Nature 2020 01 30 Part.02

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nature research | reporting summary

October 2018

Data

Policy information about availability of data

All manuscripts must include a data availability statement. This statement should provide the following information, where applicable:

• Accession codes, unique identifiers, or web links for publicly available datasets


• A list of figures that have associated raw data


• A description of any restrictions on data availability
  NCBI GEO accession ID: GSE114410 (This study) Contains bTMP, RNA:DNA hybrids, Protein ChIP-chip RAW & processed data
  NCBI GEO accession ID: GSE114444 (This study) Contains RNA-seq, H3 ChIP-seq RAW, ChIA-PET RAW & processed data
  NCBI GEO accession ID: GSE16258 (Bermejo et al., 2009) Contains Top2, Hmo1, RPB3 protein ChIP-chip data

Field-specific reporting

Please select the one below that is the best fit for your research. If you are not sure, read the appropriate sections before making your selection.

Life sciences Behavioural & social sciences Ecological, evolutionary & environmental sciences

For a reference copy of the document with all sections, see nature.com/documents/nr-reporting-summary-flat.pdf

Life sciences study design

All studies must disclose on these points even when the disclosure is negative.

Sample size 6706 RNA pol II transcribed genes

173 replication origins

Data exclusions No data excluded

Replication All experiments were performed with biological replicates

Randomization Not relevant to this study, as samples were yeast strain specific

Blinding Not relevant to this study, as samples were yeast strain specific

Reporting for specific materials, systems and methods

We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material,

system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.

Materials & experimental systems

n/a Involved in the study

Antibodies

Eukaryotic cell lines

Palaeontology

Animals and other organisms

Human research participants

Clinical data

Methods

n/a Involved in the study

ChIP-seq

Flow cytometry

MRI-based neuroimaging

Antibodies

Antibodies used anti-Flag (M2-antiflag) Antibody (Sigma-Aldrich cat no F3165, clone: M2, Lot#: SLBQ6349V)

S9.6 Monoclonal RNA:DNA Antibody (Boguslawski et al.,1986)

anti-Hstone H3 antibody (Abcam cat no 1791, Lot#:GR3236305-1)

ExtrAvidin-Peroxidase antibody (Sigma-Aldrich cat no: E2886, Lot#:015M4844V, For dot blot 1:4000 dilution is used )

Validation S9.6 Monoclonal RNA:DNA Antibody (Boguslawski et al.,1986) is validated and used in several publications including: El Hage, A.,

et al. (2010), Chan, Y. A., et al. (2014), Wahba, L., et al. (2016), Vanoosthuyse, V. (2018), El Hage, A. and D. Tollervey (2018)