RNAs anchoring replication complex control initiation and firing of DNA replication

Ummarino et al., Nature Communications, 2026 asked what decides where a human cell starts copying its DNA. Origin recognition is known to run through the ORC complex and the histone variant H2A.Z, but no consensus DNA sequence marks a mammalian origin, so something else must be selecting the sites. The authors looked at RNAs transcribed in the G1 and early S phase of the cell cycle and found a class of transcripts that hold ORC1 in place and let H2A.Z bind. They named them ANCORs, for RNAs anchoring ORC1, and they reported 81,931 predicted ANCOR-associated loci, of which 46,360 also carried H2A.Z enrichment.

The test of the mechanism came at the c-MYC locus. Repressing the local ANCOR transcript with CRISPR interference cut nascent DNA production at the c-MYC origin, but that result could have come from the DNA-bound machinery blocking the fork rather than from the loss of the RNA. To separate the two, the authors treated wild-type K562 cells with self-delivering AUMlnc sdASOs against the c-MYC ANCOR transcript, alongside a non-targeting scramble control from the same supplier. The oligonucleotides were added straight to the culture medium at 10 to 20 μM in the Methods and at 15 μM in the reported experiment, and the readout was taken 72 hours later.

The oligonucleotides reproduced the CRISPR result. c-MYC expression fell by a comparable amount, and chromatin immunoprecipitation showed both H2A.Z and ORC1 occupancy dropping at the c-MYC replication origin, with p equal to 0.0006 for H2A.Z and p equal to 0.0011 for ORC1 against the IgG control. Nascent DNA abundance at the origin fell with them, at p equal to 0.00193 against the scramble. Moving the same transcript in the opposite direction with CRISPR activation raised nascent DNA at the origin instead. Three independent ways of changing one non-coding transcript therefore moved replication at that locus in the matching direction.