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Regulation and Evolution of Transcription Initiation

    The DNA sequence of a gene needs to be copied into mRNA molecules to carry out its function, a process called transcription. Cells are highly selective in where they initiate the transcription of their genes. The mechanism of locating the starting positions of transcription is shared by most eukaryotic organisms, such as humans, plants, and fungi. Yet, a distinct way of transcription initiation has been found in a few fungal species including Baker's yeast. The main research focus of my lab is to better understand the mechanisms of transcription initiation, and to investigate how the conserved mechanisms have diverged in yeasts.

    To acheive these goals, my lab generated a large collection of high-throughput sequencing data to determine the transcription start sites (TSS) at a single-nucleotide resolution for different species and in response to environmental cues. In addition, we built a user-friendly database to visualize these TSS data, and develop new software for TSS data analysis.

Most eukaryotic genes use multiple clusters of TSS (core promoters). The use of each core promoter is regulated in response to environmental cues (called core promoter shift). (A) An example of core promoter shift (CIK1) between two growth conditions, YPD and arrest. (B) Experimental validation displays the presence and shift of two CIK1 transcript isoforms in response to changing environments ( Lu and Lin 2019 ).

YeasTSS is a public database that visulizes and integrates functional genomics data relates to transcription regulation in different yeast species (Mcmillan et al. 2019).   

Evolution of Genomes

    An organism’s genome contains the complete set of its genetic information. Changes in the sequence and structure of a genome provide raw genetic materials for functional innovation and evolutionary divergence of living organisms. A long-standing question in evolutionary biology is to determine the links between the genomic variations and the evolution of new phenotypes of new species. 

    Another research focus of my lab is to better understand the evolutionary patterns and mechanisms of the genomic sequences, gene content and genome structures, and to learn their impacts on the evolution of biological novelty and diversity through comparative analyses of genome sequence data from different lineages of organisms.  

Our study found that a higher rate of rearrangement at the genome scale might have accelerated the speciation process and increased species richness during the evolution ( Rajeh et al. 2018. )

    Ribosomal protein (RP) genes encode structural components of ribosomes, the cellular machinery for protein synthesis. We found that massive duplications of RP genes have independently occurred by different mechanisms. The sequences of most RP paralogs have been homogenized by repeated gene conversion in each species, demonstrating parallel concerted evolution, which might have facilitated the retention of their duplicates ( Mullis et al. 2018).

Our research program  is supported by:



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