Jernej Ule

Competence repression by the SPβ prophage in Bacillus subtilis revealed by transcriptomics across culture conditions

The paper uses transcriptomics to show that SPβ prophage represses competence in Bacillus subtilis under competence-inducing conditions, reducing DNA uptake and evolvability.

A combinatorial pre-mRNP retention factor network couples nuclear speckle architecture to splicing quality control

The paper identifies a network of RNA-binding proteins that retain pre-mRNPs in nuclear speckles, linking splicing status to nuclear retention and speckle organization.

PARNET: A CLIP-SEQ-BASED FOUNDATION MODEL FOR RNA SEQUENCE REPRESENTATION LEARNING

Parnet is a CLIP-seq-based foundation model for RNA sequence representation learning that outperforms existing methods in binding profile prediction and generalizes across tasks.

CDKL5 phosphorylates neuronal ELAVL proteins to promote mRNA binding, protein synthesis and visual cortex development

This study identifies CDKL5 as a kinase that phosphorylates nELAVL proteins, enhancing mRNA binding and protein synthesis, and shows its role in visual cortex development.

Short RNA chaperones promote aggregation-resistant TDP-43 conformers to mitigate neurodegeneration

Short UG-rich RNAs bind and stabilize TDP-43 RNA-recognition motifs to allosterically destabilize its prion-like domain helical region, preventing aggregation and mitigating neurodegeneration in cells and mice.

The long isoform of ZAP coordinates multiple enzymes to mediate complete decay of target transcripts

This study identifies how the long ZAP isoform recruits enzymes to degrade viral RNA through a coordinated decay pathway.

Targeted 3'-end RNA sequencing uncovers cryptic polyadenylation in Huntington's disease linked to somatic instability and CAG repeat purity

This paper introduces 3TRS, a targeted RNA sequencing method to quantify HTT transcripts in HD models, revealing cryptic polyadenylation linked to somatic instability and CAG repeat purity.

Integrative profiling of condensation-prone RNAs during early development

The paper identifies a class of condensation-prone RNAs during early development and reveals their sequence and structural features using deep learning.

Increased HCN1 activity in human excitatory neurons drives excessive network bursting in Dravet syndrome

The paper shows that increased HCN1 activity in excitatory neurons causes excessive network bursting in Dravet syndrome, suggesting HCN1 as a therapeutic target.

CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing

CAR-SPLASH identifies RNA kinetic switches that regulate alternative splicing based on transcription speed, with potential therapeutic applications using antisense oligonucleotides.

Mutual homeostasis of charged proteins

The paper identifies a homeostatic mechanism called interstasis that co-regulates the dosage of proteins with low complexity domains through RNA-based negative feedback.

Characterisation of LAMP1- and LAMP2A-positive organelles in neurons

The paper characterises LAMP1- and LAMP2A-positive organelles in neurons, finding they have distinct transport dynamics and protein compositions.

PRMT activity promotes global 3' UTR shortening in proliferating cells

This study shows PRMT activity regulates 3' UTR shortening in proliferating cells through alternative polyadenylation, impacting cancer and immune-related diseases.

Abundant capped RNAs are derived from mRNA cleavage at 3'UTR G-Quadruplexes

The paper identifies 3UTR-derived capped RNAs, showing they are abundant and originate from AGO2-mediated cleavage at G-quadruplexes, with implications for APP protein regulation.

Creation of de novo cryptic splicing for ALS/FTD precision medicine

The paper develops TDP-REG, a system using cryptic splicing to enable precise gene therapy activation in diseased neurons for ALS/FTD.

Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD

The paper shows that loss of TDP-43 function leads to the expression of de novo proteins from mis-spliced mRNA transcripts in ALS/FTD.

Subcytoplasmic location of translation controls protein output

The paper shows that subcytoplasmic mRNA localization affects protein output by determining mRNA and protein abundance through compartment-specific translation environments.

Flow: a web platform and open database to analyse, store, curate and share bioinformatics data at scale

Flow provides a web platform and database for managing and analyzing large-scale bioinformatics data, addressing challenges in data processing, quality, and accessibility.

Towards In-Silico CLIP-seq: Predicting Protein-RNA Interaction via Sequence-to-Signal Learning

RBPNet predicts CLIP crosslink count distributions from RNA sequences, outperforming existing methods and enabling variant impact scoring.

HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion

This study identifies HNRNPH1 as a key regulator of RBM3 expression through cold-induced exon skipping, offering potential therapeutic targets for neuroprotection.

A computationally-enhanced hiCLIP atlas reveals Staufen1 RNA binding features and links 3' UTR structure to RNA metabolism

The paper extends a hiCLIP atlas of Staufen1-bound duplexes by 10-fold using computational methods and reveals structural features of RNA binding and their impact on RNA metabolism.

clipplotr - a comparative visualisation and analysis tool for CLIP data

clipplotr is a command-line tool for visualizing and comparing CLIP data with annotations and functional genomic data, producing publication-quality figures.

ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins

ORC1 binds to cis-transcribed RNAs from genes with replication origins at TSSs, which is required for optimal origin activation.

Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity

This study shows that Integrator subunit INTS11 is essential for RNA polymerase II processivity during elongation, preventing antisense transcription and ensuring efficient gene expression.

Genome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides

The paper identifies genome-wide RNA binding sites of poly(PR) dipeptides and shows preferential binding to GAAGA-containing RNAs, suggesting a role in neurodegeneration.

Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP

The paper introduces PEKA, a tool for analyzing CLIP data to assess motif specificity, and shows that technical biases affect motif detection.

RNA modifications detection by comparative Nanopore direct RNA sequencing

The paper introduces Nanocompore, a method to detect RNA modifications using Nanopore direct RNA sequencing, validated on human polyA+ RNAs and non-coding RNAs.

Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs

The paper introduces SPACE and SPACEmap to identify chromatin-associated RBPs and their interactions, revealing that many bind chromatin via intrinsically disordered regions.

An improved iCLIP protocol

The paper introduces an improved CLIP protocol (iiCLIP) that produces more specific RNA binding site datasets compared to existing methods.

Acute depletion of METTL3 identifies a role for N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome

The paper shows that m6A modification affects alternative intron/exon inclusion in nascent RNA by disrupting splicing when METTL3 is depleted.