Lukas Burger

TL;DR: This study developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs and revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions.

TL;DR: It is shown that DNA-binding factors locally influence DNA methylation, enabling the identification of active regulatory regions and shows that neuronal and stem-cell methylomes are dependent on each other, as cell-type-specific LMRs are occupied by cell- type-specific transcription factors.

TL;DR: Findings reveal how sequence and chromatin cues guide de novo methyltransferase activity to ensure methylome integrity.

TL;DR: The results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect their binding sites sufficiently under the denaturing conditions used during the CLIP procedure, and show that extensive digestion with sequence-specific RNases strongly biases the recovered binding sites.

TL;DR: This map of DNase-I-hypersensitive sites in murine stem cells reveals a case of cooperativity between TFs that acts indirectly via DNA methylation, and suggests that binding of DNA-methylation-sensitive TFs relies on additional determinants to induce local hypomethylation.