# Khushi Singh > I’m Khushi Singh, a biologist studying how gene expression is controlled in early development, by chromatin regulators and by mRNA–protein condensates. Source: https://khushisingh.in/ Author: Khushi Singh (khushisingh.in). Licence: CC BY 4.0 for text and original illustrations, unless a credit says otherwise. Evidence labels used on this site: established, strong evidence, emerging, hypothesis, debated. Where a page has Simple, Curious and Expert versions, all three follow. --- Chromatin · gene regulation · epigenetics · developmental biology I study how an embryo switches on its first genes. In the hours after fertilisation, control passes from the mother’s mRNAs and proteins to the embryo’s own genome: pioneer factors open chromatin, histone marks inherited from the egg or written from metabolites decide which genes respond first, and mRNA–protein condensates keep maternal messages silent and in place until they are needed. My work connects three active questions in the field: how metabolic state reaches chromatin at genome activation, how the material state of RNA–protein granules controls when their mRNAs are read, and how the same metabolic signals shape the behaviour of the whole animal. I bring fruit-fly genetics, single-molecule imaging and quantitative image analysis. Master’s research, Max Planck Institute of Immunobiology and Epigenetics, Freiburg (2026–27): metabolism and histone modifications at the maternal-to-zygotic transition, and metabolism and behaviour. ## Gene expression across regulatory layers *[Here the web page has an interactive activity; open the source URL to use it.]* **Text description and references** One cell, four chapters. Chromatin state: a pioneer factor opens an enhancer; acetyl, lactyl and methyl marks appear, fed by acetyl-CoA, lactyl-CoA and SAM from mitochondria and gut microbes; a cohesin loop brings enhancer and promoter together. Transcriptional bursting: Pol II fires in bursts and mRNAs are exported. mRNA fate: RBPs bind; some mRNAs are deadenylated and decayed, others are held in an RNP granule that grows by fusion and later released for translation. Protein, metabolism and feedback: enzymes drive metabolic flux, metabolites and regulators return to chromatin, and metabolic state links to behaviour. Inset: maternal mRNA, zygotic mRNA and protein over developmental time (schematic). [Sun et al. 2015](https://doi.org/10.1101/gr.192542.115) · [Hug et al. 2017](https://doi.org/10.1016/j.cell.2017.03.024) · [Davidson et al. 2019](https://doi.org/10.1126/science.aaz3418) · [Bothma et al. 2014](https://doi.org/10.1073/pnas.1410022111) · [Tadros et al. 2007](https://doi.org/10.1016/j.devcel.2006.10.005) · [Bushati et al. 2008](https://doi.org/10.1016/j.cub.2008.02.081) · [Bose et al. 2022](https://doi.org/10.1016/j.cell.2022.02.022) · [Wellen et al. 2009](https://doi.org/10.1126/science.1164097) · [Zhang et al. 2019](https://doi.org/10.1038/s41586-019-1678-1) · [Krautkramer et al. 2016](https://doi.org/10.1016/j.molcel.2016.10.025) · [Leitão-Gonçalves et al. 2017](https://doi.org/10.1371/journal.pbio.2000862) ## Core interests [Open questions and landmark work →](https://khushisingh.in/research/interests/) 01 ### [Chromatin-level control of gene expression in early development](https://khushisingh.in/research/interests/#chromatin) Which factors and complexes make an enhancer competent before the genome is activated, and which act only once transcription starts? My work: [Stage 5 and the MZT](https://khushisingh.in/research/model-system/#fly-stages) · [Current project: metabolism and histone marks](https://khushisingh.in/research/gut-to-germline/) 02 ### [Spatiotemporal gene regulation by mRNA–protein condensates](https://khushisingh.in/research/interests/#condensates) How do the composition and material state of an RNP condensate set when the mRNAs inside it are translated? My work: [oskar RNA condensates and sequential smFISH](https://khushisingh.in/research/oskar-condensates/) · [Prion protein phase separation](https://khushisingh.in/research/prion-phase-separation/) ### Connected interests - [Metabolism, chromatin and developmental timingMetabolites as donors for histone marks, and metabolic state as a developmental signal](https://khushisingh.in/research/interests/#metabolism) - [Post-transcriptional control and the timing of expressionmRNA stability, decay, localisation and translation as clocks for gene expression](https://khushisingh.in/research/interests/#mrna-timing) - [Gut microbiota and host chromatinMicrobial metabolites that reach host chromatin and the germ line](https://khushisingh.in/research/interests/#microbiota) - [Metabolic state and behaviourHow metabolism and microbes shape activity, sleep and the choices an animal makes](https://khushisingh.in/research/interests/#behaviour) - [Computational biology: quantitative imaging and codeImage analysis, quantification and analysis code for embryos and molecules](https://khushisingh.in/research/interests/#computational) - [Genetic tools, biosensors and biotechnologyTissue-specific genetics, genome editing and fluorescent sensors that report molecules in real time](https://khushisingh.in/research/interests/#tools) ## Making research easier to explore I am also building this site into a platform where biology research feels easy and explorative: visual explanations of methods and ideas, and free, open tools for biologists that run in the browser, with no sign-up. Images and files you analyse stay on your own computer. - [Image lab](https://khushisingh.in/tools/image-lab/) - [Lab calculators](https://khushisingh.in/tools/lab-calculators/) - [Sequence tools](https://khushisingh.in/tools/sequence/) - [Statistics helper](https://khushisingh.in/tools/statistics/) - [Nuclei counter](https://khushisingh.in/tools/nuclei-counter/) - [AlphaFold explorer](https://khushisingh.in/tools/alphafold/) [Explore the open tools →](https://khushisingh.in/tools/)