scholarly journals Comprehensive nucleosome mapping of the human genome in cancer progression

2015 ◽  
Author(s):  
Brooke Druliner ◽  
Daniel Vera ◽  
Ruth Johnson ◽  
Xiaoyang Ruan ◽  
Lynne Apone ◽  
...  

Altered chromatin structure is a hallmark of cancer, and inappropriate regulation of chromatin structure may represent the origin of transformation. Important studies have mapped human nucleosome distributions genome wide, but the role of chromatin structure in cancer progression has not been addressed. We developed a MNase-Transcription Start Site Sequence Capture method (mTSS-seq) to map the nucleosome distribution at human transcription start sites genome-wide in primary human lung and colon adenocarcinoma tissue. Here, we confirm that nucleosome redistribution is an early, widespread event in lung (LAC) and colon (CRC) adenocarcinoma. These altered nucleosome architectures are consistent between LAC and CRC patient samples indicating that they may serve as important early adenocarcinoma markers. We demonstrate that the nucleosome alterations are driven by the underlying DNA sequence and potentiate transcription factor binding. We conclude that DNA-directed nucleosome redistributions are widespread early in cancer progression. We have proposed an entirely new hierarchical model for chromatin-mediated genome regulation.

PLoS ONE ◽  
2009 ◽  
Vol 4 (10) ◽  
pp. e7526 ◽  
Author(s):  
Alfredo Mendoza-Vargas ◽  
Leticia Olvera ◽  
Maricela Olvera ◽  
Ricardo Grande ◽  
Leticia Vega-Alvarado ◽  
...  

2008 ◽  
Vol 22 (1) ◽  
pp. 10-22 ◽  
Author(s):  
Hui Gao ◽  
Susann Fält ◽  
Albin Sandelin ◽  
Jan-Åke Gustafsson ◽  
Karin Dahlman-Wright

Abstract We report the genome-wide identification of estrogen receptor α (ERα)-binding regions in mouse liver using a combination of chromatin immunoprecipitation and tiled microarrays that cover all nonrepetitive sequences in the mouse genome. This analysis identified 5568 ERα-binding regions. In agreement with what has previously been reported for human cell lines, many ERα-binding regions are located far away from transcription start sites; approximately 40% of ERα-binding regions are located within 10 kb of annotated transcription start sites. Almost 50% of ERα-binding regions overlap genes. The majority of ERα-binding regions lie in regions that are evolutionarily conserved between human and mouse. Motif-finding algorithms identified the estrogen response element, and variants thereof, together with binding sites for activator protein 1, basic-helix-loop-helix proteins, ETS proteins, and Forkhead proteins as the most common motifs present in identified ERα-binding regions. To correlate ERα binding to the promoter of specific genes, with changes in expression levels of the corresponding mRNAs, expression levels of selected mRNAs were assayed in livers 2, 4, and 6 h after treatment with ERα-selective agonist propyl pyrazole triol. Five of these eight selected genes, Shp, Stat3, Pdgds, Pck1, and Pdk4, all responded to propyl pyrazole triol after 4 h treatment. These results extend our previous studies using gene expression profiling to characterize estrogen signaling in mouse liver, by characterizing the first step in this signaling cascade, the binding of ERα to DNA in intact chromatin.


2019 ◽  
Author(s):  
Katerina Cermakova ◽  
Eric A. Smith ◽  
Vaclav Veverka ◽  
H. Courtney Hodges

AbstractSETD2 contributes to gene expression by marking gene bodies with H3K36me3, which is thought to assist in the concentration of transcription machinery at the small portion of the coding genome. Despite extensive genome-wide data revealing the precise localization of H3K36me3 over gene bodies, the physical basis for the accumulation, maintenance, and sharp borders of H3K36me3 over these sites remains rudimentary. Here we propose a model of H3K36me3 marking based on stochastic transcription-dependent placement and transcription-independent spreading. Our analysis of the spatial distributions and dynamic features of these marks indicates that transcription-dependent placement dominates the establishment of H3K36me3 domains compared to transcription-independent spreading processes, and that turnover of H3K36me3 limits its capacity for epigenetic memory. By adding additional terms for asymmetric histone turnover occurring at transcription start sites, our model provides a remarkably accurate representation of H3K36me3 levels and dynamics over gene bodies. Furthermore, we validate our findings by revealing that loss of SPT6 impairs the transcription-coupled activity of the SETD2:IWS1:SPT6 ternary complex, thereby reducing the tight correlation between transcription and H3K36me3 levels at gene bodies.


