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Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

Peter Crisp, Alexandre Marand, Jaclyn Noshay, Peng Zhou, Zefu Lu, Robert Schmitz, Nathan Springer,

Abstract The genomic sequences of crops continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in ... Read more >>

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Cis-regulatory elements within TEs can influence expression of nearby maize genes

Jaclyn Noshay, Alexandre Marand, Sarah Anderson, Peng Zhou, Maria Katherine Mejia Guerra, Zefu Lu, Christine O’Connor, Peter Crisp, Candice Hirsch, Robert Schmitz, Nathan Springer,

Abstract Transposable elements (TEs) have the potential to create regulatory variation both through disruption of existing DNA regulatory elements and through creation of novel DNA regulatory elements. In a species with a large genome, such as maize, the many TEs interspersed with genes creates opportunities for significant allelic variation due ... Read more >>

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The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution.

Corrinne E Grover, Mengqiao Pan, Daojun Yuan, Mark A Arick, Guanjing Hu, Logan Brase, David M Stelly, Zefu Lu, Robert J Schmitz, Daniel G Peterson, Jonathan F Wendel, Joshua A Udall,

Cotton is an important crop that has made significant gains in production over the last century. Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode immunity. ... Read more >>

G3 (Bethesda) (G3 (Bethesda, Md.))
[2020, 10(5):1457-1467]

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Author Correction: Widespread long-range cis-regulatory elements in the maize genome.

William A Ricci, Zefu Lu, Lexiang Ji, Alexandre P Marand, Christina L Ethridge, Nathalie G Murphy, Jaclyn M Noshay, Mary Galli, María Katherine Mejía-Guerra, Maria Colomé-Tatché, Frank Johannes, M Jordan Rowley, Victor G Corces, Jixian Zhai, Michael J Scanlon, Edward S Buckler, Andrea Gallavotti, Nathan M Springer, Robert J Schmitz, Xiaoyu Zhang,

An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nat Plants (Nature plants)
[2020, 6(3):328]

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Widespread long-range cis-regulatory elements in the maize genome.

William A Ricci, Zefu Lu, Lexiang Ji, Alexandre P Marand, Christina L Ethridge, Nathalie G Murphy, Jaclyn M Noshay, Mary Galli, María Katherine Mejía-Guerra, Maria Colomé-Tatché, Frank Johannes, M Jordan Rowley, Victor G Corces, Jixian Zhai, Michael J Scanlon, Edward S Buckler, Andrea Gallavotti, Nathan M Springer, Robert J Schmitz, Xiaoyu Zhang,

Genetic mapping studies on crops suggest that agronomic traits can be controlled by gene-distal intergenic loci. Despite the biological importance and the potential agronomic utility of these loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic and functional molecular evidence to support the ... Read more >>

Nat Plants (Nature plants)
[2019, 5(12):1237-1249]

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The Gossypium longicalyx genome as a resource for cotton breeding and evolution

Corrinne Grover, Mengqiao Pan, Daojun Yuan, Mark Arick, Guanjing Hu, Logan Brase, David Stelly, Zefu Lu, Robert Schmitz, Daniel Peterson, Jonathan Wendel, Joshua Udall,

Abstract Cotton is an important crop that has made significant gains in production over the last century. Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode ... Read more >>

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The prevalence, evolution and chromatin signatures of plant regulatory elements.

Zefu Lu, Alexandre P Marand, William A Ricci, Christina L Ethridge, Xiaoyu Zhang, Robert J Schmitz,

Chromatin accessibility and modification is a hallmark of regulatory DNA, the study of which led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in ... Read more >>

Nat Plants (Nature plants)
[2019, 5(12):1250-1259]

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Monitoring the interplay between transposable element families and DNA methylation in maize.

Jaclyn M Noshay, Sarah N Anderson, Peng Zhou, Lexiang Ji, William Ricci, Zefu Lu, Michelle C Stitzer, Peter A Crisp, Candice N Hirsch, Xiaoyu Zhang, Robert J Schmitz, Nathan M Springer,

DNA methylation and epigenetic silencing play important roles in the regulation of transposable elements (TEs) in many eukaryotic genomes. A majority of the maize genome is derived from TEs that can be classified into different orders and families based on their mechanism of transposition and sequence similarity, respectively. TEs themselves ... Read more >>

PLoS Genet. (PLoS genetics)
[2019, 15(9):e1008291]

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Evolution of conserved noncoding sequences in Arabidopsis thaliana

Alan Yocca, Zefu Lu, Robert Schmitz, Michael Freeling, Patrick Edger,

Abstract Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome ... Read more >>

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Tiller Bud Formation Regulators MOC1 and MOC3 Cooperatively Promote Tiller Bud Outgrowth by Activating FON1 Expression in Rice.

