Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations.

Greene, Ben; Walko, R. M.; Hake, Sarah

doi:10.1093/genetics/138.4.1275

Cited by 123 publications

(16 citation statements)

References 33 publications

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“…RNA analysis: knl is strongly expressed in the meristem and stem of wild-type plants but is restricted from expression in leaves. Previous analysis has shown that the dominant Knl alleles resulting from transposon insertion are correlated with ectopic k n l expression in leaf primordia (SMITH et al 1992;GREENE et al 1994;JACKSON et al 1994; E. VOLLBRECHT and S. IIAKE, unpublished data). We isolated RNA from Knl-0 and derivatives to determine if the appearance of knots and ligule displacement was also correlated with knl expression in the leaf.…”

Section: Dna Of This Individual Revealed That Thementioning

confidence: 95%

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Mu Element-Generated Gene Conversions in Maize Attenuate the Dominant Knotted Phenotype

Mathern¹,

Hake²

1997

Genetics

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The knotted1 gene was first defined by dominant mutations that affect leaf morphology. The original allele, Kn1-O, results from a 17-kb tandem duplication. Mutator (Mu) insertions near the junction of the two repeats suppress the leaf phenotype to different degrees depending on the position of the insertion. The Mu insertions also increase the frequency of recombination at Kn1-O to create derivative alleles in which the Mu element and one copy of the repeat are lost. These derivatives are normal in appearance. Here we describe two derivatives that retained the tandem duplication but gained insertions of 1.7 and 3 kb in length in place of the Mu element. In each case, the inserted DNA is a sequence that normally flanks the distal repeat unit. Thus, each derivative consists of a tandem duplication in which the repeat unit has been extended at its distal end by the length of the new insertion. The 1.7-kb insertion dampens the phenotype, as did the original Mu insertion, whereas the 3-kb insertion completely suppresses the knotted phenotype. We propose that gene conversion, stimulated by the double-strand break of the Mu excision, gave rise to these derivatives.

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Section: Dna Of This Individual Revealed That Thementioning

confidence: 95%

“…Tissue from four to six individuals was collected for each sample. M u activity was determined by digestion with Hinff and hybridization with Mu1 and Mu8 probes (GREENE et al 1994). The probes were made radioactive using the Multiprime DNA labeling system of Amersham.…”

Section: Generation Of Derivativesmentioning

confidence: 99%

Mu Element-Generated Gene Conversions in Maize Attenuate the Dominant Knotted Phenotype

Mathern¹,

Hake²

1997

Genetics

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“…Larger intron size might result from selection favoring insertions over deletions as a way to preserve functional CREs. CRMs are, for example, found in large introns in FLOWERING LOCUS C and AGAMOUS in Arabidopsis and knotted1 in maize ( Zea mays ; Greene et al, 1994 ; Sieburth and Meyerowitz, 1997 ; Busch et al, 1999 ; Hong et al, 2003 ; Qüesta et al, 2016 ; Yuan et al, 2016 ; Liu et al, 2020 ).…”

Section: Genomic Location Of Crms: the Influence Of Genome Size And O...mentioning

confidence: 99%

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

2021

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The identification and characterization of cis-regulatory DNA sequences and how they function to coordinate responses to developmental and environmental cues is of paramount importance to plant biology. Key to these regulatory processes are cis-regulatory modules (CRMs), which include enhancers and silencers. Despite the extraordinary advances in high-quality sequence assemblies and genome annotations, the identification and understanding of CRMs, and how they regulate gene expression, lag significantly behind. This is especially true for their distinguishing characteristics and activity states. Here, we review the current knowledge on CRMs and breakthrough technologies enabling identification, characterization, and validation of CRMs; we compare the genomic distributions of CRMs with respect to their target genes between different plant species, and discuss the role of transposable elements harboring CRMs in the evolution of gene expression. This is an exciting time to study cis-regulomes in plants; however, significant existing challenges need to be overcome to fully understand and appreciate the role of CRMs in plant biology and in crop improvement.

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“…Intron-3 Z. maize Ectopic expression, improper development of the leaf mutation (Greene et al, 1994) Mutaor…”

Section: Knotted1mentioning

confidence: 99%

“…Similarly, in tomato, a Rider insertion causes the 24.7 kb duplication of the DEFL1 gene at the SUN locus resulting in elongated fruit shape (Xiao et al, 2008). There are several excellent examples in maize wherein insertion of Mutator element in the introns of the three homeobox genes Knotted1, Rough Sheath1 and Liguleless3 causes ectopic expression resulting in improper leaf development (Greene et al, 1994;Schneeberger et al, 1995;Muehlbauer et al, 1999). Moreover, in another study, a Mu11.5-kb insertion in the first intron of the Adh1-S3034 gene encoding alcohol dehydrogenase-1 (ADH1) reduced the transcript levels through inhibition of transcription (Bennetzen et al, 1984).…”

Section: Intronsmentioning

confidence: 99%

On the Role of Transposable Elements in the Regulation of Gene Expression and Subgenomic Interactions in Crop Genomes

Gill

Scossa

King

et al. 2021

Critical Reviews in Plant Sciences

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Transposable elements (TEs) represent a major and variable portion of plant genomes, and recent progress in genetics and genomics has highlighted the importance of different TE species as a useful genetic tool in crop breeding. TEs can cause changes in the pattern of gene expression, and regulate gene function by various means such as cis-up-or downregulation of nearby genes through insertion at promoter, intron, exon and down-stream regions, and trans-production of short interfering RNAs (siRNAs) via two RNA-directed DNA methylation (RdDM) pathways. siRNAs generated through different RdDM pathways differ in length and have variable effects on TEs. For instance, noncoding siRNAs of 20-60 nt produced by RNA polymerase IV (dicer-independent) and 21/22 nt by Pol II (dicer-dependent) have only minor effects on TEs compared with 24 nt siRNAs produced by Pol IV (dicerdependent pathways). Following whole-genome duplication (WGD) events after polyploidization in allopolyploids, TEs from either parent are able to induce siRNAs to regulate the complex polyploid genome. Those designated as 'controllers' usually reside in the dominant parent and affect the TEs of the recessive parent. Subgenome cross-talk thus appears to contribute to epigenetic regulation as well as reshuffling or restructuring of subgenomes and creation of novel patterns of genes expression/and variation in local or global copy number. In this review, we focus on recent progress in unraveling the role of TEs in gene expression regulation via TE-derived siRNAs in the context of polyploid plant evolution and environmental stress, and explore how ancient WGD and recent polyploidy affected the evolution of TE-induced epigenetic mechanisms.

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Mutator insertions in an intron of the maize knotted1 gene result in dominant suppressible mutations.

Cited by 123 publications

References 33 publications

Mu Element-Generated Gene Conversions in Maize Attenuate the Dominant Knotted Phenotype

Mu Element-Generated Gene Conversions in Maize Attenuate the Dominant Knotted Phenotype

Cis-regulatory sequences in plants: Their importance, discovery, and future challenges

On the Role of Transposable Elements in the Regulation of Gene Expression and Subgenomic Interactions in Crop Genomes

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