Sangam: A Confluence of Knowledge Streams

Supplementary data for the manuscript "Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic"

Show simple item record

dc.contributor The Royal Society of Edinburgh
dc.contributor Waclaw, Bartlomiej
dc.creator Waclaw, Bartlomiej
dc.creator Cholewa-Waclaw, Justyna
dc.creator Shah, Ruth
dc.creator Webb, Shaun
dc.creator Chhatbar, Kashyap
dc.creator Ramsahoye, Bernard
dc.creator Pusch, Oliver
dc.creator Yu, Miao
dc.creator Greulich, Philip
dc.creator Bird, Adrian
dc.date 2019-06-07T16:17:30Z
dc.date 2019-06-07T16:17:30Z
dc.date.accessioned 2023-02-17T20:54:05Z
dc.date.available 2023-02-17T20:54:05Z
dc.identifier Waclaw, Bartlomiej; Cholewa-Waclaw, Justyna; Shah, Ruth; Webb, Shaun; Chhatbar, Kashyap; Ramsahoye, Bernard; Pusch, Oliver; Yu, Miao; Greulich, Philip; Bird, Adrian. (2019). Supplementary data for the manuscript "Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic", [dataset]. University of Edinburgh. School of Physics and Astronomy. https://doi.org/10.7488/ds/2568.
dc.identifier https://hdl.handle.net/10283/3351
dc.identifier https://doi.org/10.7488/ds/2568
dc.identifier.uri http://localhost:8080/xmlui/handle/CUHPOERS/244179
dc.description Patterns of gene expression are primarily determined by proteins that locally enhance or repress transcription. While many transcription factors target a restricted number of genes, others appear to modulate transcription levels globally. An example is MeCP2, an abundant methylated-DNA binding protein that is mutated in the neurological disorder Rett Syndrome. Despite much research, the molecular mechanism by which MeCP2 regulates gene expression is not fully resolved. Here we integrate quantitative, multi-dimensional experimental analysis and mathematical modelling to show that MeCP2 is a novel type of global transcriptional regulator whose binding to DNA creates "slow sites" in gene bodies. Waves of slowed-down RNA polymerase II formed behind these sites travel backward and indirectly affect initiation, reminiscent of defect-induced shock waves in non-equilibrium physics transport models. This mechanism differs from conventional gene regulation mechanisms, which often involve direct modulation of transcription initiation. Our findings point to a genome-wide function of DNA methylation that may account for the reversibility of Rett syndrome in mice. Moreover, our combined theoretical and experimental approach provides a general method for understanding how global gene expression patterns are choreographed.
dc.description See Readme.txt
dc.format application/zip
dc.format application/zip
dc.format application/zip
dc.format application/zip
dc.format application/zip
dc.format text/plain
dc.format application/zip
dc.format application/zip
dc.language eng
dc.publisher University of Edinburgh. School of Physics and Astronomy
dc.rights Creative Commons Attribution 4.0 International Public License
dc.subject MeCP2
dc.subject gene expression
dc.subject transcription
dc.subject RNA-seq
dc.subject ChIP-seq
dc.subject ATAC-seq
dc.subject mathematical model
dc.subject Biological Sciences
dc.title Supplementary data for the manuscript "Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic"
dc.type dataset
dc.coverage UK
dc.coverage UNITED KINGDOM


Files in this item

Files Size Format View
ATACseq.zip 4.139Gb application/zip View/Open
ChIPseq.zip 4.314Gb application/zip View/Open
congestion_dynamic.zip 25.02Mb application/zip View/Open
congestion_slowdown.zip 77.68Mb application/zip View/Open
genome.zip 1.754Gb application/zip View/Open
main_directory.zip 216.3Mb application/zip View/Open
methylation.zip 978.5Mb application/zip View/Open
Readme.txt 6.416Kb text/plain View/Open

This item appears in the following Collection(s)

Show simple item record

Search DSpace


Advanced Search

Browse