Gaoneng Shao, Zefu Lu, Jinsong Xiong, Bing Wang, Yanhui Jing, Xiangbing Meng, Guifu Liu, Haiyan Ma, Yan Liang, Fan Chen, Yonghong Wang, Jiayang Li, Hong Yu,

Tillering in rice is one of the most important agronomic traits. Rice tiller development can be divided into two main processes: the formation of the axillary bud and its subsequent outgrowth. Several genes critical for bud formation in rice have been identified by genetic studies; however, their molecular functions and ... Read more >>

Mol Plant (Molecular plant)
[2019, 12(8):1090-1102]

Cited: 1 time

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The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family.

Mary Galli, Arjun Khakhar, Zefu Lu, Zongliang Chen, Sidharth Sen, Trupti Joshi, Jennifer L Nemhauser, Robert J Schmitz, Andrea Gallavotti,

AUXIN RESPONSE FACTORS (ARFs) are plant-specific transcription factors (TFs) that couple perception of the hormone auxin to gene expression programs essential to all land plants. As with many large TF families, a key question is whether individual members determine developmental specificity by binding distinct target genes. We use DAP-seq to ... Read more >>

Nat Commun (Nature communications)
[2018, 9(1):4526]

Cited: 4 times

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Identification of cis-regulatory elements by chromatin structure.

Zefu Lu, William A Ricci, Robert J Schmitz, Xiaoyu Zhang,

The systematic identification of cis-regulatory elements (CREs) in plant genomes is critically important in understanding transcriptional regulation during development and in response to environmental cues. Several genome-wide structure-based methods have been successfully applied to plant genomes in the past few years. Here, we review recent results on the identification and ... Read more >>

Curr. Opin. Plant Biol. (Current opinion in plant biology)
[2018, 42:90-94]

Cited: 3 times

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IPA1 functions as a downstream transcription factor repressed by D53 in strigolactone signaling in rice.

Xiaoguang Song, Zefu Lu, Hong Yu, Gaoneng Shao, Jinsong Xiong, Xiangbing Meng, Yanhui Jing, Guifu Liu, Guosheng Xiong, Jingbo Duan, Xue-Feng Yao, Chun-Ming Liu, Hongqing Li, Yonghong Wang, Jiayang Li,

Strigolactones (SLs), a group of carotenoid derived terpenoid lactones, are root-to-shoot phytohormones suppressing shoot branching by inhibiting the outgrowth of axillary buds. DWARF 53 (D53), the key repressor of the SL signaling pathway, is speculated to regulate the downstream transcriptional network of the SL response. However, no downstream transcription factor ... Read more >>

Cell Res. (Cell research)
[2017, 27(9):1128-1141]

Cited: 24 times

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Tissue-Specific Ubiquitination by IPA1 INTERACTING PROTEIN1 Modulates IPA1 Protein Levels to Regulate Plant Architecture in Rice.

Jing Wang, Hong Yu, Guosheng Xiong, Zefu Lu, Yongqing Jiao, Xiangbing Meng, Guifu Liu, Xuewei Chen, Yonghong Wang, Jiayang Li,

Plant architecture, a collection of genetically controlled agronomic traits, is one of the decisive factors that determine grain production. IDEAL PLANT ARCHITECTURE1 (IPA1) encodes a key transcription factor with pleiotropic effects on regulating plant architecture in rice (Oryza sativa), and IPA1 expression is controlled at the posttranscriptional level by microRNA156 ... Read more >>

Plant Cell (The Plant cell)
[2017, 29(4):697-707]

Cited: 17 times

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Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes.

Zefu Lu, Brigitte T Hofmeister, Christopher Vollmers, Rebecca M DuBois, Robert J Schmitz,

Chromatin structure plays a pivotal role in facilitating proper control of gene expression. Transcription factor (TF) binding of cis-elements is often associated with accessible chromatin regions. Therefore, the ability to identify these accessible regions throughout plant genomes will advance understanding of the relationship between TF binding, chromatin status and the ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2017, 45(6):e41]

Cited: 21 times

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On the origin and evolutionary consequences of gene body DNA methylation.

