Title: Comparative genomics and gene regulation in nematodes

Speaker: Monica C. Sleumer

              Postdoctoral Researcher

              Tsinghua National Laboratory for Information Science and Technology，

              Tsinghua Unversity, Beijing, China.

Host: ZHANG Zhihua

Time: 14: 00-15: 00, Sept 4, 2013

Location: First-floor seminar hall, Conference Room, BIG, CAS

Abstract: This talk details a series of investigations I have conducted over the past five years, each of which occurs at an intersection of four topics: comparative genomics, gene regulation, ribosomal protein genes, and trans-splicing in nematodes.

First, I searched for motifs in the upstream regions of orthologous genes from eight nematode species in order to find evolutionarily conserved regulatory elements. I annotated 26% of the motifs as similar to known binding sequences of transcription factors from the ORegAnno, JASPAR, and TRANSFAC transcription factor binding site databases and identified 82% of experimentally proven C. elegans regulatory elements.

I subsequently compared all motifs to each other and placed them into groups based on sequence similarity, which led to the discovery of a set of regulatory elements associated with ribosomal protein genes. One motif group was tested for regulatory function in a series of reporter gene expression experiments, revealing that the motif was necessary for the expression of nearby genes. I found that another motif group was associated with the trans-splice acceptor sites of ribosomal protein genes.

I then examined the upstream regions of all C. elegans ribosomal protein genes in detail and discovered nine motifs. Three motifs were partially similar to transcription factor binding sites from C. elegans, yeast, and Drosophila. Two of the elements had a very high rate of co-occurrence, and the distance between them displayed a complex frequency pattern that was related to their relative orientation. We tested the impact of three motifs on the expression of rpl-2 and showed that all three motifs are necessary to maintain its high natural expression level. One of the motifs was similar to the binding site of POP-1, and we showed that RNAi knockdown of pop-1 impacts the expression of rpl-2. I also investigated trans-splice acceptor site sequences and found that the trans-splice acceptor sites of ribosomal protein genes feature several four base pair patterns that occur between the splice junction and the ATG.

Lastly, I am currently involved in a multi-lab investigation of several strains of the pinewood nematode, including both pathogenic and non-pathogenic strains. I will discuss the significance of this species and share some preliminary results of the investigation.