# Resource Project

> **NIH NIH U41** · UNIVERSITY OF WASHINGTON · 2020 · $2,489,070

## Abstract

B. Research Project/Resource Production
Summary
Transcription factors (TFs) are proteins that contain site-specific DNA binding domains and regulate gene
expression during development. The complete set of TFs are known for C. elegans and D. melanogaster
and with their small genome sizes and well studied embryonic development, it is possible to determine their
in vivo binding profiles and function. The modENCODE and modERN projects have generated ChIP-seq
binding profiles for a substantial number of TFs. Our output has dramatically increased during modERN
through the use of transgenic organisms expressing tagged-TFs. This approach has proven to be more
practical than developing TF-specific antibodies, and has been adopted by other projects such as
ENCODE. These transgenic lines constitute a valuable resource to the fly and worm communities. We aim
to continue our production of GFP-tagged TFs, producing lines for the remaining 340 TFs in worm and 260
in flies. Furthermore, we will continue to use these new lines along with recently generated lines to
generate ChIP-seq data, generating binding profiles for all expressed TFs in both organisms, ~400 in each.
During the modERN project we created a pipeline to knockdown TF expression using RNAi and identified
the genes that showed differential expression using RNA-seq. While we have had success knocking-down
TFs with RNAi in Drosophila, in C. elegans we have utilized homozygous viable deletion strains. In both,
we assay expression in embryos before the onset of TF expression, at the peak of expression, and two
hours post peak or at terminal differentiation. Using these two approaches, we will continue to generate
RNA-seq data on TF loss-of-function lines, focusing on TFs with orthologs in humans or between fly and
worm.

## Key facts

- **NIH application ID:** 9944663
- **Project number:** 5U41HG007355-07
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** ROBERT H WATERSTON
- **Activity code:** U41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $2,489,070
- **Award type:** 5
- **Project period:** — → —

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9944663

## Citation

> US National Institutes of Health, RePORTER application 9944663, Resource Project (5U41HG007355-07). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9944663. Licensed CC0.

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