Seminar: Dr. Michael J. Gilchrist

Using high resolution time series data to detect transcriptional events

Date:
5 November 2014 13:30 hrs. - 14:30 hrs.
Location:
Figdor Lecture Theatre, 8th floor RIMLS Building, Geert Grooteplein 26-28, route 289
Title:
Using high resolution time series data to detect transcriptional events
Speaker(s):

Dr. Michael J. Gilchrist, MRC National Institute for Medical Research, London, UK

Host(s):

Prof. Gert Jan C. Veenstra, Dr. Simon J. van Heeringen, Dept. of  Molecular Developmental Biology, RIMLS

05-11-2014 13:30:0005-11-2014 14:30:00Europe/AmsterdamUsing high resolution time series data to detect transcriptional events  Figdor Lecture Theatre, 8th floor RIMLS Building, Geert Grooteplein 26-28, route 289Rimlsrimls@radboudumc.nl

Remarks / more information:

Gilchrist , MikeThe maternal-zygotic transition, in the early stages of animal development, marks the switch from control by maternal gene products to activation of zygotic transcription and control by the embryo. Known in part as the mid-blastula transition (MBT) in Xenopus, the process is well described in many model systems, but not fully understood at a molecular level. To explore this we have used high-resolution expression profiling to identify the timing and pattern of gene expression in Xenopus tropicalis from fertilisation through to the onset of gastrulation. In this manner we are able to dissect the process of gene expression for individual genes, and determine onset times for short periods of rapid, sustained change in expression levels, which we equate with transcriptional on-switches. In a similar manner we can detect apparent transcriptional off-switches, although the mechanisms are less clear. Using these onset times, we identify three waves of gene activity: a post-fertilisation wave involving polyadenylation of maternal mRNAs; a broad wave of zygotic transcription detectable as early as the seventh cleavage and extending beyond the MBT at the twelfth cleavage; and a shorter post-MBT wave of transcription about one hour later, as development proceeds. We show that the later wave of transcription represents, at least in part, the activation of downstream targets of transcription factors activated in the earlier wave of transcription at MBT. These time scales provide a framework for further exploration of gene regulatory networks in early vertebrate development.

Key Publications:

  • High-resolution analysis of gene activity during the Xenopus mid-blastula transition. Development. 141:1927-39, 2014
  • Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis. Genome Research 19, 1766-1775, 2009
  • Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data. BMC Bioinformatics 9, 442, 2008


<< back to all events