Undifferentiated hematopoietic cells are characterized by a genome-wide undermethylation dip around the transcription start site and a hierarchical epigenetic plasticity

2010 ◽  
Vol 2010 ◽  
pp. 209-210
Author(s):  
R.J. Arceci
Blood ◽  
2009 ◽  
Vol 114 (24) ◽  
pp. 4968-4978 ◽  
Author(s):  
Yun Shin Chung ◽  
Hye Joung Kim ◽  
Tae-Min Kim ◽  
Sung-Hyun Hong ◽  
Kyung-Rim Kwon ◽  
...  

Abstract Evidence for the epigenetic regulation of hematopoietic stem cells (HSCs) is growing, but the genome-wide epigenetic signature of HSCs and its functional significance remain unclear. In this study, from a genome-wide comparison of CpG methylation in human CD34+ and CD34− cells, we identified a characteristic undermethylation dip around the transcription start site of promoters and an overmethylation of flanking regions in undifferentiated CD34+ cells. This “bivalent-like” CpG methylation pattern around the transcription start site was more prominent in genes not associated with CpG islands (CGI−) than CGI+ genes. Undifferentiated hematopoietic cells also exhibited dynamic chromatin associated with active transcription and a higher turnover of histone acetylation than terminally differentiated cells. Interestingly, inhibition of chromatin condensation by chemical treatment (5-azacytidine, trichostatin A) enhanced the self-renewal of “stimulated” HSCs in reconstituting bone marrows but not “steady-state” HSCs in stationary phase bone marrows. In contrast, similar treatments on more mature cells caused partial phenotypic dedifferentiation and apoptosis at levels correlated with their hematopoietic differentiation. Taken together, our study reveals that the undifferentiated state of hematopoietic cells is characterized by a unique epigenetic signature, which includes dynamic chromatin structures and an epigenetic plasticity that correlates to level of undifferentiation.


2020 ◽  
Author(s):  
Zhe Sun ◽  
Alexander Yakhnin ◽  
Peter C. FitzGerald ◽  
Carl E. Mclntosh ◽  
Mikhail Kashlev

ABSTRACTPromoter-proximal pausing regulates expression of many eukaryotic genes and serves as checkpoints for assembly of elongation/splicing machinery. Little is known how broadly the pausing is employed in transcriptional regulation in bacteria. We applied NET-seq combined with RNase I footprinting for genome-wide analysis of σ70-dependent transcription pauses in Escherichia coli. Many E. coli genes appear to contain clusters of strong backtracked pauses at 10-20-bp distance from the transcription start site caused by retention of σ70 subunit in RNA polymerase. The pauses in 10-15-bp register of the promoter are dictated by binding of σ70 to canonical −10 element, 6-7 nt spacer and “YR+1Y” motif centered at transcription start site all characteristic for strong E. coli promoters. The promoters for the pauses in 16-20-bp register contain an additional −10-like sequence positioned on the same face of the DNA duplex as the original −10 element suggesting that σ70 hopping was responsible for these pauses. Our in vitro analysis reveals that RNA polymerase backtracking and DNA scrunching are involved in these pauses that are relieved by Gre transcript cleavage factors. The genes coding for transcription factors are enriched in these pauses suggesting that σ70 and Gre proteins regulate transcription in response to changing environmental cues.


BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Andrea M. Sass ◽  
Heleen Van Acker ◽  
Konrad U. Förstner ◽  
Filip Van Nieuwerburgh ◽  
Dieter Deforce ◽  
...  