Adam J Bewick, Lexiang Ji, Chad E Niederhuth, Eva-Maria Willing, Brigitte T Hofmeister, Xiuling Shi, Li Wang, Zefu Lu, Nicholas A Rohr, Benjamin Hartwig, Christiane Kiefer, Roger B Deal, Jeremy Schmutz, Jane Grimwood, Hume Stroud, Steven E Jacobsen, Korbinian Schneeberger, Xiaoyu Zhang, Robert J Schmitz,

In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (gene body methylation; gbM), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, to our knowledge the first instance for ... Read more >>

Proc. Natl. Acad. Sci. U.S.A. (Proceedings of the National Academy of Sciences of the United States of America)
[2016, 113(32):9111-9116]

Cited: 64 times

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On the Origin and Evolutionary Consequences of Gene Body DNA Methylation

Adam Bewick, Lexiang Ji, Chad Niederhuth, Eva-Maria Willing, Brigitte Hofmeister, Xiuling Shi, Li Wang, Zefu Lu, Nicholas Rohr, Benjamin Hartwig, Christiane Kiefer, Roger Deal, Jeremy Schmutz, Jane Grimwood, Hume Stroud, Steven Jacobsen, Korbinian Schneeberger, Xiaoyu Zhang, Robert Schmitz,

Abstract In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, the first known instance for an ... Read more >>

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Strigolactone Signaling in Arabidopsis Regulates Shoot Development by Targeting D53-Like SMXL Repressor Proteins for Ubiquitination and Degradation.

Lei Wang, Bing Wang, Liang Jiang, Xue Liu, Xilong Li, Zefu Lu, Xiangbing Meng, Yonghong Wang, Steven M Smith, Jiayang Li,

Strigolactones (SLs) are carotenoid-derived phytohormones that control many aspects of plant development, including shoot branching, leaf shape, stem secondary thickening, and lateral root growth. In rice (Oryza sativa), SL signaling requires the degradation of DWARF53 (D53), mediated by a complex including D14 and D3, but in Arabidopsis thaliana, the components ... Read more >>

Plant Cell (The Plant cell)
[2015, 27(11):3128-3142]

Cited: 76 times

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MONOCULM 3, an ortholog of WUSCHEL in rice, is required for tiller bud formation.

Zefu Lu, Gaoneng Shao, Jinsong Xiong, Yongqing Jiao, Jing Wang, Guifu Liu, Xiangbing Meng, Yan Liang, Guosheng Xiong, Yonghong Wang, Jiayang Li,

WUSCHEL (WUS) plays an essential role for the maintenance of meristem activity in dicots, but its function is still elusive in monocots. We isolated a new monoculm mutant, monoculm 3 (moc3), in which a point mutation causes the premature termination of rice O. sativa WUS (OsWUS). Morphological observation revealed that ... Read more >>

J Genet Genomics (Journal of genetics and genomics = Yi chuan xue bao)
[2015, 42(2):71-78]

Cited: 24 times

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Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture.

Zefu Lu, Hong Yu, Guosheng Xiong, Jing Wang, Yongqing Jiao, Guifu Liu, Yanhui Jing, Xiangbing Meng, Xingming Hu, Qian Qian, Xiangdong Fu, Yonghong Wang, Jiayang Li,

Ideal plant architecture1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, ... Read more >>

Plant Cell (The Plant cell)
[2013, 25(10):3743-3759]

Cited: 70 times

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Glabrous Rice 1, encoding a homeodomain protein, regulates trichome development in rice.

Jinjun Li, Yundong Yuan, Zefu Lu, Liusha Yang, Rongcun Gao, Jingen Lu, Jiayang Li, Guosheng Xiong,

Glabrous rice, which lacks trichomes on the rice epidermis, is regarded as an important germplasm resource in rice breeding. Trichomes are derived from aerial epidermal cells and used as a model to study the cell fate determination in plant. In Arabidopsis, the molecular mechanisms of trichome development have been well ... Read more >>

Rice (N Y) (Rice (New York, N.Y.))
[2012, 5(1):32]

Cited: 12 times

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Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice.

Yongqing Jiao, Yonghong Wang, Dawei Xue, Jing Wang, Meixian Yan, Guifu Liu, Guojun Dong, Dali Zeng, Zefu Lu, Xudong Zhu, Qian Qian, Jiayang Li,

Increasing crop yield is a major challenge for modern agriculture. The development of new plant types, which is known as ideal plant architecture (IPA), has been proposed as a means to enhance rice yield potential over that of existing high-yield varieties. Here, we report the cloning and characterization of a ... Read more >>

Nat. Genet. (Nature genetics)
[2010, 42(6):541-544]

Cited: 376 times

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