Cohesion is established during DNA replication utilising chromosome associated cohesin rings as well as those loaded de novo onto nascent DNAs.
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Same input data as the authors
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- 🟡Reported values were only indirectly comparable
- 🟡Overall, the reproduction showed a material discrepancy
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
Described well enough to reproduce 1:1. The repo ships the two final post-processing scripts (chr_position.py, filter60.py) of a calibrated ChIP-seq cohesin pipeline; GEO GSE151551 deposits the calibrated IP bigwigs named by figure panel (Fig4B: 4 genotypes x G1/S). Running the authors' own scripts on their own bigwigs reproduces the meta-centromere averaged calibrated cohesin profile and the chrIV track, and the central Fig4B claim: G1->S pericentric cohesin ladder WT(5.5x) > scc2-45(3.1x) > chl1Δ(0.77x, evicted) > chl1Δ scc2-45(0.19x, severe), i.e. chromosome-associated cohesin is evicted during S phase when the Chl1-dependent conversion pathway is absent. Independent vectorised reimplementation is bit-identical to the authors' code (max|diff|=0, r=1.0). NOT attempted: upstream Galaxy Bowtie2 alignment to sacCer3+C.glabrata spike-in and the occupancy-ratio computation (code not shipped, OR formula unspecified) -- reproduced from the deposited calibrated bigwig instead; and all wet-lab assays. Computation ran on «our HPC»; only small results copied to «host». Paper figures are qualitative so directional grades are within-tol and provisional for a human reviewer.
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Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 90assessed: 2026-06-16 ⛓ 4039399104cb
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Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-16
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-18no human curator yet
- Last updated
- 2026-09-19
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: sonnetThe paper tests whether sister chromatid cohesion during S phase is generated by conversion of cohesin complexes already associated with un-replicated DNA into cohesive structures behind the replication fork, or by nucleoplasmic cohesin loaded de novo onto nascent DNA at forks (a process dependent on Scc2), and which replisome-associated proteins each mechanism requires.
- ★ Both cohesin conversion and Scc2-dependent de novo loading mechanisms generate cohesion in S. cerevisiae, each requiring a distinct set of replisome-associated proteins. finding
- ★ Cohesion produced by cohesin conversion requires Tof1/Csm3, Ctf4 and Chl1 but not Scc2. finding
- ★ Cohesion created by de novo loading at replication forks requires Scc2 and the Ctf18-RFC complex. finding
- ★ Cohesin associated with un-replicated chromosomes is converted into cohesive structures (catenated dimers) in a fully Scc2-independent fashion. finding
- Cohesin expressed in G2/M loads onto mini-chromosomes and entraps individual DNAs (CMs) but does not form cohesive dimers (CDs) at that stage. finding
- Non-cleavable cohesin loaded during G2/M remains stably chromosome-associated through mitosis and into the subsequent G1 without requiring Scc2, unlike cohesin loaded during G1. finding
- A covalent circularization assay (BMOE crosslinking of cysteine-substituted 6C cohesin) combined with mini-chromosome IP can distinguish individual DNA entrapment (CMs) from sister DNA co-entrapment (CDs). method
- Replisome proteins involved in cohesion establishment fall into two genetic epistasis groups: Chl1/Ctf4/Csm3/Tof1 and Mrc1/Ctf18-RFC. mechanism
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Cohesin ring covalent circularization (6C cohesin, BMOE crosslinking) followed by mini-chromosome immunoprecipitation and Southern blot | S. cerevisiae, wild type (K24697) and scc2-45 temperature-sensitive mutant (K24738) strains expressing 2C-Smc1/2C-Smc3 and GALp-2C-Scc1-NC | scc2-45 conditional loss-of-function mutation (Scc2 inactivated at 37°C); GAL-induced expression of non-cleavable cohesin | Formation of catenated monomers (CMs, individual DNA entrapment) and catenated dimers (CDs, sister DNA co-entrapment) via SDS-resistant, retarded electrophoretic migration | Southern blot; BMOE crosslinker |
| Calibrated ChIP-sequencing | S. cerevisiae wild type (K24697) cells arrested in G1 after G2-phase expression of 6C non-cleavable Scc1-NC | none (time-course during prolonged G1 arrest with alpha-factor) | Genome-wide (chromosome IV) occupancy of PK-tagged Scc1-NC cohesin at time 0 vs 60 min | anti-PK antibody ChIP-seq |
| Flow cytometry (FACS) | S. cerevisiae wild type and scc2-45 strains at successive cell cycle arrest/release stages (G2/M nocodazole arrest, G1 alpha-factor arrest, S-phase release) | Cell cycle synchronization (nocodazole, alpha-factor) combined with scc2-45 temperature shift | DNA content / cell cycle stage | — |
- – In G2/M-arrested cells, similar levels of CMs (and no CDs) formed in both wild type and scc2-45 strains upon 2C-Scc1-NC induction.