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2254-2254
Author(s):  
Susan E. Shetzline ◽  
Joseph Conlon ◽  
Cezary Swider ◽  
Lindsay Thalheim ◽  
Alan M. Gewirtz

Abstract The c-myb proto-oncogene encodes a transcription factor, Myb, which is essential for the growth and survival of normal and malignant hematopoietic cells. We, and others, have previously shown that malignant hematopoietic cells are more dependent on c-Myb function than are normal hematopoietic cells. Based on these findings, we hypothesized that c-Myb regulates a unique set of genes in leukemic cells that are required for their growth. To identify Myb gene targets, we performed a transcriptome analysis using human myeloid leukemic cells engineered to express a conditionally active dominant negative Myb (MERT). Analysis of the microarray data derived from these experiments revealed that when Myb activity was inhibited, neuromedin U (NmU), a neuropeptide involved in energy homeostasis, decreased in expression 5 fold compared to control cells, a result that was confirmed by quantitative real-time PCR. Combined, the microarray and quantitative real-time PCR data suggested that Myb directly regulates NmU gene expression in hematopoietic cells. To address this question in the absence of a formally defined human NmU promoter, we examined the DNA sequence upstream of the predicted transcription start site (as noted in Genbank accession #NM_006681) for potential Myb transcription factor binding motifs. After scanning the DNA sequence (~2kb) upstream of the predicted transcription start site, eleven potential Myb response elements (MREs) were identified. Of these MREs, five were identified as canonical (PyAAC(G/C)G). Our search also identified potential AML1, PU.1, CBP, STAT3, and STAT5 binding motifs within the human NmU promoter region. To determine if any of the potential MREs within the NmU promoter were functional, we first completed in vitro assays using luciferase reporter constructs followed by in vivo assays using chromatin immunoprecipitation (ChIP) assays. The luciferase reporter constructs were generated after we determined the actual transcription start of human NmU by primer extension assays. Using a Fam-labeled NmU specific primer that annealed proximal to the predicted transcription start site, we observed a 20-nucleotide difference between the predicted and actual transcription start of NmU. When all eleven potential MREs within the NmU promoter were upstream of luciferase, a 6-fold increase in luciferase activity was observed compared to empty vector. We next systematically mutated the MREs to determine which one(s) Myb bound directly. Thus far, the in vitro luciferase assay has identified MREs at −446 and −626, which are proximal to NmU’s transcription start as important for Myb-mediated expression. To determine the physiologic relevance of our in vitro studies, we performed ChIP assays. When chromatin from K562 cells, a human myeloid leukemia cell line, was immunoprecipitated with anti-c-Myb, we observed the expected PCR product using primer pairs that flanked select MREs. These same results were obtained in our positive control ChIP experiment in which the chromatin was immunoprecipitated with anti-acetyl histone 4 indicating that the promoter region of NmU is poised for transcription. Further characterization of the regulation of NmU gene expression in normal and malignant hematopoietic cells may yield new clues to Myb’s role in leukemogenesis and could suggest new therapeutic targets in human leukemia cells.


2020 ◽  
Vol 3 (10) ◽  
pp. e202000762
Author(s):  
Oscar D Villarreal ◽  
Sofiane Y Mersaoui ◽  
Zhenbao Yu ◽  
Jean-Yves Masson ◽  
Stéphane Richard

DDX5, XRN2, and PRMT5 have been shown to resolve DNA/RNA hybrids (R-loops) at RNA polymerase II transcription termination sites at few genomic loci. Herein, we perform genome-wide R-loop mapping using classical DNA/RNA immunoprecipitation and high-throughput sequencing (DRIP-seq) of loci regulated by DDX5, XRN2, and PRMT5. We observed hundreds to thousands of R-loop gains and losses at transcribed loci in DDX5-, XRN2-, and PRMT5-deficient U2OS cells. R-loop gains were characteristic of highly transcribed genes located at gene-rich regions, whereas R-loop losses were observed in low-density gene areas. DDX5, XRN2, and PRMT5 shared many R-loop gain loci at transcription termination sites, consistent with their coordinated role in RNA polymerase II transcription termination. DDX5-depleted cells had unique R-loop gain peaks near the transcription start site that did not overlap with those of siXRN2 and siPRMT5 cells, suggesting a role for DDX5 in transcription initiation independent of XRN2 and PRMT5. Moreover, we observed that the accumulated R-loops at certain loci in siDDX5, siXRN2, and siPRMT5 cells near the transcription start site of genes led to antisense intergenic transcription. Our findings define unique and shared roles of DDX5, XRN2, and PRMT5 in DNA/RNA hybrid regulation.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 2254-2254
Author(s):  
Julia Gambone ◽  
Stephanie Dusaban ◽  
Susan Shetzline

