MOBE-ChIP: Probing Cell Type-Specific Binding Through Large-Scale Chromatin Immunoprecipitation

AbstractAnatomical methods for determining cell-type specific connectivity are essential to inspire and constrain our understanding of neural circuit function. We developed new genetically-encoded reagents for fluorescence-synapse labeling and connectivity analysis in brain tissue, using a fluorogen-activating protein (FAP)-or YFP-coupled, postsynaptically-localized neuroligin-1 targeting sequence (FAP/YFPpost). Sparse viral expression of FAP/YFPpost with the cell-filling, red fluorophore dTomato (dTom) enabled high-throughput, compartment-specific localization of synapses across diverse neuron types in mouse somatosensory cortex. High-resolution confocal image stacks of virally-transduced neurons were used for 3D reconstructions of postsynaptic cells and automated detection of synaptic puncta. We took advantage of the bright, far-red emission of FAPpost puncta for multichannel fluorescence alignment of dendrites, synapses, and presynaptic neurites to assess subtype-specific inhibitory connectivity onto L2 neocortical pyramidal (Pyr) neurons. Quantitative and compartment-specific comparisons show that PV inputs are the dominant source of inhibition at both the soma and across all dendritic branches examined and were particularly concentrated at the primary apical dendrite, a previously unrecognized compartment of L2 Pyr neurons. Our fluorescence-based synapse labeling reagents will facilitate large-scale and cell-type specific quantitation of changes in synaptic connectivity across development, learning, and disease states.

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ASCOT identifies key regulators of neuronal subtype-specific splicing

Nature Communications ◽

10.1038/s41467-019-14020-5 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 2

Author(s):

Jonathan P. Ling ◽

Christopher Wilks ◽

Rone Charles ◽

Patrick J. Leavey ◽

Devlina Ghosh ◽

...

Keyword(s):

Rna Splicing ◽

Large Scale ◽

Splice Variants ◽

Next Generation Sequencing Data ◽

Data Sets ◽

Cell Type ◽

Sequencing Data ◽

Large Scale Analysis ◽

Cell Type Specific ◽

Public Archives

AbstractPublic archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by scientists. Here, we present ASCOT, a resource that uses annotation-free methods to rapidly analyze and visualize splice variants across tens of thousands of bulk and single-cell data sets in the public archive. To demonstrate the utility of ASCOT, we identify novel cell type-specific alternative exons across the nervous system and leverage ENCODE and GTEx data sets to study the unique splicing of photoreceptors. We find that PTBP1 knockdown and MSI1 and PCBP2 overexpression are sufficient to activate many photoreceptor-specific exons in HepG2 liver cancer cells. This work demonstrates how large-scale analysis of public RNA-Seq data sets can yield key insights into cell type-specific control of RNA splicing and underscores the importance of considering both annotated and unannotated splicing events.

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The microenvironment for erythropoiesis is regulated by HIF-2α through VCAM-1 in endothelial cells

Blood ◽

10.1182/blood-2007-11-122648 ◽

2008 ◽

Vol 112 (4) ◽

pp. 1482-1492 ◽

Cited By ~ 28

Author(s):

Toshiharu Yamashita ◽

Osamu Ohneda ◽

Ai Sakiyama ◽

Fumiko Iwata ◽

Kinuko Ohneda ◽

...

Keyword(s):

Endothelial Cells ◽

Chromatin Immunoprecipitation ◽

Normocytic Anemia ◽

Reporter Assay ◽

Cell Type ◽

Erythroid Progenitors ◽

Chromatin Immunoprecipitation Assay ◽

Hematopoietic Microenvironment ◽

Cell Type Specific ◽

Vascular Adhesion

Abstract Erythropoiesis is a dynamic process regulated by oxygen in vertebrates. Recent evidence has indicated that erythropoietin (Epo) expression is regulated by hypoxia-inducible transcription factors (HIFs), HIF-2α in particular. In this study, we report that knockdown mutation of HIF-2α in mice (kd/kd) results in normocytic anemia, despite Epo induction in response to hypoxia not being severely affected. Transplantation analyses clearly demonstrated that the hematopoietic microenvironment, but not the hematopoietic cells, was altered in kd/kd. Furthermore, cell-type specific recovery of HIF-2α expression in endothelial cells (ECs) abrogated the anemic condition of the kd/kd mice, indicating that HIF-2α in EC plays an essential role in supporting erythropoiesis. In the absence of HIF-2α, the expression of vascular adhesion molecule-1 (VCAM-1) was reduced significantly and restoration of VCAM-1 expression in kd/kd ECs enhanced the development of erythroid progenitors. Finally, a chromatin immunoprecipitation assay and a reporter assay indicated that VCAM-1 gene transcription is directly regulated by HIF-2α. These data suggest that the hematopoietic microenvironment required for erythropoiesis is dynamically regulated by oxygen through the functions of HIF-2α in ECs.

