HOW CAN WE HELP YOU? Call 1-800-TRY-CHOP
Sivaramakrishnan Laboratory Research Overview
The Sivaramakrishnan Lab uses microscopic worm models of Caenorhabditis elegans to study gene expression in developing embryos. The C. elegans embryo develops through an invariant lineage; wild-type embryos follow a stereotyped pattern of cell divisions, giving rise to the exact set of 558 cells at the end of embryogenesis. The identities and lineage histories of each of these cells are very well known, providing a beautiful system to study what happens to individual cell fates when transcriptional programs are perturbed.
Learn more about our key areas of focus:
Transcription occurs through multiple intricately regulated steps. Yet, it is still unknown which steps and to what extent each step impacts the transcription rate. Based on preliminary data, three aspects are likely important to achieve the appropriate rate and mRNA dosage.
This lab will work toward determining the contributions of:
- Transcription factories
- Transcription initiation
- Elongation, in regulating transcription rate and dosage
RNA levels are affected by transcription noise. The relationship between the transcription kinetics and transcriptional precision is not well understood.
Further, mechanisms that reduce transcription noise and support the highly invariant development of the C. elegans embryo are unknown.
We are combining live RNA imaging with automated lineage analysis to link transcription dynamics directly with single-cell decisions.
Our estimates of genome-wide transcript accumulation across stages in the early C. elegans embryo determined that rates were highest at the 8-cell stage, soon after the onset of zygotic transcription and when cell sizes are relatively larger. Cell size-dependent scaling of mRNA quantities has been reported in multiple organisms, although the factors involved in scaling are not completely known.
Using RNAi and mutants that increase or decrease cell size, we will investigate the dependence of mRNA quantities on the size of cells undergoing cell fate decisions.
The ability to correlate molecular changes in individual cells with whole embryo defects provides an exciting opportunity to model human developmental disorders of transcription in the worm embryo model.
Disorders caused by mutations in genes encoding the basal transcription machinery have common phenotypes, but the molecular basis for transcription-associated developmental disorders is unclear.
In collaboration with the Arcus Omics initiative at CHOP, our lab will create worm models of pathogenic variants or variants of uncertain significance in transcriptional component genes.