Abstract Neuromedin U (NmU) is a 25-amino acid neuropeptide that is expressed at high levels in the brain, gut, and bone marrow. In the brain, NmU modulates the central control of feeding and bone mass. In the intestine, NmU regulates the contraction of smooth muscle, local blood flow, and ion transport. In the bone marrow, the physiological function of NmU remains ill-defined. To determine the physiological function of NmU in hematopoietic cells, we utilized K562-MERT cells, which express a tamoxifen-inducible dominant negative Myb (MERT), and cell culture assays. We chose to test the function of NmU in a cell line that expresses high levels of the proto-oncogene c-myb because c-Myb encodes a transcription factor that regulates cell proliferation, survival, and differentiation through the transactivation of its target genes. By inhibiting endogenous Myb activity in K562-MERT cells by tamoxifen in methylcellulose cultures, we observed a 6-fold decrease in cell number compared to untreated K562-MERT cells. Supplementing the tamoxifen treated methylcellulose cultures of K562-MERT cells with NmU resulted in a 3.6-fold increase in K562-MERT cell number compared to K562-MERT cells treated with only tamoxifen. In liquid cultures using primary cells from patients with acute myeloid leukemia, we observed more cells in the cultures with NmU than when NmU was absent from the cultures. Finally, silencing NmU gene expression in K562 cells via RNA interference decreased the proliferation of these cells. Collectively, these data demonstrate that NmU functions to promote the proliferation of hematopoietic cells. The ability of NmU to rescue cell growth in tamoxifen treated K562-MERT cells and Myb’s role in regulating hematopoietic cell proliferation led us to hypothesize that Myb mediates hematopoietic cell proliferation in part by directly regulating NmU gene expression. To test this hypothesis, we examined the DNA sequence upstream of NmU’s predicted transcription start site (as noted in Genbank accession #NM_006681) for potential Myb response elements (MREs). We identified eleven potential MREs within the first 2kb upstream of NmU’s transcription start site. Of these MREs, five were identified as canonical (PyAAC(G/T)G). Our search also identified potential Ets-2 binding motifs within the human NmU promoter region, which were of interest because Myb has been reported to cooperate with Ets-2 in the regulation of c-kit and CD34 gene expression. To determine if any of the potential MREs within the NmU promoter were functional, we first completed in vitro assays using luciferase reporter constructs followed by in vivo assays using chromatin immunoprecipitation (ChIP) assays. The luciferase reporter constructs were generated such that the first 2kb upstream of NmU’s transcription start site was inserted upstream of the luciferase gene in pGL3-basic to yield pGL3-NmU. When pGL3-NmU was co-transfected into 293T cells with a c-Myb expression construct, we observed an average of 15-fold induction of luciferase activity compared to empty vector. There was no change in luciferase activity when 293T cells were co-transfected with the c-Myb isoform B-Myb compared to empty vector, suggesting that c-Myb and not B-Myb interact with the MREs within the NmU promoter to induce its expression. Mutation of either MRE9 or 10, which are distal to NmU’s transcription start site, in pGL3-NmU prevented c-Myb from inducing luciferase gene expression, demonstrating that MRE9 and 10 are functional. When Ets-2 was co-transfected with pGL3-NmU into 293T cells, a 10-fold increase in luciferase activity was observed suggesting that Ets-2 and c-Myb may cooperate to increase the transcription of NmU. To determine the physiologic relevance of our in vitro luciferase studies, we performed ChIP assays. Following immunoprecipitation of the cross-linked chromatin with either anti-c-Myb or anti-Ets-2, a PCR product of the recovered DNA was observed using primers that flanked MRE9, MRE10, and one Ets-2 site, demonstrating that in vivo c-Myb and Ets-2 interact directly with NmU’s promoter. Studies are underway to determine whether c-Myb and Ets-2 cooperate to induce NmU gene expression. Further characterization of the regulation of NmU gene expression in normal and malignant hematopoietic cells may yield new clues to Myb’s role in leukemogenesis and could suggest new therapeutic targets in human myeloid leukemia cells.


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