Oscillatory gene expression and the maintenance of temporal patterning

NIH Pandemic-Era Grants

Pandemic Era Grants

2024

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Principal Investigator: CHRISTOPHER Martin HAMMELL
Organization: COLD SPRING HARBOR LABORATORY
Fiscal Year: 2024
Award: $415,296
Funding agency: National Institute of General Medical Sciences

Project Abstract:
Developmental gene regulation is a multidimensional problem where signals converge to generate patterns of
transcription at the proper location (spatial regulation) and correct time (temporal regulation). An equally
important feature of this regulatory process involves generating the correct amount of transcription during
development as many key regulatory genes function in dosage sensitive manners where too much or too little
expression can lead to developmental defects or disease. At present, we have only a primitive understanding
about how the transcriptional output of developmentally regulated genes is established. Experiments outlined in
this proposal aim to directly address this problem by employing an in vivo imaging system in C. elegans larva
where GFP molecules are directly tethered to nascent RNAs while they are being actively transcribed in the
nucleus. This new platform enables us to directly quantify and model the real-time expression dynamics that
ultimately dictate transcriptional output of individual genes throughout development. In Aim 1, we will use this
system to dissect the mechanisms by which two transcription factors, BLMP-1 and LIN-42, modulate features of
transcriptional bursting (including burst frequency, duration, and amplitude) to tune transcriptional levels of key
microRNAs (including lin-4 and let-7) that dictate sequential patterns of cell fate specification. We will then probe
the genomic and molecular mechanisms that BLMP-1 employs to prime future transcription by remodeling
chromatin accessibility near target gene loci. In the final Aim, we will characterize the physical and functional
interactions between LIN-42 and several conserved nuclear hormone receptors (NHR-23RORγ and NHR-85Rev-
erbβ) that mediate temporal aspects of lin-4 and let-7 transcriptional activation. This avenue of research will reveal
the principles by which chromatin remodeling and its impact on modulating the transcriptional output of cyclically
expressed genes ensures the precision and robustness of cell fate specification during development.

Terms: <ATAC sequencing><ATAC-seq><ATACseq><Address><Alleles><Allelomorphs><Animals><Assay for Transposase-Accessible Chromatin using sequencing><Autoregulation><Basal Transcription Factor><Basal transcription factor genes><Binding><C elegans><C. elegans><C.elegans><CRISPR><CRISPR/Cas system><Caenorhabditis elegans><Cell Body><Cell Communication and Signaling><Cell Nucleus><Cell Signaling><Cells><ChIP Sequencing><ChIP-seq><ChIPseq><Chromatin><Chromatin Remodeling Complex><Chromatin Remodeling Factor><Clustered Regularly Interspaced Short Palindromic Repeats><Cyclicity><DNA><DNA Binding><DNA Binding Interaction><DNA Polymerase II><DNA Polymerase epsilon><DNA bound><DNA-Binding Proteins><DNA-Dependent DNA Polymerase II><Decision Making><Defect><Deoxyribonucleic Acid><Development><Developmental Gene><Dimensions><Disease><Disorder><Dissection><Embryo Development><Embryogenesis><Embryonic Development><Enhancers><Ensure><Enzyme Gene><Enzymes><Frequencies><Funding><Future><Gene Action Regulation><Gene Copy Number><Gene Dosage><Gene Expression><Gene Expression Regulation><Gene Regulation><Gene Regulation Process><Gene Transcription><General Transcription Factor Gene><General Transcription Factors><Genes><Genetic><Genetic Alteration><Genetic Change><Genetic Transcription><Genetic defect><Genomic approach><Genomics><Homeostasis><IVIS SpectrumCT><IVIS imaging><IVIS optical imaging><IVIS spectral imaging><IVIS spectrum><IVIS system><In Vitro><Individual><Intracellular Communication and Signaling><LIN><Larva><Lobular Intraepithelial Neoplasia><Lobular Neoplasia><Location><Maintenance><Maps><Measures><Mediating><Micro RNA><MicroRNAs><Microfluidics><Molecular><Molecular Interaction><Monitor><Mutation><Non-Polyadenylated RNA><Nuclear Hormone Receptor Superfamily><Nuclear Hormone Receptors><Nucleic Acid Regulator Regions><Nucleic Acid Regulatory Sequences><Nucleosomes><Nucleus><Outcome><Output><Pathway interactions><Pattern><Periodicity><Phenotype><Physiologic pulse><Physiological Homeostasis><Pol II><Postembryonic><Process><Proteins><Pulse><RNA><RNA Expression><RNA Gene Products><Regulation><Regulator Genes><Regulatory Regions><Reporter><Repression><Research><Resolution><Rhythmicity><Ribonucleic Acid><Signal Transduction><Signal Transduction Systems><Signaling><Site><System><Technology><Time><Transcript><Transcription><Transcription Activation><Transcription Factor Proto-Oncogene><Transcription Regulation><Transcription factor genes><Transcriptional Activation><Transcriptional Control><Transcriptional Regulation><Transcriptional Regulatory Elements><assay for transposase accessible chromatin followed by sequencing><assay for transposase accessible chromatin seq><assay for transposase accessible chromatin sequencing><assay for transposase-accessible chromatin with sequencing><biological signal transduction><cell fate specification><chromatin immunoprecipitation-sequencing><chromatin modifier><chromatin remodeling><developmental><dosage><experiment><experimental research><experimental study><experiments><gene function><gene locus><gene regulatory network><genetic locus><genetic regulatory element><genome mutation><genomic effort><genomic location><genomic locus><genomic strategy><imaging approach><imaging based approach><imaging platform><in vivo imaging system><miRNA><miRNAs><mutant><novel><pathway><programs><protein function><real time model><realtime model><recruit><regulatory gene><resolutions><response><trans acting element><transcription factor><µfluidic>