How cells regulate gene expression to achieve cell type-specific outcomes is a fundamental question in biology. In recent years, it has become evident that gene regulation involves simultaneous spatiotemporal changes in 3D genome organization and transcriptome, and it is the interrelationship between them that leads to determination of cell types. One critical biological system where their interplay is central for cell type specification is early mammalian development. In early embryos, the crosstalk between newly emerging embryonic 3D nuclear architecture and gene expression drives the first, deterministic cell fate decisions leading to subsequent proper developmental progression. 

In Jachowicz lab we aim to understand how the cell-specific transcription program and 3D genome architecture arise, are controlled, and interplay to determine the fate of each individual cell in a developing embryo. Our research is directed towards the precise molecular mechanisms at work, and our goal is to provide a comprehensive picture of the regulatory molecules involved, including non-canonical factors such as "dark" genome elements. 



Dark Genome

Recent studies, including our work, show that DNA and RNA from the “dark” genome can affect genome organization and gene expression, and may act as a previously unappreciated driving force during early development. Dark elements comprise more than fifty percent of the mammalian genome and include transposons, repeats, IncRNAs, and other non-canonical genes. These elements can have functional promoters and enhancers, contain multiple binding sites in their DNA and RNAs, confer tissue-specific regulation and expression patterns, and can paste themselves into new genomic locations causing genome rearrangements.

Yet, despite clear evidence of important and unique capabilities of dark genome DNA and RNAs, their roles are not well understood. In fact, the broad functions of non-canonical RNAs in gene regulation and nuclear architecture during cell-state transitions and decrease in cell potency remain largely unexplored. In the Jachowicz lab, we are particularly fascinated by the potential of dark genome elements in shaping genome functions during early mammalian development.


Our goal is to understand how the interplay between 3D genome organization and the transcriptome regulates genome functions during early development and to uncover the role of dark genome elements in regulating events post fertilization.

We believe that our research will allow us to create a comprehensive mechanistic picture of events and factors that drive changes in cell potency and cell-state transitions following fertilization. It will provide fundamental insights into the control of genome functions at the molecular and cellular level over a period of time, corresponding to the most pronounced redesigning events taking place during early development.


Gene expression is known to be heterogenous from cell-to-cell, and early embryos are defined by a mixture of multiple distinct states. Thus, answering these biological questions requires our ability to directly relate structural dynamics to transcriptional outputs within the same individual cell. To address these challenges, we employ novel genome-wide sequencing methods based on Split-Pool Recognition of Interactions by Tag Extension (SPRITE) combined with microscopy, CRISPR technologies, and various biochemical approaches.

SPRITE-based methods can measure higher-order DNA structures with increased resolution for short- and long-range regulatory elements in single cells, detect various classes of RNAs (e.g. mRNAs, lncRNAs, small RNAs), and simultaneously capture both 3D DNA structure and RNA levels and localization. As such, they have enormous potential to detect the dynamic and heterogeneous processes of genome reorganization and transcriptome rewiring post fertilization, and allow to map how nuclear DNA and RNA composition change while cell fate is determined.

In our studies, we combine in vivo and in vitro approaches by using embryonic stem cells and early mouse embryos. These systems provide an ideal context in which to study the relationship between 3D genome structure and function because large scale remodeling of nuclear architecture occurs while at the same time, the embryonic transcription program is initiated, and the first cell fate decision is made. The reduced complexity of this model facilitates causal studies and provides clear phenotypic outcomes.

Selected Publications

Arrastia, MV., Jachowicz, JW., Ollikainen, N., Curtis, MS., Lai, C., Quinodoz, SA., Selck, DA., Ismagilov, RF., Guttman, M. (2022). Single-cell measurement of higher-order 3D genome organization with scSPRITE. Nat Biotechnol. 40(1):64-73

Jachowicz, JW., Strehle, M., Banerjee, AK., Blanco, MR., Thai, J., Guttman, M. (2022). Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome. Nat Struct Mol Biol. 29(3):239-249

Quinodoz, SA., Jachowicz, JW., Bhat, P., Ollikainen, N., Banerjee, AK., Goronzy, IN., Blanco, MR., Chovanec, P., Chow, A., Markaki, Y., Thai, J., Plath, K., Guttman, M. (2021). RNA promotes the formation of spatial compartments in the nucleus. Cell. 184(23):5775-5790.e30

Jachowicz, JW., Bing, X., Pontabry, J., Bošković, A., Rando, OJ., Torres-Padilla, ME. (2017). LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo. Nat Genet. 49(10):1502-1510

Jachowicz, JW., Santenard, A., Bender, A., Muller, J., Torres-Padilla, ME. (2013). Heterochromatin establishment at pericentromeres depends on nuclear position. Genes Dev. 27(22):2427-32