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Poly(A)+ RNA-seq from H226 cells expressing doxycycline-inducible Control (non-targeting) and p63-targeting shRNAs

ABSTRACT: Poly(A)+ RNA-seq from H226 cells expressing doxycycline-inducible Control (non-targeting) and p63-targeting shRNAs

PROVIDER: PRJNA437576 | ENA |

REPOSITORIES: ENA

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Poly(A)+ RNA-seq from H226 cells expressing doxycycline-inducible Control (non-targeting) and p63-targeting shRNAs

Project description:To determine the impact of ΔNp63α knockdown on steady-state mRNA levels, we performed poly(A)-enriched RNA-seq analysis of lung squamous cell carcinoma line H226 (inducible shControl and shp63) in the presence of 1µg/mL doxycycline to induce shRNA expression.

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sgRNA cassette sequencing and RNA-seq from H226 cells expressing doxycycline-inducible Control (non-targeting) and p63-targeting shRNAs

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LNCaP prostate cancer cells stably transfected with shRNAs targeting ADRB2

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shRNA human ME180 cells depleted for p63 versus wildtype ME180 cells

Project description:We investigated the transcriptional effects of p63 binding by analyzing ME180 cells depleted for all p63 isoforms via expression of a small hairpin RNA (shRNA) targeting the p63 oligomerization domain. Experiment Overall Design: Data were collected from three biological replicates for p63-depleted and control cells respectively.

2008-06-14 | E-GEOD-5993 | biostudies-arrayexpress

Chromatin modification is not a prerequisite for p63 binding but p63 binding can elicit chromatin remodeling

Project description:Transcription factor (TF) p63 is a master regulator playing critical roles in epidermal development and other cellular processes. Our lab’s previous research deciphered a distinct chromatin architecture at p63 bound site in keratinocytes. In order to figure out whether those chromatin modifications already exist before p63 binding, or p63 occupancy contributes to such chromatin marks, we built p63-expressing cell lines. We then obtained p63 bound regions in these overexpressing cell line, and looked at different histone marks at those sites before p63 occupancy. As shown in the results, before p63 binding, the targeting sites have barely detectable histone marks, indicating p63’s capability to approach unmodified chromatins. Moreover, there is no significant difference in chromatin marks between p63 bound sites and unbound sites when no p63 binding happens. Our in vivo findings were confirmed by examining p63 binding to unmodified nucleosomes in vitro, showing that histone modification is not indispensable for p63 binding but binding site positioning on nucleosome does play a role. Overall, our results suggest that histone modifications do not affect p63 binding, and p63 protein can bind to inaccessible, weakly modified chromatin regions in vivo.

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