Project description:Short-read sequencing of DNA fractions of the BioTAP-XL pull-downs on human EZH2 and interacting proteins. ChIP-seq-like pulldown/input samples
Project description:We report chromatin-associated protein and RNA interactions of HP1a, indentified by BioTAP-XL mass spectrometry and sequencing. We identify an extensive list of both known and novel HP1a-interacting proteins from Drosophila S2 cells and from whole organisms across embryonic, larval and adult stages. BioTAP-XL protocol was used to identify HP1a interacting proteins through mass-spectrometry analysis. ChIP-seq-like pulldown/input samples were generated using BioTAP-XL to validate genomic distribution of the HP1a-BioTAP contructs, and the newly identified interacting proteins (CG8290 and CG3680); To examine the RNAs associated with the HP1a complexes, the RNA fraction of the BioTAP-XL pulldowns was analyzed using Illumina-based RNA-seq protocols, as well as Helicos direct RNA sequencing.
Project description:Here we find that ZNF750 activates epidermal differentiation genes and represses progenitor genes as part of two distinct protein complexes Identified genomic binding sites of ZNF750 and its interacting proteins
Project description:We have combined biochemical purification of Mediator from chromatin with ChIP-sequencing to reveal Mediator occupupancy to DNA globally and to identify proteins interacting specifically with Mediator in chromatin. We find that Mediator occupy strong chromosomally interacting domain (CID) boundaries and nearly all tRNA genes. Purification of Mediator from chromatin shows that it interacts with proteins and protein complexes that have been shown to interact with CID boundaries such as RSC, Ssu72 and histone H4. We also show specific interaction between Mediator and the Arp2/Arp3, CPF, CF 1A and LSm, complexes in chromatin. These factors are involved in mRNA 3'-end processing, gene looping, actin assembly and mRNA decay.
Project description:In this study, simultaneous gene expression, of both the host and pathogen, in the incompatible interaction between rice immune line H471 and Xoo race PXO99A with strong virulence, and in compatible ones between H471’s parents and PXO99A, were analyzed in the same infected leaf blades at 1 day and 3 days post-inoculation (dpi) using the RNA-Seq technique.This study provides the first insights into the differantial gene expression profiles of both organisms interacting simultaneously in the incompatible and compatible interactions between Xanthomonas oryzae pv. oryzae and host. Gene groups of differentially expressed genes were identified for PXO99^A and H471. In the Xoo case, a set of genes associated with two-component systems, involved in Quorum sensing (QS) and protecting the cell from reactive oxygen species (ROS) and oxidative stress, and genes encoding type III secretion systems and Type III (T3) effectors were sequentially up-regulated in the incompatible interaction. In the rice case, differentially regulated genes encoding a set of signal transduction components, sixty-six transcription factors, six genes encoding PPRs and three genes encoding tetratricopeptide repeat (TPR)-like superfamily proteins, and twenty-one resistance proteins have been identified in the incompatible interaction. Among them, six rice genes encoding response regulator receivers and histone proteins in the incompatible interaction uniquely differentially up-regulated in H471 at 1 dpi
