<i>FASCIATED EAR4</i>Encodes a bZIP Transcription Factor That Regulates Shoot Meristem Size in Maize

Pautler, Michael; Eveland, Andrea L.; LaRue, Therese; Yang, Fang; Weeks, Rebecca; Lunde, China; Je, Byoung Il; Meeley, Robert B.; Komatsu, Mai; Vollbrecht, Erik; Sakai, Hajime; Jackson, David

doi:10.1105/tpc.114.132506

Cited by 129 publications

(127 citation statements)

References 71 publications

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“…ROXY proteins in Arabidopsis interact with TGA transcription factors, including TGA9/10 and PAN (Xing and Zachgo, 2008;Li et al, 2009;Murmu et al, 2010), and are thought to posttranslationally modify their activities. We found that FEA4, the maize ortholog of PAN (Pautler et al, 2015), interacts with MSCA1, suggesting that it might be a target of MSCA1. Furthermore, overlapping expression domains of the FEA4 and MSCA1 transcripts below the P 0 provides the possibility for protein interaction and modification in vivo.…”

Section: Discussionmentioning

confidence: 78%

“…We recently cloned a maize gene, FEA4, which encodes a TGA transcription factor, orthologous to PAN (Pautler et al, 2015). Loss-of-function mutations in FEA4 lead to strong fasciation in ear and tassel primordia, as well as enlarged vegetative shoot meristems, and altered phyllotaxy in certain inbred backgrounds, similar to Abph2.…”

Section: Msca1 Controls Shoot Meristem Sizementioning

confidence: 99%

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A Maize Glutaredoxin Gene,Abphyl2,Regulates Shoot Meristem Size and Phyllotaxy

et al. 2015

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Phyllotaxy describes the geometric arrangement of leaves and is important for plant productivity. Auxin is well known to regulate phyllotactic patterns via PIN1-dependent auxin polar transport, and studies of maize (Zea mays) aberrant phyllotaxy1 (abph1) mutants suggest the importance of auxin and cytokinin signaling for control of phyllotaxy. However, whether additional regulators control these patterns is poorly understood. Here, we report a new dominant maize mutant, Aberrant phyllotaxy2 (Abph2), in which the shoot meristems are enlarged and the phyllotactic pattern switches from alternate to decussate. Map-based cloning revealed that the Abph2 mutation was caused by transposition of a glutaredoxin gene, MALE STERILE CONVERTED ANTHER1 (MSCA1), which gained an altered expression pattern in Abph2 mutant embryos. msca1 loss-of-function mutants have reduced meristem size and revealed a novel function of glutaredoxins in meristem growth. In addition, MSCA1 interacts with a TGA transcription factor, FASCIATED EAR4, suggesting a novel regulatory module for regulating shoot meristem size.

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Section: Discussionmentioning

confidence: 78%

Section: Msca1 Controls Shoot Meristem Sizementioning

confidence: 99%

A Maize Glutaredoxin Gene,Abphyl2,Regulates Shoot Meristem Size and Phyllotaxy

et al. 2015

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“…To investigate the presence of enhancer RNAs in plants, we mapped intergenic open chromatin regions using published DNaseI hypersensitivity (DNase-seq) data for Arabidopsis (18) and FASCIATED EAR 4 (FEA4) ChIP-seq (19) peaks for maize (due to a lack of DNase-seq data). In total, 2,467 putative intergenic enhancers were identified in Arabidopsis and 4,665 in maize compared with 21,847 in the human lung fibroblast IMR-90 cell line.…”

Section: Significancementioning

confidence: 99%

“…In total, 2,467 putative intergenic enhancers were identified in Arabidopsis and 4,665 in maize compared with 21,847 in the human lung fibroblast IMR-90 cell line. Each site was sorted based on their GRO-seq signals, and heat maps were generated for ±1 kb from the intergenic site of (19)], and heat maps were generated ±1 kb from intergenic sites for signal from DNase-seq, GROseq, RNA-seq, H3K4me3, H3K9/27ac, and input in Arabidopsis, maize, and IMR-90 cells (8,12,(18)(19)(20)(21)(22)(23)(24)(25). Sites are sorted based on the total GRO-seq signal observed within 400 bp of the intergenic peak.…”

