Short activation domains control chromatin association of transcription factors.

Transcription factors regulate gene expression with DNA-binding domains (DBDs) and activation domains. Despite mounting evidence to the contrary, it is frequently assumed that DBDs are solely responsible for interacting with DNA and chromatin. Here, we used single-molecule tracking of transcription factors in living cells to show that short activation domains can control the fraction of molecules bound to chromatin.

Collective unstructured interactions drive chromatin binding of transcription factors.

Eukaryotic transcription factors (TFs) contain both structured DNA-binding domains (DBDs) and intrinsically disordered regions (IDRs). While the structures and sequence preferences of DBDs have been extensively characterized, the role of IDR-mediated interactions in chromatin binding and nuclear organization remains poorly understood, in part because these interactions have been difficult to measure in living cells. Here, we use a recently developed single-molecule technique, proximity-assisted photoactivation (PAPA), to investigate how IDRs influence TF associations with each other and with chromatin, focusing on the factors Sp1 and Klf1.

Assembly and Dynamics of Transcription Initiation Complexes.

Gene expression is essential for life and development, allowing the cell to modulate mRNA production in response to intrinsic and extracellular cues. Initiation of gene transcription requires a highly regulated molecular process to assemble multisubunit complexes into the preinitiation complex (PIC). Attempts to visualize these processes have been driven largely by electron microscopy, with near atomic-level resolution producing static snapshots complemented by low-resolution fluorescence cell imaging.

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis.

Mycobacterium tuberculosis (MTB) displays the remarkable ability to transition in and out of dormancy, a hallmark of the pathogen's capacity to evade the immune system and exploit susceptible individuals. Uncovering the gene regulatory programs that underlie the phenotypic shifts in MTB during disease latency and reactivation has posed a challenge. We develop an experimental system to precisely control dissolved oxygen levels in MTB cultures in order to capture the transcriptional events that unfold as MTB transitions into and out of hypoxia-induced dormancy.

Path-seq identifies an essential mycolate remodeling program for mycobacterial host adaptation.

The success of (MTB) stems from its ability to remain hidden from the immune system within macrophages. Here, we report a new technology (Path-seq) to sequence miniscule amounts of MTB transcripts within up to million-fold excess host RNA Using Path-seq and regulatory network analyses, we have discovered a novel transcriptional program for mycobacterial cell wall remodeling when the pathogen infects alveolar macrophages in mice. We have discovered that MadR transcriptionally modulates two mycolic acid desaturases / to initially promote cell wall remodeling upon macrophage infection and, subsequently, reduces mycolate biosynthesis upon entering dormancy.

Transverse dielectrophoretic-based DNA nanoscale confinement.

Confinement of single molecules within nanoscale environments is crucial in a range of fields, including biomedicine, genomics, and biophysics. Here, we present a method that can concentrate, confine, and linearly stretch DNA molecules within a single optical field of view using dielectrophoretic (DEP) force. The method can convert an open surface into one confining DNA molecules without a requirement for bonding, hydrodynamic or mechanical components.