LncRNA profile study during Human MSC adipogenic differentiation: Day0 vs Day3 vs Day6
ABSTRACT: LncRNA transcriptional profiling of human mesenchymal stem cells comparing control undifferentiated HMSC with Day3 and Day6 adipogenic differentiation stages Three-condition experiment, Day0 vs. Day3 vs Day6 cells. Day0: 4 replicates, Day3: 3 replicates and Day6: 3 replicates.
Project description:LncRNA transcriptional profiling of human mesenchymal stem cells comparing control undifferentiated HMSC with Day3 and Day6 adipogenic differentiation stages Overall design: Three-condition experiment, Day0 vs. Day3 vs Day6 cells. Day0: 4 replicates, Day3: 3 replicates and Day6: 3 replicates.
Project description:Dynamic interactions of nuclear lamins with chromatin through so-called lamin-associated domains (LADs) contribute to spatial arrangements of the genome. Here, we provide evidence for pre-patterning of differentiation-driven formation of lamin A/C LADs by domains of histone H2B modified by the nutrient sensor O-linked N-acetylglucosamine (H2BGlcNAc), which we term GADs. We demonstrate a two-step process of lamin A/C LAD formation during in vitro adipogenesis, involving (i) a spreading of lamin A/C-chromatin interactions during the transition from progenitor cell proliferation to cell cycle arrest, and (ii) a genome-scale redistribution these interactions through a process of LAD ‘exchange’ within hours of adipogenic induction. Chromatin state modeling reveals that lamin A/C LADs can be found both in active and repressive chromatin contexts which can be influenced by cell differentiation status. De novo formation of adipogenic lamin A/C LADs occurs non-randomly on GADs, consisting of megabase-size intergenic and repressive chromatin domains. Accordingly, while pre-differentiation lamin A/C LADs are gene-rich, post-differentiation LADs harbor repressive features reminiscent of lamin B1 LADs. Moreover, release of lamin A/C from genes directly involved in glycolysis concurs with their transcriptional upregulation after adipogenic induction, and with concordant downstream elevations in H2BGlcNAc levels and O-GlcNAc cycling. Our results unveil an epigenetic pre-patterning of adipogenic LADs by GADs, suggesting a coupling of developmentally regulated lamin A/C-genome interactions to a metabolically sensitive chromatin modification. Examination of LMNA and H2BGlcNAc binding in ASCs across differentiation
Project description:Background: Tissue regeneration and recovery in the adult body depends on self-renewal and differentiation of stem and progenitor cells. Mesenchymal stem cells (MSCs) that have the ability to differentiate into various cell types, have been isolated from the stromal fraction of virtually all tissues. However, little is known about the true identity of MSCs. MSC populations exhibit great tissue-, location- and patient-specific variation in gene expression and are heterogeneous in cell composition. Methodology/Principal findings: Our aim was to analyze the dynamics of differentiation of two closely related stromal cell types, adipose tissue-derived MSCs and dermal fibroblasts (FBs) along adipogenic, osteogenic and chondrogenic lineages using multiplex RNA-seq technology. We found that undifferentiated donor-matched MSCs and FBs are distinct populations that stay different upon differentiation into adipocytes, osteoblasts and chondrocytes. The changes in lineage-specific gene expression occur early in differentiation and persist over time in both MSCs and FBs. Further, MSCs and FBs exhibit similar dynamics of adipogenic and osteogenic differentiation but different dynamics of chondrogenic differentiation. Conclusion: Our findings suggest that stromal stem cells including adipose-derived MSCs and dermal FBs exploit different molecular mechanisms of differentiation to reach a common cell fate. The early mechanisms of differentiation are lineage-specific and are similar for adipogenic and osteogenic differentiation but are distinct for chondrogenic differentiation between MSCs and FBs. A total of 91 samples were analyzed by multiplex RNA-seq. Samples represented replicates from two patients, two cell types and three differentiation protocols, as indicated by the sample annotation. 5 barcodes were unused, but the corresponding FASTQ files are included for completeness.
