Biology subjects

Sudarsanam, S.

Publications and source records attributed to Sudarsanam, S..

5 recordsLinked to original sources

bioRxiv2025

Cell-type-selective synaptogenesis during the development of excitatory connectivity in the mammalian neocortex

The function of mammalian neocortex relies on the timing of axon extension and establishment of cell-type-biased patterns of excitatory synaptic connections. A subtype of excitatory neurons, layer 6 corticothalamic neurons (L6CThNs), ultimately exhibit a marked preference for synapsing onto parvalbumin-positive (PV) inhibitory interneurons over more common excitatory cells in layers 6 and 4 (L6, L4). We show that the intracortical axons of L6CThNs develop in phases, elongating within L6, then pausing before extending translaminar branches into L4. Decreasing L6CThN excitability selectively enhanced axon growth in L6 but not later elaboration in L4. For both layers, we tested whether preferential synaptogenesis onto rarer PV interneurons, or promiscuous synapse formation followed by selective pruning, generated adult connectivity. We found that L6CThNs formed functional AMPA-receptor-containing synapses preferentially onto PV interneurons. Silent L6CThN synapses were not detected. Our findings show that cell-type-biased synaptogenesis underlies the formation of functional cell-type-specific excitatory connections in the neocortex.

neuroscience↗

bioRxiv2025

ATaRVa: Analysis of Tandem Repeat Variation from Long Read Sequencing data

Tandem Repeats (TRs) are contiguous repetitions of DNA motifs whose variations modulate key cellular processes and traits. Their expansions are causally linked to over 70 neurological disorders in humans. Historically, genotyping TRs has been challenging due to their low sequence complexity and allele lengths exceeding typical short-read sequencing capabilities. While long-read sequencing improves TR genotyping by spanning large expansions and sequencing native DNA molecules, existing long-read genotypers often are inaccurate, computationally inefficient, and show platform-specific biases. Here, we present ATaRVa, a genotyper that achieves superior accuracy across both PacBio and Oxford Nanopore platforms, while running [~]15x faster than existing tools. Beyond genotyping, ATaRVa features sequence-level motif decomposition and methylation profiling. Evaluated across diverse datasets and genome-wide catalogs, ATaRVa especially excels in low coverage datasets, and accurately identifies known pathogenic expansions in clinical samples. Importantly, by quantifying uninterrupted target motifs in a population scale analysis, the tool systematically resolves false positives caused by benign, interrupted alleles. In addition, we present VisuaMiTRa, an auxiliary interface that enables interactive visualization of motif-level decomposition and base-level methylation of the TR alleles. By combining high computational efficiency with sequence-level structural awareness, ATaRVa provides a highly scalable framework for TR analysis in both population cohorts and clinical settings.

genomics↗

bioRxiv2025

Mef2c Controls Postnatal Callosal Axon Targeting by Regulating Sensitivity to Ephrin Repulsion

Cortical connectivity is contingent on ordered emergence of neuron subtypes followed by the formation of subtype-specific axon projections. Intracortical circuits, including long-range callosal projections, are crucial for information processing, but mechanisms of intracortical axon targeting are still unclear. We find that the transcription factor Myocyte enhancer factor 2-c (Mef2c) directs the development of somatosensory cortical (S1) layer 4 and 5 pyramidal neurons during embryogenesis. During early postnatal development, Mef2c expression shifts to layer 2/3 callosal projection neurons (L2/3 CPNs), and we find a novel function for Mef2c in targeting homotopic contralateral cortical regions by S1-L2/3 CPNs. We demonstrate, using functional manipulation of EphA-EphrinA signaling in Mef2c-mutant CPNs, that Mef2c downregulates EphA6 to desensitize S1-L2/3 CPN axons to EphrinA5-repulsion at their contralateral targets. Our work uncovers dual roles for Mef2c in cortical development: regulation of laminar subtype specification during embryogenesis, and axon targeting in postnatal callosal neurons. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/634300v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@108c788org.highwire.dtl.DTLVardef@163c6c3org.highwire.dtl.DTLVardef@18e6d8borg.highwire.dtl.DTLVardef@1b9f9e4_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIMef2c is required for the development of L4 and L5 neurons in the embryonic neocortex C_LIO_LIPostnatally, Mef2c is enriched in L2/3 neurons and is required for axon targeting C_LIO_LIL2/3-specific Mef2c deletion leads to EphA6 upregulation C_LIO_LIMef2c deletion in L2/3 neurons sensitizes them to EfnA5 repulsion in the contralateral cortex C_LI

neuroscience↗

bioRxiv2023

MAP1B Regulates Cortical Neuron Interstitial Axon Branching Through the Tubulin Tyrosination Cycle

