Folkert Jacobus van Werven

Cellular context restricts a promiscuous m6A reader IDR to a single functional effector interface for mRNA decay

Yeast m6A reader Pho92 uses one helical hydrophobic interface in its disordered region to engage Caf40; a single L35A substitution halts m6A-transcript decay in meiosis.

Lineage-specific retrotransposon co-option reveals a conserved ASH2L isoform as an epigenetic primer of developmental gene promoters

The paper shows that a truncated ASH2L isoform, generated via a lineage-specific retrotransposon, primes developmental gene promoters during pluripotency and is required for later developmental transitions.

Mapping and quantifying nascent transcript start sites using TT-TSS-seq

The paper introduces TT-TSS-seq, a method to map and quantify transcription start sites from nascent transcripts, revealing multiple initiation sites per gene and detecting unstable transcripts.

DNA supercoiling impacts alternative transcription start site selection in yeast

The paper shows DNA supercoiling affects alternative TSS selection in yeast, impacting 600 genes and altering TSS usage near and within open reading frames.

Multi-signal regulation of the GSK-3β homolog Rim11 governs meiosis entry in yeast

The paper shows how Rim11 integrates signals from PKA, TORC1, and Ime1 to regulate Ume6 phosphorylation and drive meiotic gene expression in yeast.

The yeast RNA methylation complex consists of conserved yet reconfigured components with m6A-dependent and independent roles

The paper identifies three novel components of the yeast m6A methyltransferase complex and reveals their distinct m6A-dependent and independent roles in meiosis and mating.

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.

RSC and GRFs confer promoter directionality by limiting divergent noncoding transcription

This study shows that RSC and GRFs control promoter directionality by reducing divergent noncoding transcription.

Integrated Genomic Analysis Reveals Key Features of Long Undecoded Transcript Isoform (LUTI)-based Gene Repression

The paper identifies LUTI candidates during meiotic prophase and shows that LUTI-based repression integrates translational and transcriptional mechanisms.

Regulated repression, and not activation, governs the cell fate promoter controlling yeast meiosis

The paper shows that repression, not activation, controls IME1 promoter activity in yeast meiosis by multiple transcription factors regulating Tup1-Cyc8 co-repressor association.

Repression of divergent noncoding transcription by a sequence-specific transcription factor

This study shows how the transcription factor Rap1 represses divergent noncoding transcription in yeast by preventing transcription initiation at cryptic promoters.