Plants are remarkably adaptable and can be found in nearly every environment on Earth, thriving in conditions ranging from complete darkness to extreme heat or cold. Our research focuses on understanding the mechanisms that allow plants this incredible plasticity and the capacity to reprogram themselves to survive and reproduce under such diverse conditions.

Shoot architecture

Plants generate different types of lateral organs (leaves and branches versus flowers) post-embryonically from stem cell descendants in the shoot apex. When flowers form is controlled by seasonal environmental cues and not only determines reproductive success in the wild and but resource allocation to different plant organs we eat. The plant specific helix-turn-helix pioneer transcription factor  LEAFY (LFY) licenses the switch to flower fate. We showed that the regulatory network downstream of LFY is comprised of a set of interlocking feed-forward loops  that integrate age, seasonal and hormonal cues to control upregulation APETALA1, a commitment factor of floral fate. Another key regulator, TERMINAL FLOWER1 promotes branch fate in lateral organs and protects the shoot apex from terminating, in opposition to LFY. It directly blocks accumulation of LFY and of APETALA1.

Organogenesis and differentiation in response to hormonal cues

The plant hormone auxin is critical for control organogenesis. We identified key targets of a master transcriptional regulator of the auxin hormone response, AUXIN RESPONSE FACTOR5/MONOPTEROS that promote flower primordium initiation and uncovered an auxin triggered chromatin state switch that is needed for primordium fate. In addition, auxin-mediated primordium initiation requires downregulation of the key pluripotency gene, SHOOT MERISTEMLESS (STM). Leaf differentiation, on the other hand, is requires lowered response to the hormone cytokinin. Our work on other hormones is listed under shoot architecture and SWI/SNF remodelers.

The role and Regulation of SWI/SNF chromatin remodeling complexes in transcriptional reprogramming in plants

ATP-dependent chromatin remodeling can change the chromatin state by using the energy derived from ATP hydrolysis to alter histone/DNA interactions. We uncovered key roles for plant SWI/SNF remodelers in development, in pluripotency (stem cell maintenance), in organogenesis and in overcoming Polycomb repression for induction of the floral homeotic genes during flower differentiation. Finally, activity of one of the SWI/SNF remodelers, BRM, restricts plant drought stress response to stress conditions, via modulation of SWI/SNF activity by signaling components that respond to the stress hormone ABA.

Polycomb silencing of gene expression programs in development and stress responses

Cell identity and response to environmental stress requires silencing of unnecessary or detrimental gene expression programs, frequently via Polycomb repression. We found that Polycomb Repressive Complexes are targeted by sequence specific binding proteins  to genetically encoded elements called Polycomb Response Elements or PREs in Arabidopsis.

The uncovered genome-encoded recruitment mechanism is very similar to that previously described in the fruitfly. Polycomb not only silences genes for flower formation until plants are ready to enter the reproductive program, it silences stem cells in flowers after all floral organs have been initiated.