Section: Significancementioning

confidence: 99%

Nascent RNA sequencing reveals distinct features in plant transcription

Hetzel

Duttke

Benner

et al. 2016

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

140

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Transcriptional regulation of gene expression is a major mechanism used by plants to confer phenotypic plasticity, and yet compared with other eukaryotes or bacteria, little is known about the design principles. We generated an extensive catalog of nascent and steadystate transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5′GRO-seq, and RNA-seq and reanalyzed published maize data to capture characteristics of plant transcription. De novo annotation of nascent transcripts accurately mapped start sites and unstable transcripts. Examining the promoters of coding and noncoding transcripts identified comparable chromatin signatures, a conserved "TGT" core promoter motif and unreported transcription factor-binding sites. Mapping of engaged RNA polymerases showed a lack of enhancer RNAs, promoter-proximal pausing, and divergent transcription in Arabidopsis seedlings and maize, which are commonly present in yeast and humans. In contrast, Arabidopsis and maize genes accumulate RNA polymerases in proximity of the polyadenylation site, a trend that coincided with longer genes and CpG hypomethylation. Lack of promoter-proximal pausing and a higher correlation of nascent and steady-state transcripts indicate Arabidopsis may regulate transcription predominantly at the level of initiation. Our findings provide insight into plant transcription and eukaryotic gene expression as a whole.plant transcription | nascent transcripts | RNA polymerase pausing | 5′GRO-seq | GRO-seq G ene expression is a hallmark of life and subject to adaptation in changing environments. Steady-state transcript levels are a result of transcription initiation, elongation, and termination, followed by maturation and decay. Much has been learned about transcriptional mechanisms using yeast and animal models. In contrast, owing to technical difficulties created by plant cell extracts, there remains a large gap in knowledge in plant transcription. Plants and animals diverged more than 1.6 billion years ago. Studying plant transcription therefore not only contributes to a better understanding of the world's largest food source but also the evolution of eukaryotic gene expression.The signals initiating transcription are ultimately integrated at the promoter. Sequence-specific transcription factors (TFs) commonly bind the proximal promoter around −150 to −50 bp upstream of the transcriptional start site (TSS) (1, 2). At the core promoter, located approximately ±50 bp relative to the TSS, basal TFs cooperate with conserved DNA sequence motifs to orchestrate recruitment of the RNA polymerase (RNAP) (1, 3). Transcription has been studied extensively in a number of species (1-3) but not in plant model systems. Studies focusing on promoterenriched sequences were hindered by the lack of precise TSSs (4, 5) but have improved dramatically through techniques such as paired end analysis of transcription start sites (3PEAT) (6) and cap analysis gene expression (CAGE) (7), but both methods are affected by RNA processing and trans...

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“…The interactions between such a protein and regulated DNA could be detected by chromatin precipitation of associated DNA followed by DNA sequencing (ChIP-Seq). In maize, there are five ChIP-Seq datasets available (Bolduc et al, 2012;Morohashi et al, 2012;Li et al, 2015a;Pautler et al, 2015;Yang et al, 2016), some of which involved lowly expressed or tissue-specific genes. For example, Opaque2 is specifically expressed in endosperm (Li et al, 2015a), Knotted1 is expressed in shoot apical meristem and floral tissues (Bolduc et al, 2012), and Pericarp Color1 has low expression except in inflorescence and seed .…”

Section: Network Performance Does Not Differ Based Upon Normalizationmentioning

confidence: 99%

Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data

et al. 2017

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ORCID IDs: 0000-0002-6182-800X (J.H.); 0000-0001-6612-3570 (S.V.); 0000-0002-9564-8146 (K.M.M.).With the emergence of massively parallel sequencing, genomewide expression data production has reached an unprecedented level. This abundance of data has greatly facilitated maize research, but may not be amenable to traditional analysis techniques that were optimized for other data types. Using publicly available data, a gene coexpression network (GCN) can be constructed and used for gene function prediction, candidate gene selection, and improving understanding of regulatory pathways. Several GCN studies have been done in maize (Zea mays), mostly using microarray datasets. To build an optimal GCN from plant materials RNA-Seq data, parameters for expression data normalization and network inference were evaluated. A comprehensive evaluation of these two parameters and a ranked aggregation strategy on network performance, using libraries from 1266 maize samples, were conducted. Three normalization methods and 10 inference methods, including six correlation and four mutual information methods, were tested. The three normalization methods had very similar performance. For network inference, correlation methods performed better than mutual information methods at some genes. Increasing sample size also had a positive effect on GCN. Aggregating single networks together resulted in improved performance compared to single networks.Maize (Zea mays) is the most widely produced crop in United States, and U.S. agriculture accounted for 36% of world maize production in 2015 (USDA, 2016). Maize has also been in the center of genetics research for more than 100 years, including McClintock's pioneering work with transposable elements (reviewed by McClintock, 1983;Fedoroff, 2012). Due to recent technological advances in nucleic acid sequencing and the availability of the maize genome sequence (Schnable et al., 2009), maize genomics research has been greatly expedited.RNA-sequencing (RNA-Seq) has become the favored technique for detecting genomewide expression patterns. RNA-Seq has some advantages over microarray analysis of gene expression, including single base-pair resolution, detection of novel transcripts, and the ability to analyze transcript abundance without existing genome information (reviewed by Wang et al., 2009;Han et al., 2015;Conesa et al., 2016). RNA-Seq data provides information about single nucleotide polymorphisms, which facilitates genomewide association studies (Fu et al., 2013;Li et al., 2013a;Lonsdale et al., 2013;Fadista et al., 2014). Because of its widespread adaptability, greater than 5000 Illumina platform Maize RNA-Seq libraries (Fig. 1A) are available in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (Leinonen et al., 2010), adding to the body of data that can be used to study the maize genome.The maize genome is large and heterogeneous, and the genome annotation is still far from complete (Cigan et al., 2005;Ficklin and Feltus, 2011). Although recent work has...

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FASCIATED EAR4Encodes a bZIP Transcription Factor That Regulates Shoot Meristem Size in Maize

Cited by 129 publications

References 71 publications

A Maize Glutaredoxin Gene,Abphyl2,Regulates Shoot Meristem Size and Phyllotaxy

A Maize Glutaredoxin Gene,Abphyl2,Regulates Shoot Meristem Size and Phyllotaxy

Nascent RNA sequencing reveals distinct features in plant transcription

Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data

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