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State-dependent control of cortical processing speed via gain modulation

10.1101/2020.04.07.030700 ◽

2020 ◽

Author(s):

David Wyrick ◽

Luca Mazzucato

Keyword(s):

Information Processing ◽

Processing Speed ◽

Visual Processing ◽

Large Scale ◽

Internal State ◽

Gain Modulation ◽

Cell Type ◽

Information Processing Speed ◽

Afferent Projections ◽

Cell Type Specific

AbstractTo thrive in dynamic environments, animals can generate flexible behavior and rapidly adapt responses to a changing context and internal state. Examples of behavioral flexibility include faster stimulus responses when attentive and slower responses when distracted. Contextual modulations may occur early in the cortical hierarchy and may be implemented via afferent projections from top-down pathways or neuromodulation onto sensory cortex. However, the computational mechanisms mediating the effects of such projections are not known. Here, we investigate the effects of afferent projections on the information processing speed of cortical circuits. Using a biologically plausible model based on recurrent networks of excitatory and inhibitory neurons arranged in cluster, we classify the effects of cell-type specific perturbations on the circuit’s stimulus-processing capability. We found that perturbations differentially controlled processing speed, leading to counter-intuitive effects such as improved performance with increased input variance. Our theory explains the effects of all perturbations in terms of gain modulation, which controls the timescale of the circuit dynamics. We tested our model using large-scale electrophysiological recordings from the visual hierarchy in freely running mice, where a decrease in single-cell gain during locomotion explained the observed acceleration of visual processing speed. Our results establish a novel theory of cell-type specific perturbations linking connectivity, dynamics, and information processing via gain modulations.

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Strain Variation in Glycosaminoglycan Recognition Influences Cell-Type-Specific Binding by Lyme Disease Spirochetes

Infection and Immunity ◽

10.1128/.67.4.1743-1749.1999 ◽

1999 ◽

Vol 67 (4) ◽

pp. 1743-1749

Author(s):

Nikhat Parveen ◽

Douglas Robbins ◽

John M. Leong

Keyword(s):

Lyme Disease ◽

Specific Binding ◽

Strain Variation ◽

Cell Type ◽

Cell Type Specific

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Large-scale determination and characterization of cell type-specific regulatory elements in the human genome

Journal of Molecular Cell Biology ◽

10.1093/jmcb/mjx058 ◽

2017 ◽

Vol 9 (6) ◽

pp. 463-476 ◽

Cited By ~ 6

Author(s):

Can Wang ◽

Shihua Zhang

Keyword(s):

Human Genome ◽

Large Scale ◽

Regulatory Elements ◽

Cell Type ◽

Cell Type Specific

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MeDeCom: discovery and quantification of latent components of heterogeneous methylomes

Genome Biology ◽

10.1186/s13059-017-1182-6 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 36

Author(s):

Pavlo Lutsik ◽

Martin Slawski ◽

Gilles Gasparoni ◽

Nikita Vedeneev ◽

Matthias Hein ◽

...

Keyword(s):

Matrix Factorization ◽

Exploratory Study ◽

Large Scale ◽

Cell Type ◽

Computational Framework ◽

Biological Interpretation ◽

Cell Type Specific ◽

Latent Components ◽

Methylation Variation ◽

Non Negative Matrix Factorization

Abstract It is important for large-scale epigenomic studies to determine and explore the nature of hidden confounding variation, most importantly cell composition. We developed MeDeCom as a novel reference-free computational framework that allows the decomposition of complex DNA methylomes into latent methylation components and their proportions in each sample. MeDeCom is based on constrained non-negative matrix factorization with a new biologically motivated regularization function. It accurately recovers cell-type-specific latent methylation components and their proportions. MeDeCom is a new unsupervised tool for the exploratory study of the major sources of methylation variation, which should lead to a deeper understanding and better biological interpretation.

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