Control of the Transition to Flowering by Chromatin Modifications

The timing of floral transition is critical to reproductive success in angiosperms and is genetically controlled by a network of flowering genes. In Arabidopsis, expression of certain flowering genes is regulated by various chromatin modifications, among which are two central regulators of flowering, namely FLOWERING LOCUS C （FLC） and FLOWERING LOCUS T（FT）. Recent studies have revealed that a number of chromatin-modifying components are involved in activation or repression of FLC expression. Activation of FLC expression is associated with various ＇active＇ chromatln modifications including acetylation of core histone tails, histone H3 lysine-4 （H3K4） methylation, H2B monoubiquitination, H3 lysine-36 （H3K36） di- and tri-methylation and deposition of the histone variant H2A.Z, whereas various ＇repressive＇ histone mod- ifications are associated with FLC repression, including histone deacetylation, H3K4 demethylation, histone H3 lysine-9 （H3K9） and H3 lysine-27 （H3K27） methylation, and histone arginine methylation. In addition, recent studies have revealed that Polycomb group gene-mediated transcriptional-silencing mechanism not only represses FLC expression, but also directly represses FTexpression. Regulation of FLC expression provides a paradigm for control of the expression of other developmental genes in plants through chromatin mechanisms.

Patterns of Chromatin-Modifications Discriminate Different Genomic Features in Arabidopsis

Dynamic regulation and packaging of genetic information is achieved by the organization of DNA into chromatin. Nucleosomal core histones, which form the basic repeating unit of chromatin, are subject to various post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitinylation. These modifications have effects on chromatin structure and, along with DNA methylation, regulate gene transcription.The goal of this study was to determine if patterns in modifications were related to different categories of genomic features, and, if so, if the patterns had predictive value. In this study, we used publically available data（ChIP-chip）for different types of histone modifications（methylation and acetylation） and for DNA methylation for Arabidopsis thaliana and then applied a machine learning based approach（a support vector machine） to demonstrate that patterns of these modifications are very different among different kinds of genomic feature categories（protein, RNA,pseudogene, and transposon elements）. These patterns can be used to distinguish the types of genomic features.DNA methylation and H3K4me3 methylation emerged as features with most discriminative power. From our analysis on Arabidopsis, we were able to predict 33 novel genomic features, whose existence was also supported by analysis of RNA-seq experiments. In summary, we present a novel approach which can be used to discriminate/detect different categories of genomic features based upon their patterns of chromatin modification and DNA methylation.

Understanding the genetic and epigenetic architecture in complex network of rice flowering pathways

Although the molecular basis of flowering time control is well dissected in the long day （LD） plant Arabidopsis, it is still largely unknown in the short day （SD） plant rice. Rice flowering time （heading date） is an important agronomic trait for season adaption and grain yield, which is affected by both genetic and environmental factors. During the last decade, as the nature of florigen was identified, notable progress has been made on exploration how florigen gene ,expression is genetically controlled. In Arabidopsis expression of certain key flowering integrators such as FLOWERING LOCUS C （FLC） and FLOWERING LOCUS T （FT） are also epige- netically regulated by various chromatin modifications, however, very little is known in rice on this aspect until very recently. This review summarized the advances of both genetic networks and chromatin modifications in rice flowering time control, attempting to give a complete view of the genetic and epigenetic architecture in complex network of rice flowering pathways.

Genetic and Epigenetic Understanding of the Seasonal Timing of Flowering

The developmental transition to flowering in many plants is timed by changing seasons,which enables plants to flower at a season that is favorable for seed production.Many plants grown at high latitudes perceive the seasonal cues of changing day length and/or winter cold(prolonged cold exposure),to regulate the expression of flowering-regulatory genes through the photoperiod pathway and/or vernalization pathway,and thus align flowering with a particular season.Recent studies in the model flowering plant Arabidopsis thaliana have revealed that diverse transcription factors engage various chromatin modifiers to regulate several key flowering-regulatory genes including FLOWERING LOCUS C(FLC)and FLOWERING LOCUS T(FT)in response to seasonal signals.Here,we summarize the current understanding of molecular and chromatin-regulatory or epigenetic mechanisms underlying the vernalization response and photoperiodic control of flowering in Arabidopsis.Moreover,the conservation and divergence of regulatory mechanisms for seasonal flowering in crops and other plants are briefly discussed.

Conserved RB functions in development and tumor suppression

The variety of human cancers in which the retinoblastoma protein pRb is inactivated reflects both its broad importance for tumor suppression and its multitude of cellular functions.Accumulating evidence indicates that pRb contributes to a diversity of cellular functions,including cell proliferation,differentiation,cell death,and genome stability.pRb performs these diverse functions through the formation of large complexes that include E2F transcription factors and chromatin regulators.In this review we will discuss some of the recent advances made in understanding the structure and function of pRb as they relate to tumor suppression,and highlight research using Drosophila melanogaster that reveals important,evolutionarily conserved functions of the RB family.

Molecular epigenetic mechanisms for the memory of temperature stresses in plants

The sessile plants encounter various stresses;some are prolonged,whereas some others are recurrent.Temperature is crucial for plant growth and development,and plants often encounter adverse high temperature fluctuations(heat stresses)as well as prolonged cold exposure such as seasonal temperature drops in winter when grown in temperate regions.Many plants can remember past temperature stresses to get adapted to adverse local temperature changes to ensure survival and/or reproductive success.Here,we summarize chromatin-based mechanisms underlying acquired thermotolerance or thermomemory in plants and review recent progresses on molecular epigenetic understanding of‘remembering of prolonged cold in winter’or vernalization,a process critical for various over-wintering plants to acquire competence to flower in the coming spring.In addition,perspectives on future study in temperature stress memories of economically-important crops are discussed.

The Polycomb Complex PRC1:Composition and Function in Plants

Polycomb group（PcG） proteins are crucial epigenetic regulators conferring transcriptional memory to cell lineages.They assemble into multi-protein complexes,e.g.,Polycomb Repressive Complex 1 and 2（PRC1,PRC2）,which are thought to act in a sequential manner to stably maintain gene repression.PRC2 induces histone H3 lysine 27（H3K27） trimethylation（H3K27me3）,which is subsequently read by PRCl that further catalyzes H2A monoubiquitination（H2Aub1）,creating a transcriptional silent chromatin conformation.PRC2 components are conserved in plants and have been extensively characterized in Arabidopsis.In contrast,PRCl composition and function are more diverged between animals and plants.Only more recently,PRC1 existence in plants has been documented.Here we review the aspects of plant specific and conserved PRC1 and highlight critical roles of PRC1 components in seed embryonic trait determinacy,shoot stem cell fate determinacy,and flower development in Arabidopsis.