In metazoans, gene expression is regulated in a tissue/cell-type-specific manner predominantly via stretches of noncoding sequence referred to as cis regulatory modules (CRMs). CRMs contain 1 or more DNA binding sites for 1 or more sequence-specific, regulatory transcription factors that function to modulate the expression of target gene(s). CRMs that activate gene expression are typically referred to as enhancers, while those that repress gene expression are referred to as silencers. Transcriptional enhancers activate gene expression in a tissue-specific manner in development and also in adult cells in response to cellular or environmental stimuli. Like enhancers, silencers can function in a cell-type-specific manner. Indeed, silencers may contribute a crucial role in the specification of precise gene expression patterns, thus enabling the establishment of sharp expression domains, such as during development. Numerous genomic and computational studies have focused primarily on predicting and characterizing enhancers. In contrast to enhancers, silencers are much less well understood. Few transcriptional silencers have been described, and there have been no large-scale efforts to catalog silencers nor to identify predictive features of silencers, such as chromatin marks. The overarching goals of this project are to identify and quantify the activities of tissue-specific silencers, to identify the chromatin signatures of silencers, and to elucidate the regulatory roles of silencer-associated (co-)repressors and DNA sequence motifs. In pursuing these goals, we will develop novel ?quantitative silencer-FACS-Seq? technology for quantitative screening of CRMs for tissue-specific silencer activity, and BioTAP-XL-TALE technology for identification of proteins found in tissue-specific chromatin assembled at specific cis-regulatory elements in cells where they act as silencers versus in cells where they act as enhancers. We will focus on the developing embryonic mesoderm in Drosophila melanogaster as our model system. We anticipate that the features and chromatin signatures of silencers identified in this project will be evolutionarily conserved across metazoans, including human.

Public Health Relevance

In metazoans, gene expression is controlled in a tissue- and cell-type specific manner through regulatory sequence elements in the genome. While elements that activate gene expression, termed transcriptional enhancers, have been studied extensively, those that suppress gene expression, termed transcriptional silencers, are poorly characterized. In this project, we will focus on Drosophila embryonic mesoderm as a model system. The goals of this project are to identify larger sets of tissue-/cell-type specific silencers and elucidate the chromatin signatures of silencers in this important developmental tissue. We anticipate that chromatin signatures of silencers in Drosophila will be conserved in mammals.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
1R01HG009723-01
Application #
9376298
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Pazin, Michael J
Project Start
2017-08-01
Project End
2021-05-31
Budget Start
2017-08-01
Budget End
2018-05-31
Support Year
1
Fiscal Year
2017
Total Cost
Indirect Cost
Name
Brigham and Women's Hospital
Department
Type
DUNS #
030811269
City
Boston
State
MA
Country
United States
Zip Code
02115