Biology subjects

Manu, M.

Publications and source records attributed to Manu, M..

3 recordsLinked to original sources

bioRxiv2018

The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages

During development, cell identity is determined by lineage-specific transcriptional programs en-coded in the cis-regulatory DNA sequence of developmental genes. The sequence-level regulatory logic--identities of bound transcription factors (TFs), TF binding sites, and TF regulatory roles--of most developmental cis-regulatory modules (CRMs) is yet to be determined. We had previously developed an approach for inferring regulatory logic de novo by training sequence-based thermo-dynamic models on comprehensive reporter activity and gene expression datasets and applied it to Cebpa, an important hematopoietic gene. Here, we experimentally test thermodynamic models to decode the cis-regulatory logic of 4 enhancers and 3 silencers neighboring Cebpa at the resolution of individual binding sites. Cebpa is expressed at high and intermediate levels in neutrophils and macrophages respectively and downregulated in non-myeloid lineages. We tested the binding sites and functional roles of inferred TFs by designing and constructing mutated CRMs and comparing theoretical predictions of their activity against empirical measurements. Reporter activity was measured in PUER cells, which can be induced to differentiate into macrophages or neutrophils. All four enhancers were found to be simultaneously active in undifferentiated PUER cells and early-stage macrophages and neutrophils, and activated by combinations of PU.1, C/EBP family TFs, Egr1, and Gfi1. We show that silencers repress the activity of the proximal promoter in a dominant manner in G1ME cells, which are derived from the red-blood cell lineage. Dominant repression in G1ME cells can be traced to binding sites for GATA and Myb, a motif shared by all of the silencers. Finally, we demonstrate that GATA and Myb act redundantly to silence the proximal promoter. The result that silencers quench the promoter selectively in non-myeloid cells indicates that dominant repression is a novel mechanism for resolving hematopoietic lineages. Furthermore, Cebpa has a fail-safe cis-regulatory architecture, featuring several functionally similar CRMs, each of which contains redundant binding sites for multiple TFs. Lastly, by experimentally demonstrating the predictive ability of our sequence-based thermodynamic models, this work highlights the utility of this computational approach for decoding the logic of mammalian gene regulation.

developmental biology↗

bioRxiv2018

Diverse nonlinear modulation of visual features by retinal amacrine cells

The prevailing hierarchical view of the visual system consists of parallel circuits that begin in the retina, which then sum effects across sequential levels, increasing in complexity. Yet a separate type of interaction, whereby one visual pattern changes the influence of another, known as modulation, has received much less attention in terms of its circuit mechanisms. Retinal amacrine cells are a diverse class of inhibitory interneurons that are thought to have modulatory effects, but we lack a general understanding of their functional types. Using dynamic causal experiments in the salamander retina perturbing amacrine cells along with an unsupervised computational framework, we find that amacrine cell modulatory effects cluster into two distinct types. One type controls ganglion cell sensitivity to individual visual features, and a second type controls the ganglion cells output gain, acting to gate all features. These results establish three separate general roles of amacrine cells - to generate primary visual features, to use context to select specific visual features and to gate retinal output.

neuroscience↗

bioRxiv2017

Synchronous inhibitory pathways create both efficiency and diversity in the retina

Visual information is conveyed from the retina to the brain by a diverse set of retinal ganglion cells. Although they have differing nonlinear properties, nearly all ganglion cell receptive fields on average compute a difference in intensity across space and time using a region known as the classical or linear surround1,2, a property that improves information transmission about natural visual scenes3,4. The spatiotemporal visual features that create this fundamental property have not been quantitatively assigned to specific interneurons. Here we describe a generalizable causal approach using simultaneous intracellular and multielectrode recording to directly measure and manipulate the sensory feature conveyed by a neural pathway to a downstream neuron. Analyzing two inhibitory cell classes, horizontal cells and linear amacrine cells, we find that rather than transmitting different temporal features, the two inhibitory pathways act synchronously to create the salamander ganglion cell surround at different spatial scales. Using these measured visual features and theories of efficient coding, we computed a fitness landscape representing the information transmitted using different weightings of the two inhibitory pathways. This theoretical landscape revealed a ridge that maintains near-optimal information transmission while allowing for receptive field diversity. The ganglion cell population showed a striking match to this prediction, concentrating along this ridge across a wide range of positions using different weightings of amacrine or horizontal cell visual features. These results show how parallel neural pathways synthesize a sensory computation, and why this architecture achieves the potentially competing objectives of high information transmission of individual ganglion cells, and diversity among receptive fields.

neuroscience↗