[Show abstract][Hide abstract] ABSTRACT: DNA methylation is important for the regulation of gene expression and the silencing of transposons in plants. Here we present genome-wide methylation patterns at single-base pair resolution for cassava (Manihot esculenta, cultivar TME 7), a crop with a substantial impact in the agriculture of subtropical and tropical regions. On average, DNA methylation levels were higher in all three DNA sequence contexts (CG, CHG, and CHH, where H equals A, T, or C) than those of the most well-studied model plant Arabidopsis thaliana. As in other plants, DNA methylation was found both on transposons and in the transcribed regions (bodies) of many genes. Consistent with these patterns, at least one cassava gene copy of all of the known components of Arabidopsis DNA methylation pathways was identified. Methylation of LTR transposons (GYPSY and COPIA) was found to be unusually high compared with other types of transposons, suggesting that the control of the activity of these two types of transposons may be especially important. Analysis of duplicated gene pairs resulting from whole-genome duplication showed that gene body DNA methylation and gene expression levels have coevolved over short evolutionary time scales, reinforcing the positive relationship between gene body methylation and high levels of gene expression. Duplicated genes with the most divergent gene body methylation and expression patterns were found to have distinct biological functions and may have been under natural or human selection for cassava traits.
Proceedings of the National Academy of Sciences 10/2015; DOI:10.1073/pnas.1519067112 · 9.67 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Availability and implementation:
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[Show abstract][Hide abstract] ABSTRACT: One of the most remarkable features of angiosperm plants is the dramatic diversity of fruit size and shape. However, our understanding of the underlying mechanisms that control fruit growth remains fragmentary. We have combined forward and reverse genetic approaches with genome-wide profiling tools to identify transcriptional and post-transcriptional regulatory modules key in controlling fruit growth. One of such module includes the riboregulator miR172 and its target APETALA2 (AP2). We have shown that MIR172C is expressed in fruit valves where it acts to prevent AP2 function, thereby allowing for fruit growth. MIR172C itself is directly activated by the FRUITFULL (FUL) MADS-domain protein and the Auxin Response Factors ARF6 and ARF8, and these transcription factors physically associate with one another to activate MIR172C expression. It will be interesting to determine if this regulatory hub, which links hormone signaling to fruit growth, occurs in diverse plant species. By combining classical and integrative genetic and molecular approaches together with genome-wide profiling and innovative genome editing tools we are also investigating additional small-RNA-dependent regulatory hubs that appear to incorporate environmental and endogenous signal responses into the control of fruit growth and morphogenesis.
FASEB conference: Mechanisms in Plant Development, Saxtons River (Vermont, USA); 08/2015
[Show abstract][Hide abstract] ABSTRACT: Growth is a major factor in any plant morphogenetic program, and it is influenced by environmental cues and endogenous signals including hormones. Recent studies have shed some light on the transcriptional regulatory pathways that modulate growth during vegetative stages, however our understanding on how growth is controlled during the reproductive phase is still fragmentary. The fruit of Arabidopsis thaliana provides an excellent platform to dissect morphogenetic processes including growth. Although a wealth of information has been accumulated on fruit patterning, maturation (or ripening), senescence and dehiscence, we are only now beginning to understand how the coordination of fruit growth is achieved mechanistically. The elongation of the fruit valves after fertilization is the most conspicuous trait during Arabidopsis thaliana fruit growth. Previous studies have shown that plant hormones are important players in regulating fruit growth, and auxin is known to play an important role in coordinating this process. Moreover, in spite of the surge of interest in the roles of small RNAs (sRNAs), their relevance to growth or how they are transcriptionally controlled in developmental contexts are topics largely unexplored. We are investigating the transcriptional and post-transcriptional regulatory circuits that orchestrate fruit growth by combining classical and integrative genetic and molecular approaches together with genome-wide profiling and innovative genome editing technologies. Interestingly we have identified several sRNA regulatory modules that play pivotal roles in fruit morphogenesis. For example, one of such modules involves the sRNA miR172. This riboregulator is key in fruit development as the growth of the fruit is blocked when the activity of miR172 is compromised. We have also revealed that the FRUITFULL (FUL) MADS-domain transcription factor and the ARF6 and ARF8 Auxin Response Factors (whose encoding genes are miR167-regulated) physically associate and interact to directly activate transcription of a miR172-encoding gene in fruit valves. In addition, we have discovered that a number of fruit regulatory genes (including sRNAs) act as regulatory hubs incorporating environmental signal responses (temperature, light regime, nutrients, …) into fruit morphogenetic pathways. Our studies define novel and evolutionary conserved sRNA-dependent regulatory modules that integrate developmental, hormone and environmental signaling pathways into the control of fruit growth.
Workshop on Mechanisms Controlling Flower Development, Aiguablava (Girona, Spain); 06/2015