The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency

A Bertero, S Brown, P Madrigal, A Osnato, D Ortmann… - Nature, 2018 - nature.com
The TGFβ pathway has essential roles in embryonic development, organ homeostasis,
tissue repair and disease,. These diverse effects are mediated through the intracellular …

A Kelch13-defined endocytosis pathway mediates artemisinin resistance in malaria parasites

J Birnbaum, S Scharf, S Schmidt, E Jonscher… - Science, 2020 - science.org
Artemisinin and its derivatives (ARTs) are the frontline drugs against malaria, but resistance
is jeopardizing their effectiveness. ART resistance is mediated by mutations in the parasite's …

RNA-centric methods: toward the interactome of specific RNA transcripts

C Gräwe, S Stelloo, FAH van Hout, M Vermeulen - Trends in biotechnology, 2021 - cell.com
RNA–protein interactions play an important role in numerous cellular processes in health
and disease. In recent years, the global RNA-bound proteome has been extensively studied …

Chromatin accessibility-based characterization of the gene regulatory network underlying Plasmodium falciparum blood-stage development

CG Toenhake, SAK Fraschka, MS Vijayabaskar… - Cell host & …, 2018 - cell.com
Underlying the development of malaria parasites within erythrocytes and the resulting
pathogenicity is a hardwired program that secures proper timing of gene transcription and …

Transcription factor proteomics—tools, applications, and challenges

J Simicevic, B Deplancke - Proteomics, 2017 - Wiley Online Library
Transcription factors (TFs) are a family of DNA‐binding proteins whose gene regulatory
capabilities are of vital importance in defining the molecular state of a cell. Despite their …

Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

NM Belliveau, SL Barnes, WT Ireland… - Proceedings of the …, 2018 - National Acad Sciences
Gene regulation is one of the most ubiquitous processes in biology. However, while the
catalog of bacterial genomes continues to expand rapidly, we remain ignorant about how …

The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences

PR Kensche, WAM Hoeijmakers… - Nucleic acids …, 2016 - academic.oup.com
In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-associated
processes and it is central to the control of gene expression. For Plasmodium falciparum, a …

Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3

J Kimmel, M Schmitt, A Sinner, PWTC Jansen… - Cell Systems, 2023 - cell.com
Taxon-specific proteins are key determinants defining the biology of all organisms and
represent prime drug targets in pathogens. However, lacking comparability with proteins in …

Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

MM Makowski, C Gräwe, BM Foster, NV Nguyen… - Nature …, 2018 - nature.com
Interaction proteomics studies have provided fundamental insights into multimeric
biomolecular assemblies and cell-scale molecular networks. Significant recent …

Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes

M Wierer, M Mann - Human molecular genetics, 2016 - academic.oup.com
High-resolution mass spectrometry (MS)-based proteomics is a powerful method for the
identification of soluble protein complexes and large-scale affinity purification screens can …