Biology subjects

Burns, D.

Publications and source records attributed to Burns, D..

4 recordsLinked to original sources

bioRxiv2023

Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency

The concentration and stoichiometry of transcription factors (TFs) determine cellular identity and can be manipulated to drive cell state transitions. Understanding how changes in TF concentration regulate chromatin state and expression across cell state transitions remains a challenge. We investigated this relationship by profiling chromatin accessibility and gene expression at single-cell resolution across a densely sampled time course of reprogramming human fibroblasts to induced pluripotent stem cells via ectopic expression of OCT4, SOX2, KLF4, and MYC (OSKM). Using deep learning sequence models of base-resolution chromatin accessibility profiles across cell states, we deciphered predictive transcription factor (TF) motif syntax in regulatory elements, inferred affinity- and concentration-dependent dynamics of TF footprints, linked peaks to putative target genes, and elucidated rewiring of cis-regulatory networks. Our models reveal that early in reprogramming, OSK, at supraphysiological concentrations, rapidly open transient regulatory elements by occupying non-canonical low-affinity binding sites. As OSK concentration falls, the accessibility of these transient elements decays as a function of motif affinity. We find that these OSK-dependent transient elements sequester the somatic TF AP-1. This redistribution is strongly associated with the silencing of fibroblast-specific genes within individual nuclei. Together, our integrated single-cell resource and models reveal insights into the cis-regulatory code of reprogramming at unprecedented resolution. We establish a quantitative, predictive framework that links TF stoichiometry, motif syntax, and somatic silencing to provide new perspectives on the control of cell identity by TFs during fate transitions.

genetics↗

bioRxiv2023

Temperature-Sensitive Contact Modes Allosterically Gate TRPV3

TRPV Ion channels are sophisticated molecular sensors designed to respond to distinct temperature thresholds. The recent surge in cryo-EM structures has provided numerous insights into the structural rearrangements accompanying their opening and closing; however, the molecular mechanisms by which TRPV channels establish precise and robust temperature sensing remain elusive. In this work we employ molecular simulations, multi-ensemble contact analysis, graph theory, and machine learning techniques to reveal the temperature-sensitive residue-residue interactions driving allostery in TRPV3. We find that groups of residues exhibiting similar temperature-dependent contact frequency profiles cluster at specific regions of the channel. The dominant mode clusters on the ankyrin repeat domain and displays a linear melting trend while others display non-linear trends. These modes describe the residue-level temperature response patterns that underlie the channels functional dynamics. With network analysis, we find that the community structure of the channel changes with temperature. And that a network of high centrality contacts connects distant regions of the protomer to the gate, serving as a means for the temperature-sensitive contact modes to allosterically regulate channel gating. Using a random forest model, we show that the contact states of specific temperature-sensitive modes are indeed predictive of the channel gates state. Supporting the physical validity of these modes and networks are several residues identified with our analyses that are reported in literature to be functionally critical. Our results offer high resolution insight into thermo-TRP channel function and demonstrate the utility of temperature-sensitive contact analysis.

biophysics↗

bioRxiv2022

Heart cockle shells transmit sunlight for photosynthesis using bundled fiber optic cables and condensing lenses

Many animals convergently evolved photosynthetic symbioses. In bivalves, giant clams (Cardiidae: Tridacninae) gape open to irradiate their symbionts, but heart cockles (Cardiidae: Fraginae) stay closed because sunlight passes through transparent windows in their shells. Here, we show that heart cockles (Corculum cardissa and spp.) use biophotonic adaptations to transmit sunlight for photosynthesis. Heart cockles transmit 11-62% of photosynthetically active radiation (mean=31%) but only 5-28% of potentially harmful UV radiation (mean=14%) to their symbionts. Beneath each window, microlenses condense light to penetrate more deeply into the symbiont-rich tissue. Within each window, aragonite forms narrow fibrous prisms perpendicular to the surface. These bundled "fiber optic cables project images through the shell with a resolution of >100 lines/mm. Parameter sweeps show that the aragonite fibers size ([~]1{micro}m diameter), morphology (long fibers rather than plates), and orientation (along the optical c-axis) transmit more light than many other possible designs. Heart cockle shell windows are thus: (i) the first instance of fiber optic cable bundles in an organism to our knowledge; (ii) a second evolution, with epidermal cells in angiosperm plants, of condensing lenses for photosynthesis; and (iii) a photonic system that efficiently transmits useful light while protecting photosymbionts from UV radiation.

evolutionary biology↗

bioRxiv2022

Temperature Sensitive Contacts in Disordered Loops Tune Enzyme I Activity

Homologous enzymes with identical folds often exhibit different thermal and kinetic behaviors. Understanding how enzyme sequence encodes catalytic activity at functionally optimal temperatures is a fundamental problem in biophysics. Recently it was shown that the residues that tune catalytic activities of thermophilic/mesophilic variants of the C-terminal domain of bacterial Enzyme I (EIC) are largely localized within disordered loops, offering a model system with which to investigate this phenomenon. In this work, we employ molecular dynamics simulations and mutagenesis experiments to reveal a mechanism of sequence-dependent activity tuning of EIC homologs. We find that a network of contacts in the catalytic loops is particularly sensitive to changes in temperature, with some contacts exhibiting distinct linear or non-linear temperature-dependent trends. Moreover, these trends define structurally clustered dynamical modes and can distinguish regions that tend toward order or disorder at higher temperatures. Assaying several thermophilic EIC mutants, we show that complementary mesophilic mutations to the most temperature-sensitive positions exhibit the most enhanced activity while mutations to relatively temperature insensitive positions exhibit the least enhanced activities. These results provide a mechanistic explanation of sequence-dependent temperature tuning and offer a computational method for rational enzyme modification. SignificanceTemperature affects the catalytic rates of all enzymes. The impact of temperature on the catalytic activity of an enzyme, however, is convoluted from contributions of protein sequence, structure, and dynamics. As such, understanding and designing the molecular features of enzymes which tune catalytic rates at different temperatures remains a fundamental challenge in biophysics. In this work we have employed molecular simulations and mutagenesis experiments to reveal the temperature tuning mechanism of mesophilic and thermophilic homologues of the C domain of bacterial Enzyme l. We find that enzymes can be tuned to their physiological temperatures through a network of temperature-sensitive residue contacts localized in the disordered loops. Furthermore, we find that among temperature-sensitive contacts some exhibit linear and others non-linear dependence on temperature. These clues offer a promising physics-based approach for tuning enzyme activity.

biophysics↗