The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family

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

doi:10.1038/s41467-018-06977-6

Cited by 163 publications

(183 citation statements)

References 72 publications

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“…Therefore, these tissue-specific accessibility maps can help drive computational-based predictions of TF binding and refine results from in vitro methods such as DNA Affinity and Purification sequencing (DAP-seq) [8,90]. Along with co-expression networks of genes from the same tissue type, the accessible chromatin maps provide a basis for strengthening TF-DNA interaction predictions.…”

Section: Discussionmentioning

confidence: 98%

The regulatory landscape of early maize inflorescence development

Parvathaneni

Bertolini

Shamimuzzaman

et al. 2019

Preprint

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The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. Here, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen-and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profiled accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classified approximately 1.6 percent of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3' ends of maize genes. This approach mapped regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor (TF) occupancy data were used to annotate regulatory factors, such as combinatorial TF binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based only on functional regions delineated by MNase hypersensitivity revealed new SNP-trait associations in known regulators of inflorescence development as well as new candidates. These analyses provide a comprehensive look into the cisregulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

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Section: Discussionmentioning

confidence: 98%

The regulatory landscape of early maize inflorescence development

Parvathaneni

Bertolini

Shamimuzzaman

et al. 2019

Preprint

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“…Interestingly, 14/15 of these significant terms were associated with "binding" activities, including protein, nucleoside, and ribonucleoside binding. Furthermore, we found these exonic DMRs were enriched at transcription factor binding sites which were identified using DAP-seq [48] (Permutation P-value < 0.001).…”

Section: Hypomethylated Regions In Maize Are Involved In Distal Gene mentioning

confidence: 93%

Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

Lyu

et al. 2020

Preprint

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DNA methylation is a ubiquitous chromatin feature -in maize, more than 25% of cytosines in the genome are methylated. Recently, major progress has been made in describing the molecular mechanisms driving methylation, yet variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here we leveraged whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to investigate the adaptive and phenotypic consequences of methylation variations in maize. By using a novel estimation approach, we inferred the methylome site frequency spectrum (mSFS) to estimate forward and backward methylation mutation rates and selection coefficients. We only found weak evidence for direct selections on methylations in any context, but thousands of differentially methylated regions (DMRs) were identified in population-wide that are correlated with recent selections. Further investigation revealed that DMRs are enriched in 5' untranslated regions, and that maize hypomethylated DMRs likely helped rewire distal gene regulation. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, our HiChIP data indicated that the interactive loops between DMRs and respective downstream genes were present in B73, a modern maize line, but absent in teosinte. And functional analyses suggested that these DMRs likely served as cis-acting elements that modulated gene regulation after domestication. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.

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“…SEMs of the leaf surface showed that the epicuticular wax crystal deposition defects of ad1-ref were enhanced by the fdl1 mutation ( Figure 5D). To investigate the hypothesis that FDL1/MYB94 could directly regulate the expression of AD1 and other KCS genes, we performed DAP-seq, an in vitro DNA-TF binding assay that captures genomic DNA binding events in their native sequence context (O'Malley et al, 2016;Galli et al, 2018). In vitro expressed HALO-FDL1 proteins were incubated with maize genomic DNA libraries and FDL1bound DNA fragments were identified using next-generation sequencing.…”

Section: The Myb Transcription Factor Fused Leaves1 Positively Regulamentioning

confidence: 99%

“…Reads were mapped to the B73v3 genome as described in Galli et al, 2018(Galli et al, 2018. In brief, fastq files were trimmed using trimmomatic with the following bam Coverage with 10bp bin size and FPKM normalization.…”

Section: Dap-seq Read Mapping Filtering and Peak Callingmentioning

confidence: 99%

The FUSED LEAVES1/ADHERENT1Regulatory Module Is Required For Maize Cuticle Development And Organ Separation

Liu

Bourgault

Strable

et al. 2020

Preprint

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ORCID IDs: 0000-0002-9928-7114 (X.Liu); 0000-0002-0260-8285 (J. Strable); 0000-0002-1901-2971 (A. Gallavotti) Running title: maize cuticle formationOne sentence summary: The classic maize mutant adherent1, first isolated a century ago, is affected in an enzyme responsible for cuticle formation that is regulated by the MYB transcription factor FUSED LEAVES1. ABSTRACTIn land plants all aerial epidermal cells are covered by the cuticle, an extracellular hydrophobic layer. The cuticle represents a primary barrier between cells and the 4 Cutin is a polyester matrix composed mainly of glycerol and long-chain (C16

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The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family

Cited by 163 publications

References 72 publications

The regulatory landscape of early maize inflorescence development

The regulatory landscape of early maize inflorescence development

Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

The FUSED LEAVES1/ADHERENT1Regulatory Module Is Required For Maize Cuticle Development And Organ Separation

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