Transposable elements play an important role during cotton genome evolution and fiber cell development

Wang, Kun; Huang, Gai; Zhu, Yu-Xian

doi:10.1007/s11427-015-4928-y

Cited by 51 publications

(34 citation statements)

References 55 publications

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“…The A subgenome also has higher proportions of copia-type retrotransposons adjacent to coding genes . Among above three cotton species, the fiber yield and quality vary significantly (Wang et al, 2016). The cultivated allotetraploid cottons produce longer and better fibers than its two diploid ancestors.…”

Section: Te-derived Small Rnas Act As Regulators In Cis or Transmentioning

confidence: 99%

“…Further, it is found that TEs may regulate unbalanced expression pattern of some important genes involved in fiber development from two cotton subgenomes. For examples, a copia-type retrotransposon and a LINE retrotransposon located at the promoter of the MYB-domain transcription factor (MYB) and ethylene response factor (ERF) gene, respectively, and they both enhanced the transcription of nearby gene, which plays key role in cotton fiber development (Wang et al, 2016).…”

Section: Te-derived Small Rnas Act As Regulators In Cis or Transmentioning

confidence: 99%

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The effect of transposable elements on phenotypic variation: insights from plants to humans

Wei

Cao

2016

Sci. China Life Sci.

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Transposable elements (TEs), originally discovered in maize as controlling elements, are the main components of most eukaryotic genomes. TEs have been regarded as deleterious genomic parasites due to their ability to undergo massive amplification. However, TEs can regulate gene expression and alter phenotypes. Also, emerging findings demonstrate that TEs can establish and rewire gene regulatory networks by genetic and epigenetic mechanisms. In this review, we summarize the key roles of TEs in fine-tuning the regulation of gene expression leading to phenotypic plasticity in plants and humans, and the implications for adaption and natural selection. transposable elements, gene expression, phenotypic variation Citation:Wei, L., and Cao, X. (2016). The effect of transposable elements on phenotypic variation: insights from plants to humans. Sci China Life Sci 59, 24 -37.

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Section: Te-derived Small Rnas Act As Regulators In Cis or Transmentioning

confidence: 99%

Section: Te-derived Small Rnas Act As Regulators In Cis or Transmentioning

confidence: 99%

The effect of transposable elements on phenotypic variation: insights from plants to humans

Wei

Cao

2016

Sci. China Life Sci.

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“…cacao and A . thaliana , more repeat elements were inserted near (within 1 kb) genes in cotton [33], and repeat elements were more likely to be methylated [34]. CpG islands are usually located near gene promoters and can also appear within or at the 3’- end of genes in the human genome [5].…”

Section: Discussionmentioning

confidence: 99%

Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq

et al. 2017

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DNA methylation is an important epigenetic modification regulating gene expression, genomic imprinting, transposon silencing and chromatin structure in plants and plays an important role in leaf senescence. However, the DNA methylation pattern during Gossypium hirsutum L. cotyledon senescence is poorly understood. In this study, global DNA methylation patterns were compared between two cotyledon development stages, young (J1) and senescence (J2), using methylated DNA immunoprecipitation (MeDIP-Seq). Methylated cytosine occurred mostly in repeat elements, especially LTR/Gypsy in both J1 and J2. When comparing J1 against J2, there were 1222 down-methylated genes and 623 up-methylated genes. Methylated genes were significantly enriched in carbohydrate metabolism, biosynthesis of other secondary metabolites and amino acid metabolism pathways. The global DNA methylation level decreased from J1 to J2, especially in gene promoters, transcriptional termination regions and regions around CpG islands. We further investigated the expression patterns of 9 DNA methyltransferase-associated genes and 2 DNA demethyltransferase-associated genes from young to senescent cotyledons, which were down-regulated during cotyledon development. In this paper, we first reported that senescent cotton cotyledons exhibited lower DNA methylation levels, primarily due to decreased DNA methyltransferase activity and which also play important role in regulating secondary metabolite process.

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“…TEs may establish and rewire gene regulatory networks by genetic and epigenetic mechanisms to modulate stem cell development (Wei and Cao, 2016;Wang et al, 2016). In human embryonic stem cells, about 20% of the transcription factor binding sites were reported to be associated with TE insertions (Kunarso et al, 2010).…”

Section: Perspectivesmentioning

confidence: 99%

Recent advances in the research for the homolog of breast cancer associated gene AtROW1 in higher plants

Jiao

Zhang

Zhu

2016

Sci. China Life Sci.

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BARD1 (BRCA1 associated RING domain protein 1), as an important animal tumor suppressor gene associated with many kinds of cancers, has been intensively studied for decades. Surprisingly, homolog of BARD1 was found in plants and it was renamed AtROW1 (repressor of Wuschel-1) according to its extremely important function with regard to plant stem cell homeostasis. Although great advances have been made in human BARD1, the function of this animal tumor-suppressor like gene in plant is not well studied and need to be further elucidated. Here, we review and summarize past and present work regarding this protein. Apart from its previously proposed role in DNA repair, recently it is found essential for shoot and root stem cell development and differentiation in plants. The study of AtROW1 in plant may provide an ideal model for further elucidating the functional mechanism of BARD1 in mammals.

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Transposable elements play an important role during cotton genome evolution and fiber cell development

Cited by 51 publications

References 55 publications

The effect of transposable elements on phenotypic variation: insights from plants to humans

The effect of transposable elements on phenotypic variation: insights from plants to humans

Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq

Recent advances in the research for the homolog of breast cancer associated gene AtROW1 in higher plants

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