The human DNA ends proteome uncovers an unexpected entanglement of functional pathways

Abstract

DNA ends get exposed in cells upon either normal or dysfunctional cellular processes or molecular events. Telomeres need to be protected by the shelterin complex to avoid junctions occurring between chromosomes while failing topoisomerases or clustered DNA damage processing may produce double-strand breaks, thus requiring swift repair to avoid cell death. The rigorous study of the great many proteins involved in the maintenance of DNA integrity is a challenging task because of the innumerous unspecific electrostatic and/or hydrophobic DNA—protein interactions that arise due to the chemical nature of DNA. We devised a technique that discriminates the proteins recruited specifically at DNA ends from those that bind to DNA because of a generic affinity for the double helix. Our study shows that the DNA ends proteome comprises proteins of an unexpectedly wide functional spectrum, ranging from DNA repair to ribosome biogenesis and cytoskeleton, including novel proteins of undocumented function. A global mapping of the identified proteome on published DNA repair protein networks demonstrated the excellent specificity and functional coverage of our purification technique. Finally, the native nucleoproteic complexes that assembled specifically onto DNA ends were shown to be endowed with a highly efficient DNA repair activity.

Proteomic Analysis of DNA Synthesis on a Structured DNA Template in Human Cellular Extracts: Interplay Between NHEJ and Replication‐Associated Proteins

“…In addition to these DNA repair and DNA replication‐associated proteins, a number of proteins belonging to the family of Dynamins, involved in the cytoskeleton dynamics, are specifically recruited onto the substrate. A similar result has already been noticed in a proteomic study of DNA‐ends specific proteins, [ 13 ] but the functional relevance of this unexpected association awaits further investigations. Finally, some heterogeneous nuclear ribonucleoproteins were recovered that reflects their ability to bind to ssDNA with high affinity.…”

Tyrosine kinase c-Abl couples RNA polymerase II transcription to DNA double-strand breaks

“…However, the mechanism that underlays MRN-dependent accumulation of RNAPII at DSBs remains elusive. RNAPII components were also detected as DNA end-binding proteins by mass spectrometry (73). The majority of DSBs in asynchronous cells are repaired by non-homologous end joining (NHEJ), which involves minimal resection by Mre11 3′-5′exonuclease (74,75).…”

A Novel Pyrazolopyrimidine Ligand of Human PGK1 and Stress Sensor DJ1 Modulates the Shelterin Complex and Telomere Length Regulation

“…We found most of these in TRF2 immunoprecipitates. Berthelot et al also previously identified glyceraldehyde-3-phosphate dehydrogenase as a telomere associated factor using affinity chromatography based on capture by telomeric oligonucleotides [57].…”