The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis

Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remains largely unexplored. Here, we show that suppression of the RNA helicase DDX6 endows human and mouse primed embryonic stem cells (ESCs) with a differentiation-resistant, “hyper-pluripotent” state, which readily reprograms to a naive state resembling the preimplantation embryo. We further demonstrate that DDX6 plays a key role in adult progenitors where it controls the balance between self-renewal and differentiation in a context-dependent manner. Mechanistically, DDX6 mediates the translational suppression of target mRNAs in P-bodies. Upon loss of DDX6 activity, P-bodies dissolve and release mRNAs encoding fate-instructive transcription and chromatin factors that re-enter the ribosome pool. Increased translation of these targets impacts cell fate by rewiring the enhancer, heterochromatin, and DNA methylation landscapes of undifferentiated cell types. Collectively, our data establish a link between P-body homeostasis, chromatin organization, and stem cell potency

Dynamics of BAF- Polycomb Complex Opposition on Heterochromatin in Normal and Oncogenic States

The opposition between polycomb repressive complexes (PRC) and BAF (mSWI/SNF) complexes plays critical roles in development and disease. Mutations in the genes encoding BAF subunits contribute to over 20% of human malignancy, yet the underlying mechanisms remain unclear owing largely to a lack of assays to assess BAF function in vivo. To address this, we have developed a widely applicable recruitment assay system and find that BAF opposes PRC by rapid, ATP-dependent eviction, leading to the formation of accessible chromatin. Reversing this process results in reassembly of facultative heterochromatin. Surprisingly, BAF-mediated PRC eviction occurs in the absence of PolII occupancy, transcription, and replication. Further, we find that tumor suppressor and oncogenic BAF complex mutations result in differential effects on PRC eviction. These studies define a mechanistic sequence underlying the resolution and formation of facultative heterochromatin and demonstrate that BAF opposes polycomb complexes on a minute-by-minute basis to provide epigenetic plasticity

Gender & Sex in Methods and Measurement - Tool 2: Effective Recruitment Strategies

Once we have determined who will be eligible for our research studies, we need to develop a recruitment strategy – a clear plan for identifying and reaching prospective participants, providing them with information about the study, and enrolling them into it. This tool will explore considerations to take into account when recruiting people who are marginalized and minoritized based on their genders, sexes and sexualities

Gender & Sex in Methods and Measurement - Tool 4: Asking About and Measuring Participants' Genders & Sexes

This tool helps researchers understand whether, when and how to ask participants about their genders & sexes. There is no single, correct way to measure people’s genders and sexes, in part because these terms have multiple meanings. This tool serves as a guide to walk researchers through some common approaches to gender and sex measurement with a focus on intentionality, precision and harm reduction

Gender & Sex in Methods and Measurement - Tool 3: Sampling Plans and Data Analyses

When we recruit participants to our research studies, they become a part of our sample – the group of people we will collect data from, or who we will generate data with, to answer our research questions or test our hypotheses. There are several points to consider about sampling in relationship to gender, sex, and sexuality. Here, we offer questions for researchers to ask themselves, issues to carefully consider, and some illustrative example situations

Gender & Sex in Methods and Measurement - Tool 6: Working with Pre-Existing, Secondary and Older Data

Researchers aren’t always working with primary data, they often work with pre-existing, secondary and older data. Sometimes, this means that the data being used was not collected in a way that aligns with recommended practices for measuring gender, sex and sexuality. How should researchers deal with these issues? Tool #6 provides some strategies and tips