Athma A. Pai

Formation of an RNA-mediated nuclear compartment

The paper identifies RNA as the molecular glue forming a stable chromatin compartment associated with nuclear speckles, independent of speckles themselves.

CRYPTID-exon: streamlined detection of cryptic exons from RNA-seq data

CRYPTID-exon identifies cryptic exons in human RNA-seq data, showing their impact on mRNA stability and gene expression through ASO targeting.

SPARK: in silico simulations for benchmarking nascent RNA sequencing experiments

SPARK generates simulated nascent RNA sequencing data to benchmark computational tools for analyzing transcriptional dynamics.

mRNA initiation and termination are spatially coordinated

The paper identifies a spatial coordination between mRNA initiation and termination sites, proposing a 'Positional Initiation-Termination Axis' that influences isoform diversity.

Pol II degradation activates cell death independently from the loss of transcription

The paper shows that loss of Pol II protein, specifically Rbp1, triggers apoptosis independently of transcriptional loss, revealing a new apoptotic response mechanism contributing to cancer therapy efficacy.

Pervasive noise in human splice site selection

The paper tracks splicing intermediates in human cells using ultra-deep sequencing and finds pervasive usage of low-fidelity splice sites associated with genomic features that promote splicing noise.

High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes

The paper measures mRNA and protein levels in single cells for synthetic promoters, finding that promoter strength affects both transcription and translation, and introduces a framework for comparing gene regulation.

Raver1 links Ripk1 RNA splicing to caspase-8-mediated pyroptotic cell death, inflammation, and pathogen resistance

This study identifies Raver1 as a regulator of Ripk1 RNA splicing, which affects caspase-8-mediated pyroptosis, inflammation, and resistance to Yersinia infection.

Challenges in identifying mRNA transcript starts and ends from long-read sequencing data

This paper evaluates the accuracy of identifying mRNA transcript start and end sites from long-read sequencing data and introduces a method to improve terminal end identification.

Genome-wide kinetic profiling of pre-mRNA 3' end cleavage

The paper estimates genome-wide 3' end cleavage rates using metabolic labeling, sequencing, and modeling, finding fast but variable cleavage with associations to sequence elements and RNA Polymerase II localization.

A cohesin traffic pattern genetically linked to gene regulation

The paper identifies three types of chromatin boundaries that regulate cohesin traffic, which guides enhancer-promoter interactions and affects gene regulation.

High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets

The paper analyzes circular ANRIL isoforms in human pancreatic islets and finds higher circular:linear ANRIL ratios in T2D risk allele carriers, linked to reduced beta cell proliferation.

Widespread occurrence of hybrid internal-terminal exons in human transcriptomes

The paper identifies hybrid internal-terminal exons in human transcriptomes using a new pipeline and shows their tissue-specific usage and association with RNA splicing genes.

Precision Cas9 Genome Editing in vivo with All-in-one, Self-targeting AAV Vectors

This paper develops single-AAV vectors for precise in vivo genome editing using Nme2Cas9 with HDR templates or multiple sgRNAs, showing efficacy in treating HT-I and MPS-I mouse models.

Numerous recursive sites contribute to accuracy of splicing of long introns in flies

The paper identifies hundreds of novel recursive splicing sites in Drosophila introns, showing they are more accurately spliced and often located in long introns involved in development.

The kinetics of pre-mRNA splicing in the Drosophila genome: influence of gene architecture

The paper measures splicing rates genome-wide in Drosophila to understand how gene architecture affects splicing efficiency and accuracy.

Environmental Perturbations Lead To Extensive Directional Shifts In RNA Processing

The paper shows environmental changes cause widespread shifts in RNA processing across multiple cell types and identifies trans factor regulation of these changes.