Regulation of directed axon guidance and branching during development is essential for the generation of neuronal networks. However, the molecular mechanisms that underlie interstitial axon branching in the mammalian brain remain unresolved. Here, we investigate interstitial axon branching in vivo using an approach for precise labeling of layer 2/3 callosal projection neurons (CPNs), allowing for quantitative analysis of axonal morphology at high acuity and also manipulation of gene expression in well-defined temporal windows. We find that the GSK3{beta} serine/threonine kinase promotes interstitial axon branching in layer 2/3 CPNs by releasing MAP1B-mediated inhibition of axon branching. Further, we find that the tubulin tyrosination cycle is a key downstream component of GSK3{beta}/MAP1B signaling. We propose that MAP1B functions as a brake on axon branching that can be released by GSK3{beta} activation, regulating the tubulin code and thereby playing an integral role in sculpting cortical neuron axon morphology. HIGHLIGHTS- GSK3{beta} activation induces excessive interstitial axon branching in excitatory cortical neurons - MAP1B, acting as a brake, is a downstream effector of GSK3{beta}-mediated axon branching - MAP1B inhibition of axon branching is released by GSK3{beta} phosphorylation - GSK3{beta}/MAP1B regulation of interstitial axon branching is through modification of the tubulin code

neuroscience↗

bioRxiv2023

Drebrin Regulates Collateral Axon Branching in Cortical Layer II/III Somatosensory Neurons

Proper cortical lamination is essential for cognition, learning, and memory. Within the somatosensory cortex, pyramidal excitatory neurons elaborate axon collateral branches in a laminar-specific manner that dictates synaptic partners and overall circuit organization. Here, we leverage mouse models, single-cell labeling and imaging approaches to identify intrinsic regulators of laminar-specific collateral, also termed interstitial, axon branching. We developed new approaches for the robust, sparse, labeling of layer II/III pyramidal neurons to obtain single-cell quantitative assessment of axon branch morphologies. We combined these approaches with cell-autonomous loss-of-function (LOF) and over-expression (OE) manipulations in an in vivo candidate screen to identify regulators of cortical neuron axon branch lamination. We identify a role for the cytoskeletal binding protein drebrin (Dbn1) in regulating layer II/III cortical projection neuron (CPN) collateral axon branching in vitro. LOF experiments show that Dbn1 is necessary to suppress the elongation of layer II/III CPN collateral axon branches within layer IV, where axon branching by layer II/III CPNs is normally absent. Conversely, Dbn1 OE produces excess short axonal protrusions reminiscent of nascent axon collaterals that fail to elongate. Structure-function analyses implicate Dbn1S142 phosphorylation and Dbn1 protein domains known to mediate F-actin bundling and microtubule (MT) coupling as necessary for collateral branch initiation upon Dbn1 OE. Taken together, these results contribute to our understanding of the molecular mechanisms that regulate collateral axon branching in excitatory CPNs, a key process in the elaboration of neocortical circuit formation. Significance StatementLaminar-specific axon targeting is essential for cortical circuit formation. Here, we show that the cytoskeletal protein drebrin (Dbn1) regulates excitatory layer II/III cortical projection neuron (CPN) collateral axon branching, lending insight into the molecular mechanisms that underlie neocortical laminar-specific innervation. To identify branching patterns of single cortical neurons in vivo, we have developed tools that allow us to obtain detailed images of individual CPN morphologies throughout postnatal development and to manipulate gene expression in these same neurons. Our results showing that Dbn1 regulates CPN interstitial axon branching both in vivo and in vitro and may aid in our understanding of how aberrant cortical neuron morphology contributes to dysfunctions observed in Autism Spectrum Disorder (ASD) and epilepsy.

neuroscience↗