Mats E. Ljungman

The paper identifies widespread readthrough transcription in human cells and shows that depletion of specific factors increases its extent.

This study shows that HSF1 forms stress-induced condensates with divergent transcriptional outcomes, impacting transcriptional responses during different stress conditions.

The paper identifies fedratinib as a drug that increases endoplasmic reticulum-mitochondria contact sites by inhibiting BRD4, revealing a novel epigenetic pathway linking ERMCS to cellular metabolism.

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

This study identifies STK19 as a factor facilitating the transition from initial TCR complex assembly to downstream repair steps by enabling RNAPII clearance.

The paper profiles RNA dynamics in 16 human cell lines using Bru-seq and BruChase-seq, showing gene and pathway-specific RNA turnover and isoform regulation.

The paper identifies nascent transcription patterns of PROMPTs, eRNAs, and readthrough transcripts in 16 human cell lines using Bru-seq and finds they are regulated by sequence and chromatin features, suggesting they are functionally important.

This study identifies autophagy as a critical survival pathway in mIDH1 gliomas and shows that inhibiting autophagy enhances radiosensitivity and tumor regression in preclinical models.

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

This study identifies MTMR5 as a neuron-specific autophagy suppressor, showing its role in limiting autophagy and its potential as a therapeutic target for neurodegenerative diseases.

The paper identifies a non-canonical role of HIRA in transcription restart after DNA damage, independent of H3.3 deposition, by stabilizing UBN2 and reducing ATF3 expression.

This study identifies ELOF1 as a factor that directs CRL4CSA to ubiquitylate RNAPII at K1268, facilitating TCR and protecting CSB-deficient cells from transcription-replication collisions.

The paper identifies how human PUM proteins regulate gene expression by RNA stability and develops a rulebook to predict functional PREs using machine learning.

The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.

The paper investigates parental allele-specific genome architecture and transcription dynamics during the cell cycle in lymphoblastoid cells, identifying allele-biased expression and chromatin organization features.