- – 2C-Scc1-NC cohesin loaded during G2/M remained chromosome-associated as CMs through mitosis into the subsequent G1 arrest in both strains.
- – Calibrated ChIP-seq showed median genome-wide cohesin occupancy did not change during a prolonged G1 arrest.
- – Upon release into S phase, both SCC2 wild-type and scc2-45 (Scc2-inactivated) cells produced CDs in similar amounts.
- ▼ In scc2-45 cells, CD formation upon replication was accompanied by a reduction in the fraction of CMs.
- ▲ Higher levels of CMs were retained in SCC2 wild-type cells than in scc2-45 cells after replication, suggesting additional Scc2-dependent de novo loading.
- count 20–25% (Fraction of 6C cohesin crosslinked at all three ring interfaces (Smc1, Smc3, Scc1) during covalent circularization)
- other 45 min (Duration of galactose induction of 2C-Scc1-NC expression in G2/M-arrested cultures)
- other 60 min (Duration of prolonged G1 arrest (alpha-factor) used for calibrated ChIP-seq time course)
- other 37°C (Restrictive temperature used to inactivate Scc2 in the scc2-45 mutant during S-phase release)
Statistical methods review
Model: opusA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
The study uses a qualitative, assay-based experimental design in S. cerevisiae, relying on biochemical and molecular readouts (BMOE crosslinking of '6C' cohesin followed by mini-chromosome immunoprecipitation and Southern-blot detection of catenated monomers/dimers, calibrated ChIP-sequencing, and FACS cell-cycle profiling) rather than formal hypothesis-testing statistics. Results are reported descriptively, with key blots stated to be representative of independent biological repeats (e.g., three for the Figure 2 conversion assay). No inferential statistical tests, p-values, or formal effect-size estimates are reported in the available text.
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Key results are presented as representative gels/blots described as reproduced across three independent biological repeats.↳ Could also: Quantifying band intensities (e.g., CM and CD fractions) across all replicates and plotting the individual replicate values with a measure of spread, optionally with a test such as a paired t-test or non-parametric Wilcoxon comparison. — Showing per-replicate quantification alongside the representative image would convey the magnitude and consistency of the observed changes and let readers see the spread across repeats.
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The ChIP-seq supplement summarizes cohesin retention using the median level across chromosome IV.↳ Could also: Reporting the median together with an interquartile range or a bootstrap confidence interval, and/or showing the genome-wide distribution. — Adding a dispersion or interval estimate around the median would communicate the variability of occupancy across the chromosome in addition to its central tendency.
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Genotype/condition differences (e.g., SCC2 vs scc2-45 CM/CD levels) are described in qualitative terms such as 'similar' or 'a reduction'.↳ Could also: Defining a quantitative outcome metric per replicate and reporting an effect size (e.g., difference or ratio with a 95% CI). — An effect-size-based summary would put a number on the size of the described differences and complement the descriptive narrative.
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Sample size is conveyed as a fixed number of biological repeats (e.g., n=3) without a stated power or sample-size rationale.↳ Could also: Briefly stating the basis for the chosen number of replicates, and reporting the exact n for each panel in the legend. — An explicit per-panel n and a short note on replicate choice would make the basis of the reported reproducibility transparent to readers.
Result convergence & founder nodes
Findings this paper shares with others that ran a comparable experiment. A node’s strength is how many independent papers report it (replication breadth) — not how often it is cited, so a heavily-replicated but under-cited founder still stands out.
