structure, which is composed of nucleosomes. Nucleosomes are formed by the interaction of proteins, called histones, with DNA. An octamer of core histones, containing two molecules each of the proteins H2A, H2B, H3 and H4, interacts with 146 base pairs (bp) of DNA that is wrapped around the octamer [36]. This organization allows for complete accommodation of the DNA in the nucleus and for the regulation of gene activity. According to the level of condensation, chromatin can be classified into two groups: euchromatin and heterochromatin. The condensed chromatin, known as heterochromatin, is characterized by holding transcriptionally silent repeats and transposons. A very large proportion of genomic DNA is found in the heterochromatin state. Open chromatin, denominated euchromatin, is characterized as gene rich and transcriptionally active [37]. Changes of transcriptional states are coupled with chromatin remodeling, which is accompanied by epigenetic marks. These epigenetic marks represent heritable and reversible changes that do not alter the original DNA sequence. Several types of modifications have been reported as epigenetic marks, mainly DNA methylation, histone modifications and small RNAs. Epigenetic marks have great importance in adaptation to environmental changes that require a complex orchestration of the transcriptional output of the genome.
==Projects List==

{|class="wikitable sortable" style="width:100%;text-align:center"
|-
!Project Title
!Species
!Published years
!Academic Journal
!RiceWiki Project ID
|-
|'''High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression '''
|''Oryza sativa'' L. ssp. ''Japnoica''
|2008
|The Plant Cell
|[[IC4R001-Epigenomic-2008-18263775]]
|-
|'''Local DNA hypomethylation activates genes in rice endosperm'''
|''Oryza sativa cultivars''
|2010
|Proceedings of the National Academy of Sciences
|[[IC4R002-Epigenomic-2010-20937895]]
|-
|'''Comparison of Four ChIP-Seq Analytical Algorithms Using Rice Endosperm H3K27 Trimethylation Profiling Data'''
|''Oryza sativa'' L. ssp. ''Japnoica''
|2011
|PLoS ONE
|[[IC4R003-Epigenomic-2011-21984925]]
|-
|'''Transcriptome and methylome interactions in rice hybrids'''
|''Oryza sativa'' L. ssp. ''Japnoica''
|2012
|Proceedings of the National Academy of Sciences
|[[IC4R004-Epigenomic-2012-22778444]]
|-
|'''Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice'''
|''Oryza sativa'' L. ssp. ''Japnoica''
|2010
|The Plant Journal
|[[IC4R005-Epigenomic-2016-20487381]]
|-
|'''High-resolution mapping of open chromatin in the rice genome'''
|''Oryza sativa'' L. ssp. ''Japnoica''
|2016
|Genome Research
|[[IC4R006-Epigenomic-2016-22110044]]
|}
==References==
<references>
<ref name="ref1">
https://en.wikipedia.org/wiki/Epigenome
</ref>
</references>

@@ Line 66: / Line 66: @@
 |''Oryza sativa''
 |2012
-|J Genet Genomics
+|Journal of Genetics and Genomics
 |'''[[IC4R008-Epigenomic-2012- 22835977]]'''
 |-
@@ Line 72: / Line 72: @@
 |''Oryza sativa''
 |2013
-|Curr Opin Plant Biol
+|Current Opinion in Plant Biology
 |'''[[IC4R009-Epigenomic-2013-23562565]]'''
 |-
@@ Line 84: / Line 84: @@
 |''Oryza sativa''
 |2015
-|Mol Breeding
+|Molecular Breeding
 |'''[[IC4R011-Epigenomic-2015-11001567]]'''
 |}

@@ Line 56: / Line 56: @@
 |Genome Research
 |'''[[IC4R006-Epigenomic-2016-22110044]]'''
 |}

