Aarthi Ramakrishnan

KMT2E recruitment by H3 serotonylation regulates neurodevelopmental chromatin dynamics

This study identifies KMT2E as a reader of H3K4me3Q5ser, showing its role in regulating chromatin dynamics and neurodevelopmental gene expression in ODLURO syndrome.

Quinone reductase 2 reads H3 serotonylation to support human cortical neuron development

This study identifies QR2 as a reader of H3Q5ser, showing its role in human neuron development through transcriptional and electrophysiological effects.

A shared transcriptional network in the nucleus accumbens supports resilience to chronic stress across sex.

The paper identifies a shared transcriptional network in the nucleus accumbens that supports stress resilience in both sexes and shows causal effects of hub genes.

Guidance receptor-mediated mechanocompliance of GBM cells facilitates immune-silent invasion

This study identifies how GBM cells use Plexin-D1 and Plexin-B2 to gain mechanocompliance, enabling immune-silent invasion through tissue.

Epigenetic editing of Cartpt promotes acquisition and extinction of cocaine memory

The paper uses CRISPR-based epigenetic editing to manipulate Cartpt expression in mice, showing it affects cocaine memory acquisition and extinction.

AlphaGenome Enhances Personal Gene Expression Prediction but Retains Key Limitations

AlphaGenome improves gene expression prediction over Enformer but still underperforms compared to models trained on individual-level data.

3D Brain Vascular Niche Model Captures Invasive Behavior and Gene Signatures of Glioblastoma

This paper develops a 3D brain vascular niche model to study GBM invasion and gene signatures, revealing glia-vascular contact influences transcriptional adaptation and poor prognosis.

ZBTB7A regulates MDD-specific chromatin signatures and astrocyte-mediated stress vulnerability in orbitofrontal cortex

The paper identifies ZBTB7A as a key regulator of MDD-specific chromatin signatures and astrocyte-mediated stress vulnerability in the orbitofrontal cortex.

Cell-Type-Specific Epigenetic Priming of Gene Expression in Nucleus Accumbens by Cocaine

This study identifies a novel epigenetic mechanism by which chronic cocaine exposure alters gene expression in nucleus accumbens neurons through H2A.Z depletion and chromatin changes.

Monomethylation of Lysine 27 at Histone 3 Confers Lifelong Susceptibility to Stress

This study identifies H3K27me1 as a chromatin scar that mediates lifelong stress susceptibility through its role in altering gene expression in the nucleus accumbens.

Transcriptional signatures in the rat medial prefrontal cortex associated with vulnerability and resilience across distinct phases of opioid use disorder

Serotonin transporter-dependent histone serotonylation in placenta contributes to the neurodevelopmental transcriptome

The paper shows that serotonin transporter-dependent H3 serotonylation in placenta regulates neurodevelopmental gene networks in embryos.

DeepRegFinder: Deep Learning-Based Regulatory Elements Finder

DeepRegFinder uses deep learning to predict enhancers and promoters from genomic data, outperforming existing methods across multiple cell types.

AhR restricts axon regeneration by balancing neuronal stress and growth response after injury

This study identifies AhR as a regulator of axon regeneration by balancing stress and growth responses after injury, showing that its inhibition promotes regeneration in nerve and spinal cord injury models.

Transcriptional signatures of heroin intake and seeking throughout the brain reward circuit

This study identifies transcriptional changes in the brain reward circuit across heroin exposure and seeking behaviors in mice, revealing molecular mechanisms and potential therapeutic targets for opioid use disorder.

Histone H3 serotonylation dynamics in dorsal raphe nucleus contribute to stress- and antidepressant-mediated gene expression and behavior

The paper investigates how serotonin modifies histone H3K4me3Q5ser dynamics in the dorsal raphe nucleus under stress and antidepressant exposure, showing its role in gene expression and behavior.

Histone monoaminylation dynamics are regulated by a single enzyme and promote neural rhythmicity

A single enzyme, TGM2, bidirectionally controls H3 monoaminylation dynamics, which, in turn, facilitate neural rhythmicity.

The Long Noncoding RNA FEDORA is a Cell-Type- and Sex-Specific Regulator of Depression

The paper identifies FEDORA, a lncRNA with sex- and cell-type-specific effects on depression in females.

ATAC and histone H3K9me3 landscapes revealed the altered epigenome by fetal-neonatal iron deficiency in the adult male rat hippocampus

This study examines how fetal-neonatal iron deficiency and prenatal choline supplementation affect epigenetic marks in adult rat hippocampi, revealing altered chromatin accessibility and H3K9me3 enrichment linked to gene dysregulation.

Plexin-B2 is a key regulator of cell mechanics during multicellular organization

This study identifies Plexin-B2 as a regulator of cell mechanics during multicellular organization, showing its role in modulating cell stiffness, contractility, and differentiation in human stem and progenitor cells.

Repeated morphine exposure activates synaptogenesis and other neuroplasticity-related gene networks in the prefrontal cortex of male and female rats

This study identifies gene networks and pathways activated by repeated morphine exposure in rat prefrontal cortex, revealing sex-specific differences in neuroplasticity-related gene expression.

Adolescent Social Isolation Reprograms the Medial Amygdala: Transcriptome and Sex Differences in Reward

The paper shows that adolescent social isolation causes sex-specific changes in the medial amygdala's transcriptome and behavior, with Crym playing a key role in these effects.

Early life stress alters transcriptomic patterning across reward circuitry in male and female mice

This study shows that early life stress alters transcriptomic patterns in reward circuitry of male and female mice, increasing sensitivity to adult stress.

Brg1 controls neurosensory cell fate commitment and differentiation in the mammalian inner ear

This study identifies Brg1's role in specifying neurosensory lineage and differentiation in the mammalian inner ear by interacting with Eya1/Six1 and regulating chromatin structure.

Zfp189 Mediates Stress Resilience Through a CREB-Regulated Transcriptional Network in Prefrontal Cortex

The paper identifies Zfp189 as a key driver of a transcriptional network promoting stress resilience in prefrontal cortex neurons through CREB regulation.