Temporal regulation of head-on transcription at replication initiation sites.

Michael Kronenberg, Michael F Carey

Open access · goldAbstract read

In one paragraph

Article in iScience, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

–field-weighted citation impact, top 88% of its field

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 0 citations in OpenAlex.

Induced DNA double strand breaks by genotoxic drugs occur at active transcription H3K36 tri-methylation sites.Communications biology · 2026
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors at 1 institution in 1 country.

Michael KronenbergDepartment of Biological Chemistry, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA.

Michael F CareyDepartment of Biological Chemistry, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA.

University of California, Los Angeles · US

Funding

Interplay Between Chromatin and Co-Activator ComplexesR01GM074701 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CAREY, MICHAEL F · 2005 to 2025

$6.7M

NIGMS NIH HHS R01 GM074701

6 · The paper itself

Abstract

Head-on (HO) collisions between the DNA replication machinery and RNA polymerase over R-loop forming sequences (RLFS) are genotoxic, leading to replication fork blockage and DNA breaks. Current models suggest that HO collisions are avoided through replication initiation site (RIS) positioning upstream of active genes, ensuring co-orientation of replication fork movement and genic transcription. However, this model does not account for pervasive transcription, or intragenic RIS. Moreover, pervasive transcription initiation and CG-rich DNA is a feature of RIS, suggesting that HO transcription units (HO TUs) capable of forming R-loops might occur. Through mining phased GRO-seq data, and developing an informatics strategy to stringently identify RIS, we demonstrate that HO TUs containing RLFS occur at RIS in MCF-7 cells, and are downregulated at the G1/S phase boundary. Our analysis reveals a novel spatiotemporal relationship between transcription and replication, and supports the idea that HO collisions are avoided through transcriptional regulatory mechanisms.

Indexed as

BioinformaticsMolecular biologyMolecular mechanism of gene regulationTranscriptomics

Identifiers

PMID36594032

DOI10.1016/j.isci.2022.105791

PMCPMC9803852

OpenAlexW4311255523

What OpenQuestion holds

Textmetadata

LicenceCC BY-NC-ND

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.