Research Summary

Plants have the fascinating ability to constantly adapt their development according to changes in the surrounding environment. This plasticity is provided by meristems, small groups of undifferentiated self-regenerating stem cells, continuously formed throughout development. Meristem number, position and activity are a major source of variability in the architecture of different plant species, since they determine if, when and how branches and flowers are formed during both vegetative and reproductive development. Plant architecture, extensively modified during the domestication of crop species, still represents a major target of selection in modern breeding. In particular, in cultivated grasses, the major worldwide food source, vegetative and reproductive branching represents a major component of yield. 

Our research is aimed at understanding: i) how pluripotent meristematic cells are formed during development; ii) how meristem fate and organ initiation are regulated; iii) the role of the plant hormone auxin in shaping plant architecture and regulating meristem function (; iv) the molecular mechanisms of plant domestication and evolution.  

In my laboratory we investigate the molecular mechanisms behind the formation and activity of meristems, by combining the strength of traditional forward and reverse genetics with molecular biology. We use maize mutants affected in branch and flower formation to identify and understand the genes and gene networks controlling plant architecture. We isolated several genes affecting branching in both tassels and ears, the male and female inflorescences of maize. Among these, we identified two transcription factors (BARREN STALK1 and BARREN STALK FASTIGIATE1), an auxin biosynthetic enzyme (SPARSE INFLORESCENCE1) involved in the formation of new meristems, and a transcriptional corepressor (RAMOSA1 ENHANCER LOCUS2) that regulates the decision of meristems to form either a branch or a flower during development. To move towards a systemic understanding of the molecular mechanisms regulating plant architecture, it is essential to achieve a more comprehensive view of the relationships of these genes and pathways, and for this purpose we are using different genomic approaches. We also pursue functional comparative analysis, by using different model plant systems (maize and Arabidopsis thaliana) to highlight the similarities and differences at the origin of the variability in plant architectures observed in natural and domesticated environments.

Currently funded projects:

IOS-1546873 Genomic and synthetic approaches linking auxin signaling to functional domains in maize

IOS-1456950  Characterizing the role of transcriptional repression in maize development and domestication


Recent Publications

Bartlett, A, O'Malley R, Huang SC, Galli M, Nery JR, Gallavotti A, Ecker JR.  2017.  Mapping genome-wide transcription factor binding sites using DAP-seq. Nature Protocols. 12(8):1659-1672. AbstractWebsite
To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX). The resulting DNA library is incubated with an affinity-tagged in vitro-expressed TF, and TF–DNA complexes are purified using magnetic separation of the affinity tag. Bound genomic DNA is eluted from the TF and sequenced using next-generation sequencing. Sequence reads are mapped to a reference genome, identifying genome-wide binding locations for each TF assayed, from which sequence motifs can then be derived. A researcher with molecular biology experience should be able to follow this protocol, processing up to 400 samples per week.
Chatterjee, M, Liu Q, Menello C, Galli M, Gallavotti A.  2017.  The Combined Action of Duplicated Boron Transporters Is Required for Maize Growth in Boron Deficient Conditions. Genetics. AbstractWebsite
The micronutrient boron is essential in maintaining the structure of plant cell walls and is critical for high yields in crop species. Boron can move into plants by diffusion or by active and facilitated transport mechanisms. We recently showed that mutations in the maize boron efflux transporter ROTTEN EAR (RTE) cause severe developmental defects and sterility. RTE is part of a small gene family containing five additional members (RTE2-RTE6) that show tissue specific expression. The close paralogous gene RTE2 encodes a protein with 95% amino acid identity with RTE and is similarly expressed in shoot and root cells surrounding the vasculature. Despite sharing similar functions with RTE, mutations in the RTE2 gene do not cause growth defects in the shoot, even in boron deficient conditions. However, rte2 mutants strongly enhance the rte phenotype in soils with low boron content, producing shorter plants that fail to form all reproductive structures. The joint action of RTE and RTE2 is also required in root development. These defects can be fully complemented by supplying boric acid, suggesting that diffusion or additional transport mechanisms overcome active boron transport deficiencies in the presence of an excess of boron. Overall, these results suggest that RTE2 and RTE function are essential for maize shoot and root growth in boron deficient conditions.
O’Malley, RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR.  2016.  Cistrome and epicistrome features shape the regulatory DNA landscape. Cell. 165:1280-1292. AbstractWebsite
The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TF-specific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism.
Galli, M and Gallavotti, A.  2016.  Expanding the regulatory network for meristem size in plants. Trends in Genetics. 32(6):372-383. AbstractWebsite
The remarkable plasticity of post-embryonic plant development is due to groups of stem-cell-containing structures called meristems. In the shoot, meristems continuously produce organs such as leaves, flowers, and stems. Nearly two decades ago the WUSCHEL/CLAVATA (WUS/CLV) negative feedback loop was established as being essential for regulating the size of shoot meristems by maintaining a delicate balance between stem cell proliferation and cell recruitment for the differentiation of lateral primordia. Recent research in various model species (Arabidopsis, tomato, maize, and rice) has led to discoveries of additional components that further refine and improve the current model of meristem regu- lation, adding new complexity to a vital network for plant growth and productivity.