Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome binding profile of TFIIH helicases XPB and XPD in HT1080 cells

ABSTRACT: The conserved TFIIH helicases XPB and XPD play key roles in transcription initiation and DNA repair. To investigate the functions of these helicases on a genome-wide scale, we performed ChIP-seq of endogenous XPB and XPD in the HT1080 human fibrosarcoma cell line. 2 ChIP samples and 1 unenriched input control from the same crosslinked chromatin pool

ORGANISM(S): Homo sapiens

SUBMITTER: Lucas Gray

PROVIDER: E-GEOD-44849 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD.

Gray Lucas T LT Vallur Aarthy C AC Eddy Johanna J Maizels Nancy N

Nature chemical biology 20140309 4

G4 motifs are greatly enriched near promoters, suggesting that quadruplex structures may be targets of transcriptional regulation. Here we show, by ChIP-Seq analysis of human cells, that 40% of the binding sites of the transcription-associated helicases, XPB and XPD, overlap with G4 motifs. The highly significant overlap of XPB and XPD binding sites with G4 motifs cannot be explained by GC richness or parameters of the genomewide analysis, but instead suggests that these proteins are recruited t ...[more]

PMID: 24609361

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Project description:In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-related processes. For P. falciparum, the causative agent of human malaria, the nucleosome landscape of the extremely AT-rich intergenic regulatory regions is largely unexplored. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit. We observe strong positioning of nucleosomes around splice sites that could aid co-transcriptional splicing events. In addition, nucleosome depleted regions are apparent hallmarks of transcription start sites (TSSs) and may support pre-initiation complex assembly. Moreover, we reveal nucleosome occupancy dynamics on strong TSSs during intraerythrocytic development, which correlate with gene expression changes and we observe a characteristic nucleosome architecture of functional - but not inert - TGCATGCA DNA motifs. Collectively, these findings highlight the regulatory capacity of the nucleosome landscape of this deadly human pathogen. Mnase-seq during the intra-erythrocytic asexual cycle of Plasmodium falciparum var2csa-panned 3D7 parasites for 8 time-points, every 5 hours starting from 5 hours post invasion until 40 hours post-invasion (T5-T40). Cycle length of these parasites is ~43 hours, synchronicity window is ~ 8 hours. T40 has 2 technical replicates (independent digestions; T40A, T40B). Additionally, pellet control sample (T15), histone H4-ChIP control (T40A) and sonicated and amplified genomic DNA. Chromatin was digested using a combined MNase + exonuclease III treatment. Libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification. Strand-specific RNA-seq for expression quantification during the intra-erythrocytic asexual cycle of Plasmodium falciparum var2csa-panned 3D7 parasites for 8 time-points every 5 hours starting from 5 hours post invasion invasion until 40 hours post-invasion (T5-T40). Cycle length of these parasites is ~43 hours, synchronicity window is ~ 8 hours. These samples are originating from the exact same batch of parasites as are the MNase-Seq libraries. Libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification.

Dataset Information

Genome binding profile of TFIIH helicases XPB and XPD in HT1080 cells

Publications

G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD.

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