Raj Chari

Optogenetic induction of TAD boundary pairing promotes gene activity

This study uses OptoTet to manipulate TAD boundaries and shows that boundary pairing enhances gene activity for ERRFI1 but not MYC.

QuantiTrack: A unified software to study protein dynamics in living cells

QuantiTrack, a MATLAB GUI, unifies single-molecule detection, tracking, quality control and mobility analyses; for glucocorticoid receptor, hormone washout cut bound fraction, dwell times and low-mobility occupancy.

Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy

The paper uses PhIX-MS and cryo-EM to map transient interactions at proteasomes, revealing structural details of proteins like TXNL1 and PSMD5.

Engineering CAR T Cells for Hepatocellular Carcinoma Recurrence after Liver Transplantation

This paper develops GPC3-targeted CAR T cells resistant to immunosuppressive drugs and with reduced alloreactivity, showing efficacy in preclinical models and feasibility for clinical use post-liver transplantation.

Disruption of CTCF binding by germline non-coding variants in CDKN2B suppress CDKN2A expression and predispose to melanoma

The paper identifies non-coding variants in CDKN2B that disrupt CTCF binding, reduce CDKN2A expression, and increase melanoma risk in families.

Large distant deletion disrupts CDKN2A enhancer and predisposes to melanoma

The paper identifies a large distant deletion in DMRTA1 upstream of CDKN2A that predisposes to melanoma by disrupting regulatory sequences and reducing p16 expression.

CRISPR-Based Gene Dependency Screens reveal Mechanism of BRAF Inhibitor Resistance in Anaplastic Thyroid Cancer

This study identifies TAZ deficiency as synthetically lethal with BRAF inhibitors in anaplastic thyroid cancer, revealing a mechanism of resistance and a potential therapeutic target.

Orderly mitosis shapes interphase genome organization

The paper identifies molecular regulators of centromere distribution by screening nuclear proteins and shows that mitosis influences interphase genome organization.

Functional characterization of the 9q34.13 locus identifies RAPGEF1 as modulating risk for melanoma and nevi via RAS activation

This study identifies RAPGEF1 as a gene modulating melanoma and nevi risk through RAS activation, using fine-mapping, expression data, and functional assays.

Weak SLP-76-PLC-γ1 interaction in the LAT-nucleated multi-protein complex fine-tunes TCR signal strength to optimize T cell responsiveness

The paper shows that a weak SLP-76-PLC-γ1 interaction fine-tunes TCR signal strength, optimizing T cell responsiveness by controlling PLC-γ1 activity.

Metastatic organotropism in small cell lung cancer

This study identifies key cellular programs and pathways driving metastatic organotropism in small cell lung cancer using preclinical models and multiomic profiling.

Structural perturbation of chromatin domains with multiple developmental regulators can severely impact gene regulation and development

The paper shows that disrupting chromatin domain boundaries with multiple developmental regulators can cause severe gene dysregulation and developmental defects in mice.

The ubiquitin ligase HUWE1 enhances WNT signaling by antagonizing destruction complex-mediated β-catenin degradation and through a mechanism independent of β-catenin stability

This study identifies HUWE1 as a regulator of WNT signaling through two mechanisms: antagonizing destruction complex-mediated β-catenin degradation and an independent pathway, both requiring HUWE1's ubiquitin ligase activity.

In vivo CRISPR screening identifies NF1/RASA1/TP53 co-mutations and downstream MEK signaling as a common key mechanism of sinonasal tumorigenesis

This study identifies NF1/RASA1/TP53 co-mutations and MEK signaling as key drivers of sinonasal tumorigenesis through in vivo CRISPR screening and drug response testing.

p53-induced RNA-binding protein ZMAT3 inhibits transcription of a hexokinase to suppress mitochondrial respiration

This study identifies ZMAT3 as a regulator of HKDC1 transcription through JUN, suppressing mitochondrial respiration in colorectal cancer cells.

Transfer RNA acetylation regulates in vivo mammalian stress signaling

This study shows that tRNA acetylation regulates stress signaling in mammals by affecting ribosome function and interacting with the Gcn2 kinase.

Mapping chromatin interactions at melanoma susceptibility loci and cell-type specific dataset integration uncovers distant gene targets of cis-regulation

The paper identifies candidate causal variants and genes at melanoma risk loci using capture-HiC and integrates multi-omics data to prioritize cis-regulatory interactions.

Genetic regulation of TERT splicing contributes to reduced or elevated cancer risk by altering cellular longevity and replicative potential

This study identifies VNTR6-1 and rs10069690 as regulators of TERT splicing and expression, influencing cancer risk and telomere dynamics through altered telomerase isoform ratios.

Targeting the sphingolipid rheostat in IDH1mut glioma alters cholesterol homeostasis and triggers apoptosis via membrane degradation

This study shows that altering sphingosine levels in IDH1mut glioma cells disrupts cholesterol homeostasis, leading to apoptosis through effects on cholesterol synthesis, uptake, and efflux.

AVENGERS: Analysis of Variant Effects using Next Generation sequencing to Enhance BRCA2 Stratification

The paper develops AVENGERS, a method using CRISPR-Cas9 to classify BRCA2 variants as functional or nonfunctional, improving the interpretation of variants of uncertain significance.

AGO2 silences mobile transposons in the nucleus of quiescent cells

The paper shows AGO2 localizes to the nucleus in quiescent cells to silence mobile transposons via RNA interference.

High affinity enhancer-promoter interactions can bypass CTCF/cohesin-mediated insulation and contribute to phenotypic robustness

The paper shows that high affinity enhancer-promoter interactions can bypass CTCF/cohesin insulation and maintain gene expression in some tissues but not others.

Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma

The paper identifies a chemical scaffold targeting hRpn13, revealing a DEUBAD-lacking isoform upregulated in multiple myeloma and demonstrating its potential as a therapeutic target.

A UVB-responsive common variant at chr7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor gene (AHR)

This paper identifies rs117132860 as a functional variant at 7p21.1 that regulates AHR expression in response to UVB, contributing to melanoma risk and tanning ability.

The Dystonia Gene THAP1 Controls DNA Double Strand Break Repair Choice

This study identifies a transcriptional network involving THAP1 that regulates SHLD1 expression, affecting DNA repair choice and linking DNA damage to dystonia.

dbGuide: A database of functionally validated guide RNAs for genome editing in human and mouse cells

dbGuide compiles over 4000 functionally validated guide RNA sequences for CRISPR/Cas9-based knockout in human and mouse, enabling more reliable guide RNA selection.

Massively parallel reporter assays combined with cell-type specific eQTL informed multiple melanoma loci and identified a pleiotropic function of HIV-1 restriction gene, MX2, in melanoma promotion

The paper identifies multiple melanoma susceptibility genes and variants by integrating MPRA with eQTL data, revealing MX2's role in melanoma promotion.

Structure of E3 ligase E6AP with a novel proteasome-binding site provided by substrate receptor hRpn10

The paper identifies a novel proteasome-binding site in E6AP mediated by hRpn10, showing E6AP's unique interaction with the proteasome for substrate ubiquitination.