Project description:Adipose stem cells (ASCs) and adipocytes play a crucial role in maintaining energy balance. We aim to examine the temporal relationship between gene expression and histone modification transitions during in vitro differentiation of human ASCs into adipocytes. Here, we examine by RNAseq proliferating ASCs (Day -2 prior to adipogenic induction), confluent ASCs (Day 0, adipogenic induction), pre-adipocytes (Day 3) and maturing adipocytes (Day 9). We find 1060, 5452 and 2216 genes differentially expressed between D-2/D0, D0/D3 and D3/D9 respectively. We identify gene clusters with distinct and dynamic expression patterns. In particular, adipogenic induction is marked by temporal waves of gene induction and downregulation. We report two types of transcriptional waves: (i) those showing transient induction or inactivation at D0, D3 or D9, and involved in sensory perception and immune response functions; and (ii) those showing long-lived induction or repression at these time points. Our data reveal a dynamic network of gene regulation during adipogenesis, involving signaling, immune and developmental processes. We identify 15 unique epigenetic states using Hidden Markov Modeling which reflects an epigenetically highly organised genome showing enhancer states are commonly consecutive. A heatmap for the abundance of epigenetic states for the expression clusters reveals a link between expression and epigenetic marking of the state suggesting an increase in the number of number of chromatin states with increase in expression. Our data point to a model of increased epigenetic complexity associated with gene expression. Examination of expression of profiles of ASCs across differentiation
Project description:Anaylsis differentially expressed genes of mouse peri-implanted uteri comparing pre-implantation uteri (Day2, Day3 and Day4) with post-implantation uteri (Day6, Day7 and Day8) by microassay. This study has built a meaningful basis for future investigation in elucidating the molecular nature of maternal-fetal interactions during pregnancy establishment and maintenance. Pre-implantation uteri VS. Post-implantation uteri. Three biological replicates of each experiments: pre-implantation uteri (Day2, Day3 and Day4): 234, 234①, 234②; 3 mixture of post-implantation uteri (Day6, Day7 and Day8): 678, 678①, 678②. Two hybridizations were performed by using a reverse fluorescence strategy (Cy3, Cy5) for each sample.
Project description:Anaylsis differentially expressed genes of mouse peri-implanted uteri comparing pre-implantation uteri (Day2, Day3 and Day4) with post-implantation uteri (Day6, Day7 and Day8) by microassay. This study has built a meaningful basis for future investigation in elucidating the molecular nature of maternal-fetal interactions during pregnancy establishment and maintenance. Overall design: Pre-implantation uteri VS. Post-implantation uteri. Three biological replicates of each experiments: pre-implantation uteri (Day2, Day3 and Day4): 234, 234①, 234②; 3 mixture of post-implantation uteri (Day6, Day7 and Day8): 678, 678①, 678②. Two hybridizations were performed by using a reverse fluorescence strategy (Cy3, Cy5) for each sample.
Project description:HEK293T cells grown to confluence in media +10% fetal bovine serume. Media was removed and replaced with serum free media, and cultured for 3 days. RNA was harvested from day0 (serum supplemented), control, and day3 (serum starved) cultures, experiment. Overall design: The analysis compared RNAs from serum supplemented cultures to cultures grown in serum free media for 3 days. Each array was hybridized to a day0 sample and a day3 serum starved sample. There are a total of four arrays with 2 arrays each for dye swap.
Project description:The experiment was designed to generate a time series for epithelial model during development. Each time point had 3 replicates. The data set contained 5 time points over 10 days. They are day0, day3, day5,day7,day10.
Project description:The molecular mechanisms of cerebral vasopasm after SAH are not totally understood. In the present study, we analyzed gene expression profile in rabbit basilar artery after SAH using cDNA microarrays. Total RNA was extracted from rabbit basilar arteries (12 samples: day0 n=3, day3 n=3, day5 n=3, and day7 n=3). They were analyzed by microarray.