IkBa associates with histone H2A in human keratinocytes
Ontology highlight
ABSTRACT: Here, we demonstrate that IkBa displays a predominant and unique nuclear localization in normal basal keratinocytes. This nuclear IkBa binds the chromatin through direct interaction of the ankyrin repeats with histone H2A and associates with the promoter and regulatory regions of several developmental-related genes including HOXA10, HOXB2 and HOXB9. Most importantly, IkBa dictates the competence of these HOX genes to be activated upon TNFa stimulation. Examination of IkBalpha location in keratinocyte cells
Project description:Cell samples of undifferentiated human umbilical cord mesenchymal stem cells (1-3) and cells that have been cultured in smooth muscle differentiation medium for 6 hours (4-6) and 24 hours (7-9) were collected and subjected to miRNA array. Exploration of miRNA involved smooth muscle differentiation mechanism would offer potential therapeutic choices for improving performance of vascular grafts engineered with umbilical cord mesenchymal stem cells.
Project description:The Inhibitor of the NFkB, IkBa, is the main regulator of the NFkB pathway. Our data has demonstrated that there is an alternative function for IkBa in the chromatin that affects HOX and other developmental genes. Keywords: CHIP-chip Chip-on-chip analysis has demonstrated that IkBa associates to the promoters of several genes. Chromatin fragments were obtained from NIH-3T3 cells and precipitated with 3 different IkBa comercial antibodies (raised in mouse, goat and rabbit), and fold enrichment was compared to input.
Project description:The experiment aimed at investigating the profiles of two histone marks (H3K27me3 and H3K4me3) in muscle tissues (Pectoralis major) of 35 days-old control (n=3) and thermally-manipulated (cyclic rise in egg incubation temperature of 1.5°C from days 7 to 16 of embryogenesis; n=3) chickens.
Project description:To gain insight into ncRNAs functionality in bacteria, we studied the correlation of gene expression from Mycoplasma pneumoniae's ncRNAs with their overlapping ORFs over 10 different time points. This experiment contains RNAseq pair-end data from this 10 time points along Mycoplasma pneumoniae growth cycle.
Project description:The discovery of small open reading frames (smORFs) encoding for polypeptides (SEPs; <100aa) highlights that the coding capacity of the genomes has been underestimated. Most ORF-finding algorithms have historically set a minimum threshold length of 100 aa. As consequence, some transcripts encoding for SEPs, were erroneously discarded or classified as non-coding RNAs (ncRNAs). With this experiments we try to experimentally assess the existence and complexity of these small proteins. The experimental design includes: After growing each Mycoplasma for 6h at 37°C, cells were washed twice with PBS and lysed with 700 µl of Qiazol buffer. Then, samples were lysed with 700 µl of Qiazol buffer. RNA extractions were performed by using the miRNeasy mini Kit (Qiagen) following the instructions of the manufacturer. Libraries for RNA-seq were prepared following directional RNA-seq library preparation and sequencing. Briefly, 1 µg of total RNA was fragmented to ~100-150 nt using NEB Next Magnesium RNA Fragmentation Module (ref. E6150S, NEB). Treatments with Antarctic phosphatase (ref. M0289S, NEB) and PNK (ref. M0201S, NEB) were performed in order to make the 5’ and 3’ ends of the RNA available for adapter ligation. Samples were further processed using the TruSeq small RNA Sample Prep Kit (ref. RS-200-0012, Illumina) according to the manufacturer's protocol. In summary, 3’ adapters and subsequently 5’ adapters were ligated to the RNA. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and a specific primer (RNA RT Primer) complementary to the 3’ RNA adapter. cDNA was further amplified by PCR using indexed adapters supplied in the kit. Finally, size selection of the libraries was performed using 6% Novex® TBE Gels (ref. EC6265BOX, Life Technologies). Fragments with insert sizes of 100 to 130 bp were cut from the gel, and cDNA was precipitated and eluted in 10 µl of elution buffer. Double-stranded templates were cluster amplified and sequenced on an Illumina HiSeq 2000.
Project description:Whole genome sequencing was performed on E. coli BL21 (DE3) evolved at 25°C in pH 9 terrific broth media buffered with Tris-HCl (pH 9). The evolved E. coli was characterized and compared to the parent strain.
Project description:Hepatitis C virus (HCV) remains a significant public health threat as new 1.75 million HCV infections emerged worldwide. The majority of these infections become persistently infected, while around 30 % spontaneously eliminate the virus. Clinical factors for viral clarification are related to HCV interaction with host immune system, but little is known about the consequences after HCV spontaneous resolution. These individuals are difficult to recruit and study as acute infection is usually asymptomatic, and they will not be identified unless it progress to chronic infection. The study of peripheral blood mononuclear cells (PBMCs) of these patients is crucial, as PBMCs are one of the main HCV extrahepatic reservoirs, and its transcriptional profile provide us information of innate and adaptive immune response against HCV infection. Our research shows novel insight on molecular consequences of spontaneous resolution after an acute HCV infection. 96 Individuals with different HCV exposure status were recruited: spontaneous resolved, chronic infected and healthy controls; and the microRNA profile of their PBMCs were analyzed. Our results indicate similar disruption of miRNA expression on HCV chronic patients and those who spontaneously clarified the infection, compared to control patients. The disrupted miRNAs formed a signature of 21 miRNAs that mainly regulate lipid metabolism. This is the first report showing miRNA profile similarities between chronic HCV patients and spontaneous resolved individuals. Thus, our results suggest that HCV infection promotes molecular alterations in PBMCs that will last longer after HCV spontaneous eradication. This evidences open up new prospects in the management of individuals who spontaneously clarified infection, as they should be monitored and followed to dismiss future HCV-related complications, such us liver diseases complications. The identified miRNA signature could be used as biomarker to monitor HCV fingerprint on HCV-exposed patients.
Project description:The experiment aimed at investigating the profiles of two histone marks (H3K27me3 and H3K4me3) in hypothalamus tissues of 35 days-old control (n=3) and thermally-manipulated (cyclic rise in egg incubation temperature of 1.5°C from days 7 to 16 of embryogenesis; n=3) chickens.
Project description:The activation of NFkB pathway is commonly observed in many neurodegenerative disease and contributes to the disease pathogenesis. However, with hundreds of target genes expressed in the brain, the mechanism of NFkB signaling transduction pathway is bearly understood. We were interested in revealing the downstream mediators of NFkB in the brain and chose the IkBa-dificient model as our tool. IkBa is the essential negative regulator of NFkB activity and deletioon of IkBa induced NFkB hyperactivation. We used Nestin-Cre to conditionally knockout IkBa in the brain cells of neural lineage and performed the microarray to give us candidate genes.