John S. Mattick

The long noncoding RNA Dory is required for female but not male spatial learning and memory

This study identifies the lncRNA Dory as essential for female spatial memory and balance, with no effect in males, using CRISPR and RNA sequencing in mice.

FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling

FIRST-seq uses nanopore cDNA sequencing to profile RNA modifications and structures by analyzing RT errors, achieving single-nucleotide resolution without PCR or second-strand synthesis.

Frequent functional orthology of long noncoding RNAs and genomic loci associated with complex traits and disorders

The paper links GWAS-associated haplotype blocks to lncRNAs and their mammalian orthologs, showing strong functional associations with complex traits.

Specificity of the stabilising interaction between intrinsically disordered protein sequences and G-quadruplexes in RNA

The paper shows how intrinsically disordered protein sequences selectively stabilize specific RNA G-quadruplex structures through weak interactions, without relying on high-affinity binding or cations.

ECSFinder: Optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences

ECSFinder improves prediction of evolutionarily conserved RNA structures by combining machine learning with thermodynamic and covariation features from existing tools.

Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing

Nano3P-seq quantifies RNA abundance, tail composition, and tail length dynamics at single-read resolution without PCR or adapters.

On the discovery of ADRAM, an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3

The paper identifies ADRAM, an experience-dependent lncRNA that interacts with 14-3-3 to regulate Nr4a2 expression and fear extinction memory in mice.

Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

The paper introduces a method to quantify RNA modifications using nanopore sequencing, revealing novel modification sites and dynamics in yeast under environmental stress.

Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation

The paper investigates the subcellular relocalization of TRMT1 and TRMT1L during neuronal activation and identifies their role in RNA modification dynamics and neuronal plasticity.

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

The paper identifies tissue- and cancer-specific RNA modification machinery (RMP) expression patterns and dysregulation across 32 tissues, 10 species, and 13,358 tumor-normal samples.

Best practices for genome-wide RNA structure analysis: combination of mutational profiles and drop-off information

This paper shows that combining mutational profiles and drop-off information improves RNA structure analysis by capturing complementary structural information and reducing false positives.

Accurate detection of m6A RNA modifications in native RNA sequences

This paper demonstrates the detection of m6A RNA modifications in native RNA sequences using Oxford Nanopore Technologies with high accuracy.

Targeted, High-Resolution RNA Sequencing Of Non-Coding Genomic Regions Associated With Neuropsychiatric Functions

The paper identifies novel non-coding RNAs in human brain tissue associated with neuropsychiatric traits using targeted RNA capture and long-read sequencing.

Transcription initiation RNAs are associated with chromatin activation mark H3K4me3

The paper identifies tiRNAs as small RNAs associated with H3K4me3-marked chromatin in murine macrophages, showing their enrichment near transcription initiation sites.

Universal Alternative Splicing Of Noncoding Exons

The paper identifies that nearly all noncoding exons undergo alternative splicing, generating a vast repertoire of regulatory RNAs and highlighting conserved splicing patterns across species.