Abstract
The human K562 chronic myeloid leukemia cell line has long served as an experimental paradigm for functional genomic studies. To systematically and functionally annotate the human genome, the ENCODE consortium generated hundreds of functional genomic data sets, such as chromatin immunoprecipitation coupled to sequencing (ChIP-seq). While ChIP-seq analyses have provided tremendous insights into gene regulation, spatiotemporal insights were limited by a resolution of several hundred base pairs. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq that overcomes this limitation by providing higher precision mapping of protein-DNA interactions. To study the interplay of transcription initiation and chromatin, we profiled the genome-wide locations for RNA polymerase II (Pol II), the histone variant H2A.Z, and the histone modification H3K4me3 using ChIP-seq and ChIP-exo. In this Data Descriptor, we present detailed information on parallel experimental design, data generation, quality control analysis, and data validation. We discuss how these data lay the foundation for future analysis to understand the relationship between the occupancy of Pol II and nucleosome positions at near base pair resolution.
Highlights
Background & SummaryControl of eukaryotic transcription patterns involves the interplay of RNA polymerase II (Pol II) and chromatin
Once Pol II initiates transcription, it rapidly transitions to a regulated paused state, 30-50 base pairs downstream of the transcription start site (TSS)[1]
Chromatin immunoprecipitation coupled to high throughput sequencing (ChIP-seq) is a powerful tool to study mechanisms of gene regulation by selectively enriching for DNA fragments that interact with a given protein in living cells
Summary
Control of eukaryotic transcription patterns involves the interplay of RNA polymerase II (Pol II) and chromatin. Once Pol II initiates transcription, it rapidly transitions to a regulated paused state, 30-50 base pairs (bp) downstream of the transcription start site (TSS)[1]. The +1 nucleosome is enriched with the histone variant H2A.Z and tri-methylation of the fourth N-terminal lysine on the histone H3 tail (H3K4me[3]) It has been known for several decades that Pol II must overcome nucleosomal obstacles during transcription[4]. Chromatin immunoprecipitation coupled to high throughput sequencing (ChIP-seq) is a powerful tool to study mechanisms of gene regulation by selectively enriching for DNA fragments that interact with a given protein in living cells. A more recently developed technology, called ChIP-exo, improves upon ChIP-seq by providing near base pair mapping resolution for protein-DNA interactions. Given its high base pair resolution, ChIP-exo is uniquely capable of spatially resolving divergent, initiating, paused, and elongating RNA polymerase II on a genome-wide scale.
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