@@ Line 7: / Line 7: @@
 == Epigenetic changes in stress==
-* Natural plant populations are constantly exposed to environmental changes. Because they are sessile organisms, they cannot move away from stressful environments. For this reason, plants have developed intricate mechanisms enabling them to respond and adapt to recurring biotic and abiotic stresses [6]. In nature, stresses do not generally arise in isolation but often cross-talk with each other. Plants can mitigate the effects of stresses by regulating various genes of diverse and shared pathways, which allows them to combat and tolerate stress conditions. The basic information that determines the biological behavior of a plant is contained in its genome. New gene combinations, arising from genetic recombination, can enhance the plant's tolerance or resistance to environmental stresses. However, the rate of environmental change is faster than the rate of new gene combinations [13].In this context, genetic changes in plant genomes have to cope with the different types of stress to which they are exposed.
+* Natural plant populations are constantly exposed to environmental changes. Because they are sessile organisms, they cannot move away from stressful environments. For this reason, plants have developed intricate mechanisms enabling them to respond and adapt to recurring biotic and abiotic stresses [6]. In nature, stresses do not generally arise in isolation but often cross-talk with each other. Plants can mitigate the effects of stresses by regulating various genes of diverse and shared pathways, which allows them to combat and tolerate stress conditions. The basic information that determines the biological behavior of a plant is contained in its genome. New gene combinations, arising from genetic recombination, can enhance the plant's tolerance or resistance to environmental stresses. However, the rate of environmental change is faster than the rate of new gene combinations [13].In this context, genetic changes in plant genomes have to cope with the different types of stress to which they are exposed.<br><br>
 [[File: IC4R-Epigenomic-overview-2.png|center|thumb|870px|'''Figure 2. Cross-talk between epigenetic changes to promote gene regulation for stress tolerance. Stress signals can activate or repress gene expression, which can also be modulated by epigenetic changes. DNA methylation, histone modifications and npcRNAs may work together or alone to target negative gene regulators of stress tolerance. They may also induce target positive gene regulators of stress tolerance, resulting in the accumulation of gene products. Both mechanisms will lead to stress tolerance of the plant.''']]
 * Nuclear DNA has important levels of organization responsible for perpetuating genetic information across generations. This organization is provided by the chromatin structure, which is composed of nucleosomes. Nucleosomes are formed by the interaction of proteins, called histones, with DNA. An octamer of core histones, containing two molecules each of the proteins H2A, H2B, H3 and H4, interacts with 146 base pairs (bp) of DNA that is wrapped around the octamer [36]. This organization allows for complete accommodation of the DNA in the nucleus and for the regulation of gene activity. According to the level of condensation, chromatin can be classified into two groups: euchromatin and heterochromatin. The condensed chromatin, known as heterochromatin, is characterized by holding transcriptionally silent repeats and transposons. A very large proportion of genomic DNA is found in the heterochromatin state. Open chromatin, denominated euchromatin, is characterized as gene rich and transcriptionally active [37]. Changes of transcriptional states are coupled with chromatin remodeling, which is accompanied by epigenetic marks. These epigenetic marks represent heritable and reversible changes that do not alter the original DNA sequence. Several types of modifications have been reported as epigenetic marks, mainly DNA methylation, histone modifications and small RNAs. Epigenetic marks have great importance in adaptation to environmental changes that require a complex orchestration of the transcriptional output of the genome.
 ==Projects List==

@@ Line 24: / Line 24: @@
 |2008
 |The Plant Cell
-|[[IC4R001-Epigenomic-2008-18263775]]
+|'''[[IC4R001-Epigenomic-2008-18263775]]'''
 |-
 |'''Local DNA hypomethylation activates genes in rice endosperm'''
@@ Line 30: / Line 30: @@
 |2010
 |Proceedings of the National Academy of Sciences
-|[[IC4R002-Epigenomic-2010-20937895]]
+|'''[[IC4R002-Epigenomic-2010-20937895]]'''
 |-
 |'''Comparison of Four ChIP-Seq Analytical Algorithms Using Rice Endosperm H3K27 Trimethylation Profiling Data'''
@@ Line 36: / Line 36: @@
 |2011
 |PLoS ONE
-|[[IC4R003-Epigenomic-2011-21984925]]
+|'''[[IC4R003-Epigenomic-2011-21984925]]'''
 |-
 |'''Transcriptome and methylome interactions in rice hybrids'''
@@ Line 42: / Line 42: @@
 |2012
 |Proceedings of the National Academy of Sciences
-|[[IC4R004-Epigenomic-2012-22778444]]
+|'''[[IC4R004-Epigenomic-2012-22778444]]'''
 |-
 |'''Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice'''
@@ Line 48: / Line 48: @@
 |2010
 |The Plant Journal
-|[[IC4R005-Epigenomic-2016-20487381]]
+|'''[[IC4R005-Epigenomic-2016-20487381]]'''
 |-
 |'''High-resolution mapping of open chromatin in the rice genome'''
@@ Line 54: / Line 54: @@
 |2016
 |Genome Research
-|[[IC4R006-Epigenomic-2016-22110044]]
+|'''[[IC4R006-Epigenomic-2016-22110044]]'''
 |}
 ==References==
 <references>