Project description:The protein Yin-Yang 1 (YY1) is a ubiquitous multifunctional transcription factor. Interestingly, there are several cellular functions controlled by YY1 that could play a role in Leishmania pathogenesis. Leishmaniasis is a human disease caused by protozoan parasites of the genus Leishmania. This study examined the potential role of macrophage YY1 in promoting Leishmania intracellular survival. Knockdown of YY1 resulted in attenuated survival of Leishmania in infected macrophages, suggesting a role of YY1 in Leishmania persistence. Biochemical fractionation studies revealed Leishmania infection caused redistribution of YY1 to the cytoplasm from the nucleus where it is primarily located. Inhibition of nuclear transport by leptomycin B attenuates infection-mediated YY1 redistribution and reduces Leishmania survival. This suggests that Leishmania induces the translocation of YY1 from the nucleus to the cytoplasm of infected cells, where it may regulate host molecules to favour parasite survival. A label-free quantitative whole proteome approach showed that the expression of a large number of macrophage proteins was dependent on the YY1 level. Interestingly, several of these proteins were modulated in Leishmania-infected cells, revealing YY1-dependent host response and suggesting their potential role in Leishmania pathogenesis. Together, these findings identify YY1 as a novel and essential virulence factor by proxy that promotes Leishmania survival.
Project description:This SuperSeries is composed of the following subset Series: GSE31784: Expression changes in Yy1 knock down mouse embryonic stem cells GSE31785: Yy1 occupancy of mouse ES cell genome Refer to individual Series
Project description:Yin Yang 1 (YY1) is a multifunctional transcription factor with critical roles in carcinogenesis and metastasis. However, its biological role and clinical impact in colorectal cancer (CRC) remain unclear. This study aimed to elucidate the oncological role of YY1 in CRC. To indentify the target genes of YY1, microarray analysis was performed on siYY1 and siControl transfected cells.
Project description:The proportion of pathogenic Th17 (pTh17) cells were significantly higher in RA than that in control individuals and showed a potential relevance with YY1 expression. Increased YY1 expression was observed in pTh17, and the pTh17 differentiation was hampered by YY1 knockdown. We used microarrays to detail the gene expression changes of pTh17 transfected with YY1 shRNA lentivirus and tried to elucidate the potential mechanisms how YY1 can affect pTh17 cell differentiation in RA.
Project description:These data include the genome wide location analyses of Yy1 by bioChIPs of Fbio-Yy1. Streptavidin precipitation of formaldehyde cross-linked chromatin prepared from Fbio-Yy1 and control expressing mouse ES cells
Project description:Yin Yang 1 (YY1) is a multifunctional transcription factor with critical roles in carcinogenesis and metastasis. However, its biological role and clinical impact in colorectal cancer (CRC) remain unclear. This study aimed to elucidate the oncological role of YY1 in CRC. To indentify the target genes of YY1, microarray analysis was performed on siYY1 and siControl transfected cells.
Project description:We mesured YY1 binding in isolated mouse crypt epihtelium using ChIP-seq Jejunal crypt epithelia were isolated and processed for ChIP using YY1 antibody Santa Cruz, SC-1703, lot E0511
Project description:We have determined the global gene expression upon loss of function of the Yy1 transcription factor in mouse embryonic stem cells Total RNA was extracted from ES cells transiently transfected with yy1-specific or scrampled-control siRNA oligos 48 hr post-transfection.
Project description:R-loops are three-stranded nucleic acid structures consisting of a DNA-RNA hybrid and a displaced single-stranded DNA (ssDNA). R-loops are facilitators of gene expression and genome stability that play both regulatory and potentially deleterious roles in cells. To elucidate the protein-based mechanisms of R-loop regulation, we developed an APEX-based proximity proteomics using a catalytically inactive mutant of RNase H1 (APEX-RNH1D210N) to profile the proximal proteome of R-loops in cells. Our proteomics results identified a list of known and potential R-loop-binding proteins with diverse molecular functions, and confirmed YY1 as a novel R-loop-binding protein through a series of in-vitro binding assays. YY1 is a DNA-binding protein recognizing a consensus motif or G-quadruplex (G4) structure. Our binding results indicated YY1's notably stronger affinity for R-loops compared to RNA/DNA hybrid, DNA G4 and DNA without a consensus motif, implying R-loops' role in YY1 recruitment to genomic regions lacking a YY1-binding motif. To investigate YY1-R-loop interaction in cells, we introduced R-loop structures into specific genomic regions vis CRISPR-dCas9 targeting, followed by DRIP-qPCR, YY1-ChIP-qPCR and RT-qPCR experiments. Increased R-loop levels corresponded with heightened YY1 occupancy and differential gene expression, suggesting YY1-R-loop interactions contribute to transcriptional regulation. More importantly, our RNA-seq and YY1-ChIP-seq results revealed that the interactions between YY1 and promoter R-loops were involved in global transcriptional regulation, especially in the positive regulation of transcription. Together, we identified YY1 as a novel R-loop-binding protein and uncovered a mechanism wherein YY1-R-loop interactions regulate gene expression.
Project description:To investigate the functions of JMJD2/KDM4 family in mouse embryonic stem cells (mESCs), we treat the the conditional triple-knockout mESCs of Jmjd2a/Kdm4a, Jmjd2b/Kdm4b and Jmjd2c/Kdm4c with 4-hydroxytamoxifen (4-OHT) for 72h. Further, to investigate whether JMJD2/KDM4 phase separation affects chromatin binding of YY1, we generated IDR-truncated JMJD2C/KDM4C (Mut) to disrupt its phase separation ability, and rescued it by by fusing two IDRs in other species (hIDR1 and hIDR2). We overexpressed those phase separation mutants in the aboved mESCs separately and TKO endogenous Jmjd2 by adding 4-OHT 72h.
