The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

Hanada, Kousuke; Vallejo, Verónica; Nobuta, Kan; Slotkin, R. Keith; Lisch, Damon; Meyers, Blake C.; Shiu, Shin-Han; Jiang, Ning

doi:10.1105/tpc.108.063206

Cited by 90 publications

(110 citation statements)

References 69 publications

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“…One mechanism of chimeric gene formation is the transposition of genic sequences captured by flanking MULE DNA transposons in rice 68,69 . MULE-derived loci (MDLs) accounted for 7% of Oryzeaeand species-specific genes.…”

Section: −6mentioning

confidence: 99%

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

et al. 2018

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Section: −6mentioning

confidence: 99%

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

et al. 2018

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“…Finally, GC-rich sequences tend to augment bendability and the ability to undergo a B-Z transition of DNA helical structure, which is often associated with open chromatin and active transcription (46). This might explain why the fraction of expressed Pack-MULEs is much higher than other transposable elements, including the autonomous elements of MULEs (10). It is also interesting to note that a de novo insertion of Mu1 (a GC-rich Pack-MULE) in the 5′ UTR of one of the tandemly duplicated p1 genes in maize induced the expression of other p1 genes in the same cluster, possibly through the alteration of DNA methylation and chromatin structure (20).…”

Section: Discussionmentioning

confidence: 99%

“…The procedure for the annotation of Pack-MULEs in the three genomes was similar to that described previously (10). The sequences for rice pseudomolecules and gene annotation information were downloaded from the rice annotation group at Michigan State University (http://rice.plantbiology.msu.…”

Section: Methodsmentioning

confidence: 99%

“…In rice, there are nearly 3,000 PackMULEs, of which 22% are transcribed and at least 1% are translated (10). Pack-MULEs are frequently associated with small RNAs, which may suppress the expression of themselves and the parental genes from which the gene fragments are derived (10). This suggests that Pack-MULEs have a great potential in regulating gene expression and providing unique resources for coding sequences.…”

mentioning

confidence: 99%

“…First isolated in maize (5,6), Pack-MULEs can amplify genes or gene fragments on a massive scale (4,5,(7)(8)(9). In rice, there are nearly 3,000 PackMULEs, of which 22% are transcribed and at least 1% are translated (10). Pack-MULEs are frequently associated with small RNAs, which may suppress the expression of themselves and the parental genes from which the gene fragments are derived (10).…”

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confidence: 99%

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Pack- Mutator –like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

Jiang

Ferguson

Slotkin

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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In monocots, many genes demonstrate a significant negative GC gradient, meaning that the GC content declines along the orientation of transcription. Such a gradient is not observed in the genes of the dicot plant Arabidopsis. In addition, a lack of homology is often observed when comparing the 5′ end of the coding region of orthologous genes in rice and Arabidopsis. The reasons for these differences have been enigmatic. The presence of GC-rich sequences at the 5′ end of genes may influence the conformation of chromatin, the expression level of genes, as well as the recombination rate. Here we show that Pack-Mutator-like transposable elements (PackMULEs) that carry gene fragments specifically acquire GC-rich fragments and preferentially insert into the 5′ end of genes. The resulting Pack-MULEs form independent, GC-rich transcripts with a negative GC gradient. Alternatively, the Pack-MULEs evolve into additional exons at the 5′ end of existing genes, thus altering the GC content in those regions. We demonstrate that Pack-MULEs modify the 5′ end of genes and are at least partially responsible for the negative GC gradient of genes in grasses. Such a unique and global impact on gene composition and gene structure has not been observed for any other transposable elements.gene duplication | gene modification

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Plant Transposable Elements

Jiang

2016

Encyclopedia of Life Sciences

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Transposable elements (TEs) were first discovered by Barbara McClintock in maize. As the most abundant and dynamic component of the plant genomes, the activity of TEs is responsible for genome size expansion, alteration of gene expression, duplication and amplification of normal genes. There are many different types of elements in the plant genomes, with each of them occupying a specific niche, including genic regions, intergenic regions and centromeres. Particularly, the centromere‐specific elements may play critical roles in the formation of new plant species. Most TEs are quiescent in normal development but are turned on by various biotic or abiotic stresses, thus favouring the survival of host organisms under undesirable conditions. In addition to their roles in genome evolution, TEs can be useful tools for gene cloning, mapping and transformation. Key Concepts Transposable elements are the largest components of plant genomes. They have target specificity. Transposable elements play roles in speciation. Transposition activity is tightly regulated. Transposable elements influence expression of other genes. They are genetic and molecular tools.

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The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

Cited by 90 publications

References 69 publications

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Pack- Mutator –like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

Plant Transposable Elements

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