Journal of Genetics and Genomics

Abstract:
MicroRNAs (miRNAs) are a class of about 20–24 nt small non-coding RNAs that can regulate their target gene expression transcriptionally and posttranscriptionally. There are an increasing number of studies describing the identification of new components and regulatory mechanisms involved in the miRNA biogenesis and effector pathway as well as new functions of miRNAs in plant development. This review mainly focuses on the components involved in this pathway, and the developmental defects associated with the corresponding mutations. Some functions of important miRNAs in plant development, together with the modes of miRNA action, are also discussed in this review to describe the recent advance in this area.

The Polycomb Complex PRC1: Composition and Function in Plants

Anne Molitor, Wen-Hui Shen

2013, 40(5): 231-238. doi: 10.1016/j.jgg.2012.12.005

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Abstract:
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 PRC1 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, PRC1 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.

Imprinting in Plants and Its Underlying Mechanisms

Hongyu Zhang, Abed Chaudhury, Xianjun Wu

2013, 40(5): 239-247. doi: 10.1016/j.jgg.2013.04.003

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Abstract:
Genomic imprinting (or imprinting) refers to an epigenetic phenomenon by which the allelic expression of a gene depends on the parent of origin. It has evolved independently in placental mammals and flowering plants. In plants, imprinting is mainly found in endosperm. Recent genome-wide surveys in Arabidopsis, rice, and maize identified hundreds of imprinted genes in endosperm. Since these genes are of diverse functions, endosperm development is regulated at different regulatory levels. The imprinted expression of only a few genes is conserved between Arabidopsis and monocots, suggesting that imprinting evolved quickly during speciation. In Arabidopsis, DEMETER (DME) mediates hypomethylation in the maternal genome at numerous loci (mainly transposons and repeats) in the central cell and results in many differentially methylated regions between parental genomes in the endosperm, and subsequent imprinted expression of some genes. In addition, histone modification mediated by Polycomb group (PcG) proteins is also involved in regulating imprinting. DME-induced hypomethylated alleles in the central cell are considered to produce small interfering RNAs (siRNAs) which are imported to the egg to reinforce DNA methylation. In parallel, the activity of DME in the vegetative cell of the male gametophyte demethylates many regions which overlap with the demethylated regions in the central cell. siRNAs from the demethylated regions are hypothesized to be also transferred into sperm to reinforce DNA methylation. Imprinting is partly the result of genome-wide epigenetic reprogramming in the central cell and vegetative cell and evolved under different selective pressures.

An Integrated Workflow for DNA Methylation Analysis

Pingchuan Li, Feray Demirci, Gayathri Mahalingam, Caghan Demirci, Mayumi Nakano, Blake C. Meyers

2013, 40(5): 249-260. doi: 10.1016/j.jgg.2013.03.010

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Abstract:
The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes. DNA methylation has a demonstrated role in the genome stability and protection, regulation of gene expression and many other aspects of genome function and maintenance. BS-seq is a relatively unbiased method for profiling the DNA methylation, with a resolution capable of measuring methylation at individual cytosines. Here we describe, as an example, a workflow to handle DNA methylation analysis, from BS-seq library preparation to the data visualization. We describe some applications for the analysis and interpretation of these data. Our laboratory provides public access to plant DNA methylation data via visualization tools available at our “Next-Gen Sequence” websites (http://mpss.udel.edu), along with small RNA, RNA-seq and other data types.

An in vivo Transient Expression System Can Be Applied for Rapid and Effective Selection of Artificial MicroRNA Constructs for Plant Stable Genetic Transformation

Basdeo Bhagwat, Ming Chi, Li Su, Haifeng Tang, Guiliang Tang, Yu Xiang

2013, 40(5): 261-270. doi: 10.1016/j.jgg.2013.03.012

Abstract (57) HTML PDF (1)

Abstract:
The utility of artificial microRNAs (amiRNAs) to induce loss of gene function has been reported for many plant species, but expression efficiency of the different amiRNA constructs in different transgenic plants was less predictable. In this study, expressions of amiRNAs through the gene backbone of Arabidopsis miR168a were examined by both Agrobacterium-mediated transient expression and stable plant genetic transformation. A corresponding trend in expression of amiRNAs by the same amiRNA constructs between the transient and the stable expression systems was observed in the experiments. Plant genetic transformation of the constructs that were highly expressible in amiRNAs in the transient agro-infiltration assays resulted in generation of transgenic lines with high level of amiRNAs. This provides a simple method for rapid and effective selection of amiRNA constructs used for a time-consuming genetic transformation in plants.

2013 Vol. 40, No. 5