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Chromosomal Scc1/Mcd1 occupancy across chromosome IV does not change during prolonged G1 arrest, indicating negligible de novo cohesin loading from the nucleoplasmic pool in G1.ChIP-seq s-cerevisiae none 2020×1papers★ This paper is the founder (earliest)
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Cohesin catenated dimer formation during replication is equivalent in SCC2 and scc2-45 cells, demonstrating that cohesion establishment from chromosome-associated cohesin rings is Scc2-independent.other s-cerevisiae up 2020×1papers★ This paper is the founder (earliest)
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Cohesin catenated monomer levels decrease concomitantly with catenated dimer accumulation during replication in scc2-45 cells, consistent with direct conversion of pre-loaded cohesin rings into cohesion.other s-cerevisiae down 2020×1papers★ This paper is the founder (earliest)
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Cohesin catenated monomer levels are equivalent in SCC2 and scc2-45 cells in G2/M prior to replication, with no catenated dimers detected, indicating cohesion is not established before S phase.other s-cerevisiae none 2020×1papers★ This paper is the founder (earliest)
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Cohesin catenated monomer levels are higher in SCC2 wild-type than scc2-45 cells following replication, indicating Scc2-dependent de novo loading of cohesin onto nascent DNA.other s-cerevisiae up 2020×1papers★ This paper is the founder (earliest)
Citation network
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Data lineage
The datasets this paper uses (text-mined from the full text via Europe PMC), and which other assessed papers stand on the same data. A shared dataset is a factual link — not a judgement.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
scope.md — pmid-32515737
Paper: Srinivasan, Fumasoni, Petela, Murray, Nasmyth. "Cohesion is established during DNA replication utilising chromosome associated cohesin rings as well as those loaded de novo onto nascent DNAs." eLife 2020;9:e56611. Code: github.com/naomipetela/nasmythlab-ngs @ d7509c6 (chr_position.py, filter60.py) Data: GEO GSE151551 (calibrated ChIP-seq, S. cerevisiae sacCer3, Ion Torrent Proton)
Pipeline-derived results (IN SCOPE)
The repo ships the two post-processing scripts of the calibrated-ChIP pipeline:
chr_position.py— pads per-chromosome samtools-mpileup pileups to full sacCer3 length, assigning value 0 to unrepresented positions.filter60.py— extracts read depth for all positions ±60 kb of CDEIII for all 16 chromosomes, averages each relative position across chromosomes, and multiplies by the sample's occupancy ratio (OR) -> meta-centromere averaged calibrated cohesin profile (avgchr60.tabular). GEO deposits the calibrated IP bigwig for each sample (the pipeline's output upstream of these scripts). Samples are named by figure panel: Fig4B (4 strains K24697/K24738/K28061/K28175 × G1/S, IP+WCE) and Fig2-figsupp1 (K24697 G10/G160). Only IP tracks were deposited as bigwig (WCE = NONE).
IN SCOPE (attempted, reproduced):
- R1 Fidelity: run authors' chr_position.py + filter60.py on a deposited bigwig and confirm the meta-centromere average matches an independent vectorised reimpl.
- R2 Meta-centromere averaged calibrated cohesin profile (filter60 output) for the 8 Fig4B IP samples.
- R3 Fig4B biological claim: G1->S change in pericentric cohesin per genotype.
- R4 chrIV calibrated cohesin track (the Fig4B chromosome-IV view).
- R5 Geometry: repo's hard-coded sacCer3 chromosome lengths and ±60 kb CDEIII window coordinates vs the reference / SGD CEN annotation.
OUT OF SCOPE (not attempted)
- Upstream raw-read steps (Galaxy Bowtie2 alignment to sacCer3 + C. glabrata spike-in, OR computation, samtools mpileup): code not shipped (Galaxy GUI tool versions, exact OR formula not given). The deposited bigwig IS that step's calibrated output, so we reproduce from it.
- Wet-lab: minichromosome/cohesion assays, ChIP antibodies, strain construction, fitness assay (Source data 1), microscopy. Not computational.
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
Reproduction ran the authors' own post-processing scripts on the authors' own deposited calibrated bigwigs (GSE151551) and is bit-identical (max|diff|=0, r=1.0, peak 86.875), with the central Fig4B claim fully reproduced — the S/G1 pericentric ladder WT 5.47 > scc2-45 3.12 > chl1Δ 0.77 (<1, evicted) > chl1Δ scc2-45 0.19. No deviation sits on the authors' side and every value is derivable from shared data. The two caveats are entirely explainable and not defects: Fig4B is qualitative (no printed numbers, so comparison is directional) and the upstream alignment + occupancy-ratio step was not re-run because that code/formula was not deposited. Overall a strong, honest reproduction graded yellow only for the qualitative endpoint and partial-pipeline coverage.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.