rates_m6A

"Slow RNAPII transcription elongation rate, low levels of RNAPII pausing, and elevated histone H1 content at promoters associate with higher m6A deposition on nascent mRNAs"

Genes 2022, 13, 1652. https://doi.org/10.3390/genes13091652

Alicia Gallego, José Miguel Fernández-Justel, Sara Martín-Vírgala, Magdalena M Maslon, María Gómez

contact: agallego@cbm.csic.es, mgomez@cbm.csic.es

SEQUENCING EXPERIMENTS INCLUDED:

• 4sUDRBseq: scripts for processing transcription elongation rates (data from this work, some scripts based on Fuchs et al. 2014).
• ChMeRIPseq: scripts for processing information about m6A levels in chromatin-enriched RNAs (ChMeRIP) (data from Fernandez-Justel et al. 2021).
• CheRNAseq: scripts for processing expression levels in chromatin-enriched RNAs (cheRNA) (data from Fernandez-Justel et al. 2021).
• Elongation_rate_data_Maslon: scripts for processing information about transcription elongation rates (data from Maslon et al. 2019) and m6A levels across Ensembl protein-coding genes.
• H1c_H1d_data_Cao: scripts for processing information about levels of H1c and H1d histone variants (data from Cao et al. 2013) across RefSeq protein-coding genes.
• Histone_marks_data_Geeven: scripts for processing information about histone marks H3K4me3, H3K9me3, and H3K27me3 (data from Geeven et al. 2015) across RefSeq protein-coding genes.
• MNase_seq: scripts for processing positioned nucleosomes (data from this work) across RefSeq protein-coding genes.
• RNAPII_ChIPseq: scripts for processing RNAPII occupancies and RNAPII pausing indexes (RNAPII-ChIP sequencing) (data from Fernandez-Justel et al. 2021).

REFERENCES

· Cao K., et al., 2013. High-Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells. PLOS Genet. 9, e1003417. https://doi.org/10.1371/journal.pgen.1003417
· Fernández-Justel JM., et al., 2021. Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner. https://doi.org/10.1101/2021.10.12.464039
· Fuchs G., Voichek Y., et al., 2015. Simultaneous measurement of genome-wide transcription elongation speeds and rates of RNA polymerase II transition into active elongation with 4sUDRB-seq. Nat. Protoc. 10, 605–618. https://doi.org/10.1038/nprot.2015.035
. Geeven G., et al. 2015. Local compartment changes and regulatory landscape alterations in histone H1-depleted cells. Genome Biol 16, 289. https://doi.org/10.1186/s13059-015-0857-0
· Maslon MM., et al., 2019. A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes. EMBO J. 38, e101244. https://doi.org/10.15252/embj.2018101244