We study cell division and fate in plants and yeasts. Gene networks controlled by rice transcription factors for flowering stem and flower development is a research focus. Post-transcriptional processes fine-tune genomic expression. We examine links between splicing, chromatin status and cell division in yeast with implications for plant gene expression.
- Rice RFL regulates inflorescence form; OsMADS1 a regulatory hub for flowers
- Contextual roles for essential splicing factors in splicing, chromatin and cell division
Genetic regulators of flowering: Developmental of multicellular eukaryotes can be controlled by master regulators with cascading effects on cell and tissue fate. In higher plants, flowering requires a dramatic change in the fate of organs that emerge from the apical meristem- a plant growth center. Remarkable diversity exists in flowering time, form and function of the flowering stem (inflorescence) and floral organs. Yet, how evolutionarily conserved regulators confer different architectures are not well understood. Rice, a genetically tractable cereal-grass model, produces modified flowers on higher-order inflorescence branches. Its unique floral organs are the lemma, palea and lodicules (Figure 1A) whose homology to dicot organs is debated. We study rice inflorescence and flower development with the overall goal to identify networks of transcription factors, chromatin regulators, and signaling pathways for meristem and organ fate.
In Arabidopsis LFY triggers the floral program; yet as LFY orthologs have species-specific expression patterns this opens several conceptual questions. Our work on rice RFL showed unique cis- enhancers drive its dynamic expression in inflorescence branch meristems, which is important for branching (Figure 1A). Intriguingly, RFL had a general role as a meristem factor as it promoted basal axillary meristems outgrowth as secondary shoots. We hypothesize that RFL controls plant architecture and reproduction by meristem specific mechanisms.
The stereotypic position of floral organs is largely determined by combined activity of MADS-domain transcription factors. We studied functions for rice OsMADS1, a MADS factor belonging to the SEP clade, by comparative phenotypic and transcriptomic studies of loss-of-function mutants, transgenics with induced overexpression and the wild type. We deciphered its pivotal role for floral meristem fate, in organ differentiation and timely meristem termination (Figure 1C). The OsMADS1 transcriptome and its chromatin occupancy demonstrate its temporally varied effects on downstream transcription factors, chromatin modifiers, protein and RNA homeostasis factors, and hormonal pathways. These snapshots of OsMADS1 driven gene networks (Figure 1C) give leads on pathways that ensure proper floral development.
Pre-mRNA splicing and links to regulated gene expression and cellular processes: RNA splicing, an essential step in eukaryotic gene expression, generates functional RNAs from a genes primary transcript. Splicing requires precise excision of non-functional intronic segments and this can expand the complexity of expressed information from any genome. Defects in splicing cause diseases and developmental disorders. Our research on fission yeast factors, Prp18, Slu7 and Prp16, deciphered their intron-context-dependent roles for accurate splice-site selection and for alternative splice isoforms under diverse growth and stress conditions. Further, some splicing factors, mediate centromeric heterochromatinzation and thereby influence cell division and mitosis. As fission yeast gene exon-intron architectures closely resemble those in higher plants, our findings preview how post-transcriptional mechanisms may fine-tune developmental gene expression.
We will further our investigations of key regulatory networks during rice inflorescence and flower development. Broad aims are to probe spatial and temporal pathways downstream to hub factors like RFL, OsMADS1 and some of their key target genes (Figure 1B, C). Our preliminary data indicate RNA binding and RNA modification factors could influence floral developmental gene expression; these leads will be examined in rice and mechanistic studies could rely on fission yeast as a surrogate. We will continue probing roles for spliceosomal proteins in splicing dependent, and independent pathways (Figure 2) that lead to constitutive and/ or facultative heterochromatinzation using fission yeast as a model system.
Project Title: Investigating partners of rice transcription factors and their target genes during floret development
Aniket Girish Parab
Project Title: Gene targets of OsMADS1 and RFL in Rice inflorescence and floral development – understanding the transcriptional and epigenetic regulator of gene target
Project Title: Understanding the differential action of fission yeast splicing factors and its impact on transcriptome diversity and cellular response
Project Title: Developmental regulators of unique grass floret organs: organ differentiation and position of the lodicule; a modified grass petal analogue
Project Title: Investigating the role of rice RFL in meristem fate: vegetative axillary meristems vs. reproductive inflorescence with floral meristems
Project Title: Deciphering non canonical roles of splicing factors in model yeasts
Project Title: Gene regulatory network for control of flowering; fine-tuning expression by post transcription epigenetic factors.
currently UGC Kothari fellow
Project Title: Characterization and identification of protein partners of OsMADS1 transcription factor in developing Rice panicle
Project Title: Mutational analyses of pre-mRNA splicing factors spprp18 and spprp16 to decipher their splicing functions and interacting partners)
Project Title: Functional characterization of OSMADS2 B- class transcription factor in rice [Oryza sativa])
Project Title: Deciphering the mechanism of action of RFL, a gene involved in rice tillering and panicle branching
D Narsimha Murthy
Junior Scientific Assistant