2021 ◽  
Vol 7 (31) ◽  
pp. eabi6508
Author(s):  
Seung-Gi Jin ◽  
Dean Pettinga ◽  
Jennifer Johnson ◽  
Peipei Li ◽  
Gerd P. Pfeifer

Sunlight-associated melanomas carry a unique C-to-T mutation signature. UVB radiation induces cyclobutane pyrimidine dimers (CPDs) as the major form of DNA damage, but the mechanism of how CPDs cause mutations is unclear. To map CPDs at single-base resolution genome wide, we developed the circle damage sequencing (circle-damage-seq) method. In human cells, CPDs form preferentially in a tetranucleotide sequence context (5′-Py-T<>Py-T/A), but this alone does not explain the tumor mutation patterns. To test whether mutations arise at CPDs by cytosine deamination, we specifically mapped UVB-induced cytosine-deaminated CPDs. Transcription start sites (TSSs) were protected from CPDs and deaminated CPDs, but both lesions were enriched immediately upstream of the TSS, suggesting a mutation-promoting role of bound transcription factors. Most importantly, the genomic dinucleotide and trinucleotide sequence specificity of deaminated CPDs matched the prominent mutation signature of melanomas. Our data identify the cytosine-deaminated CPD as the leading premutagenic lesion responsible for mutations in melanomas.


2016 ◽  
Author(s):  
Christophe D Chabbert ◽  
Lars M Steinmetz ◽  
Bernd Klaus

The genome–wide study of epigenetic states requires the integrative analysis of histone modification ChIP–seq data. Here, we introduce an easy–to–use analytic framework to compare profiles of enrichment in histone modifications around classes of genomic elements, e.g. transcription start sites (TSS). Our framework is available via the user–friendly R/Bioconductor package DChIPRep. DChIPRep uses biological replicate information as well as chromatin Input data to allow for a rigorous assessment of differential enrichment. DChIPRep is available for download through the Bioconductor project at http://bioconductor.org/packages/DChIPRep. Contact [email protected]


2019 ◽  
Vol 47 (13) ◽  
pp. 6714-6725 ◽  
Author(s):  
Chen Chen ◽  
Jie Shu ◽  
Chenlong Li ◽  
Raj K Thapa ◽  
Vi Nguyen ◽  
...  

Abstract SPT6 is a conserved elongation factor that is associated with phosphorylated RNA polymerase II (RNAPII) during transcription. Recent transcriptome analysis in yeast mutants revealed its potential role in the control of transcription initiation at genic promoters. However, the mechanism by which this is achieved and how this is linked to elongation remains to be elucidated. Here, we present the genome-wide occupancy of Arabidopsis SPT6-like (SPT6L) and demonstrate its conserved role in facilitating RNAPII occupancy across transcribed genes. We also further demonstrate that SPT6L enrichment is unexpectedly shifted, from gene body to transcription start site (TSS), when its association with RNAPII is disrupted. Protein domains, required for proper function and enrichment of SPT6L on chromatin, are subsequently identified. Finally, our results suggest that recruitment of SPT6L at TSS is indispensable for its spreading along the gene body during transcription. These findings provide new insights into the mechanisms underlying SPT6L recruitment in transcription and shed light on the coordination between transcription initiation and elongation.


2019 ◽  
Vol 48 (3) ◽  
pp. 1206-1224
Author(s):  
Julie M J Lepesant ◽  
Carole Iampietro ◽  
Eugenia Galeota ◽  
Benoit Augé ◽  
Marion Aguirrenbengoa ◽  
...  

Abstract The histone demethylase LSD1 is a key chromatin regulator that is often deregulated in cancer. Its ortholog, dLsd1 plays a crucial role in Drosophila oogenesis; however, our knowledge of dLsd1 function is insufficient to explain its role in the ovary. Here, we have performed genome-wide analysis of dLsd1 binding in the ovary, and we document that dLsd1 is preferentially associated to the transcription start site of developmental genes. We uncovered an unanticipated interplay between dLsd1 and the GATA transcription factor Serpent and we report an unexpected role for Serpent in oogenesis. Besides, our transcriptomic data show that reducing dLsd1 levels results in ectopic transposable elements (TE) expression correlated with changes in H3K4me2 and H3K9me2 at TE loci. In addition, our results suggest that dLsd1 is required for Piwi dependent TE silencing. Hence, we propose that dLsd1 plays crucial roles in establishing specific gene expression programs and in repressing transposons during oogenesis.


2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi110-vi110
Author(s):  
Tathiane Malta ◽  
Thais Sarraf Sabedot ◽  
Carlos Carlotti jr ◽  
Houtan Noushmehr

Abstract Meningiomas are mostly benign brain tumors but have a substantial risk of recurrence, sometimes to more aggressive subtypes. Recently, a DNA methylation signature in meningioma was described as able to stratify patients by recurrence risk (favorable and unfavorable). It is well recognized that epigenetic deregulation at distinct genomic elements can affect changes in gene expression and contribute to cancer initiation and progression. Our goal for this study is to define genes that are actively expressed or repressed by both DNA methylation and chromatin histone modification (defined by H3K4me3). For this pilot study, we selected two favorable (grades I and II) and two unfavorable (grades II and III) meningioma primary tumor samples (N=4) and mapped H3K4me3 genome-wide and whole-genome DNA methylation, in an attempt to identify active transcription start sites at known promoters. After data alignment, preprocessing and peak calling, we identified 29,514 consensus peaks for H3K4me3. The differential binding analysis resulted in 5,752 H3K4me3 regions that distinguish favorable from unfavorable meningioma, mostly gain of peaks in the unfavorable group. We identified 1,505 peaks overlapping with known promoters, 51% associated with gain of peaks in the unfavorable group. Promoter-associated chromatin changes coincided with hypomethylation in 23 unique genes in the unfavorable group. Genes such as MET, PTEN, and the long non-coding RNA RP11-60L3.1 were identified as potential regulators of meningioma recurrence. Our preliminary results describe the identification of distinct genome-wide changes in chromatin associated with meningioma patient with high risk for recurrence. Identification of candidate genes will provide knowledge of the role of epigenomics in the development of malignant meningioma and of opportunities for targeted therapy.


Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 3398-3398 ◽  
Author(s):  
Maria Gkotzamanidou ◽  
Masood Shammas ◽  
Vassilis L. Souliotis ◽  
Weihua Song ◽  
Jagannath Pal ◽  
...  

Abstract Multiple Myeloma (MM) is characterized by genomic heterogeneity that contributes to differences in clinical outcome. Mis - or unrepaired DNA damage poses a serious threat to genomic stability, potentially leading to the formation of oncogenic mutations, including translocations, deletions and amplifications. Spontaneous endogenous DNA damage represents an essential portion of DNA lesions; therefore, a thorough knowledge of its types and prevalence is of high importance for its impact on myelomagenesis, its interaction with exogenous DNA damaging sources, and consequently, at improving the clinical outcome of myeloma patients. First, we evaluated the occurrence of spontaneous DNA damage in a panel of 4 MM cell lines, 4 CD138+ primary MM patients samples and in 4 solid tumor cell lines. Using single-cell gel electrophoresis (comet assay) under neutral and alkaline conditions we observed high levels of olive tails moments indicative of DNA damage in all MM cell lines (mean±SD, MM1S 47.56±7.1, OPM2 60.92±7.9) and primary MM cells as well as solid tumor cell lines, compared to normal cell controls (PBMCs 6.283±3.56, HEEC 1.448±0.2, BJ 0.64±0.58) (P=.0001). Significantly higher signal of the most widely used marker of DNA damage γH2ax phosphorylated at serine139, 53BP1 and RPA32 as indicator of Single strand breaks (SSB) was observed by immunoblotting in all MM cell lines compared to normal controls confirming the high occurrence of DNA damage in MM in absence of any exogenous genotoxic insult. These results were further confirmed by immunocytochemistry with γH2Ax, ku70/80, 53BP1, Rad51. Remarkably, the Non homologous end joining (NHEJ) marker ku70/80 was co-localized with γH2Ax and was present in ~80% of cells, indicating the activation of NHEJ throughout the cell cycle. To further elucidate the differential spontaneous DNA damage in MM, we detected and quantified the abasic sites by using an ELISA-based assay. The distribution of abasic sites showed same pattern as the DSBs in all the MM cell types analyzed, indicating that abasic sites constitute an important portion of spontaneous DNA damage (OPM2 57.3/105, PBMCs 12/105bp). On the basis of these findings, we hypothesized that the increased stimulation by endogenous oxidative stress or possible inactivation of DNA damage repair mechanisms might be implicated to this observed high occurrence of DSBs in MM. By using our chromosomally integrated green fluorescent protein reporter construct-based assay, we observed that NHEJ and homologous recombination (HR) were significantly more active in all MM cells compared to normal controls. Moreover, we found that increased stimulation by endogenous oxidative stress was present in all MM cells evaluated, while a strong correlation between the levels of oxidative stress and the spontaneous DSBs was observed (r=0.85, P<.0001). As the information conveyed by epigenetic modifications play a key role in the regulation of DNA processes including DNA damage and repair, we performed Chip-seq analysis for γH2ax. After performing peak calling on γH2ax ChIP-seq data, we sought to determine whether γH2ax enrichment regions tend to occur in previously reported common fragile sites or early replicating sites. Interestingly, we found that spontaneous DNA damage is equally representative in replicating fragile sites and random sites throughout genome. Next, we performed sequential double chip-seq analysis for γH2ax for the first Chip and a total 5 different epigenetic marks for the re-Chip. We performed peak-calling analysis on each data type, and strikingly, we found that similar numbers of peaks can be found across re-ChIP dataset with H3K27ac having the greatest number of peaks (653). Of the 5 marks evaluated, we observed that only H4K20me2 showed significant enrichment in promoter regions relative to random chance (P=.039) within 1kb of transcription start sites. A similar trend is also observed for the region within 3kb of transcription start sites (P=.026), and 2kb of transcription start sites (P=.084, weakly significant), indicating a possible role of methylation of K20 in proper chromatin organization in proximity of DSBs. In conclusion, our study demonstrates the higher occurrence of ongoing spontaneous DNA damage in MM and provides insights into possible relationship between the aberrant epigenome and spontaneous DNA damage revealing mechanism that might be dysregulated promoting genomic instability. Disclosures Anderson: Celgene: Consultancy; Sanofi-Aventis: Consultancy; Onyx: Consultancy; Acetylon: Scientific Founder, Scientific Founder Other; Oncoprep: Scientific Founder Other; Gilead Sciences: Consultancy. Dimopoulos:Celgene: Consultancy, Honoraria.


Sign in / Sign up

Export Citation Format

Share Document