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Heider MR, Sun J, Sexton BS, Langhorst BW, Gray A, Higgins L, Chen L, Apone L, Evans TC, Nichols NM, Liu P. Abstract 249: A novel suite of enzyme mixes enable robust hybrid capture sequencing from low quality FFPE DNA. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
In cancer genomics, a common source of DNA is formalin-fixed, paraffin-embedded (FFPE) tissue from patient surgical samples, where in most cases high-quality fresh or frozen tissue samples are not available. FFPE DNA poses many notable challenges for preparing NGS libraries, including low input amounts and highly variable damage from fixation, storage, and extraction methods. Due to the high cost of sequencing and variability of coverage, regions of interest are often specifically enriched using hybrid capture-based approaches, but these methods require a high input of diverse, uniform DNA library to achieve the coverage required for somatic mutation identification in tumor samples. We developed a new DNA repair enzyme mix, enzymatic fragmentation mix, and library amplification PCR master mix, optimizing the activities of these mixes using FFPE samples ranging from DIN 1.8 to 6.8 to maximize yield, WGS library quality, and target enrichment library performance. Combining DNA damage repair and a novel enzymatic fragmentation mix upstream of library preparation reduced the false positive rate in somatic variant detection by repairing damage-derived mutations, and also improved the library yield, quality metrics (including mapping, chimeras, and properly-paired reads), complexity, coverage uniformity, and hybrid capture library quality metrics. The new PCR master mix boosts the library yield without compromising library quality in FFPE-derived samples, allowing flexibility in the PCR cycles used to accommodate high-throughput processing of FFPE samples of highly varied quality. This library prep workflow was evaluated with multiple sequencing platforms including Illumina, MGI, and Element Biosciences. This new suite of enzyme mixes allows even highly damaged FFPE samples to achieve high-quality libraries with sufficient input for hybrid capture. Increasing the useable reads and coverage enables robust detection of somatic variants as demonstrated using both reference standard DNA and patient-derived FFPE samples. Finally, the use of enzymatic fragmentation and a flexible PCR master mix make this FFPE library prep workflow compatible with high-throughput and automation-based workflows.
Citation Format: Margaret R. Heider, Jian Sun, Brittany S. Sexton, Bradley W. Langhorst, Andrew Gray, Lauren Higgins, Lixin Chen, Lynne Apone, Thomas C. Evans, Nicole M. Nichols, Pingfang Liu. A novel suite of enzyme mixes enable robust hybrid capture sequencing from low quality FFPE DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 249.
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Affiliation(s)
| | - Jian Sun
- 1New England Biolabs, Inc., Ipswich, MA
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Sexton BS, Heider M, Williams L, Langhorst B, Dimalanta E, Apone L. Abstract 58: Novel enzymatic fragmentation for challenging samples and methods. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Next Generation Sequencing (NGS) requires fragmentation of DNA molecules upstream of sequencing. Current methods for fragmentation include mechanical shearing and enzymatic fragmentation for NGS library preparation. Mechanical shearing requires costly instruments, can be difficult to automate for high throughput labs, and results in sample loss. In comparison, enzymatic fragmentation methods do not require expensive instruments and are automation friendly. However, current enzymatic fragmentation methods on the market can remove DNA modifications such as methylation, cement DNA damage resulting from formalin fixation in final libraries and can introduce sequencing artifacts or bias. Therefore, while many fragmentation methods are commercially available, challenges remain for sequencing samples such as FFPE DNA or for detecting DNA modification (e.g., 5-methylcytosine).
We have developed a novel enzymatic fragmentation method that can be used upstream of library preparation for DNA methylation assessment or FFPE DNA. The novel enzymatic fragmentation method is quick and robust, taking as little as 20 minutes. It is automation-friendly and can be used to generate DNA fragments ranging from as small as 50 bp up to over 1000 bp.
Here we demonstrate the use of the novel enzymatic fragmentation method upstream of 5mC library preparation methods. This fragmentation method maintained the methylation marks. These libraries showed improvements in GC bias, library yield, library complexity and other sequencing metrics over libraries generated with mechanically sheared DNA.
The use of the novel enzymatic fragmentation method with FFPE DNA library preparation resulted in improvements in sequencing metrics (increased proper pairs, etc.). There was reduced FFPE-damage-derived mutations compared to mechanical shearing or other enzymatic fragmentation methods.
Fragmenting DNA to defined sizes for diverse applications and sample types remains a challenging aspect of NGS library preparation. This new, robust enzymatic fragmentation method overcomes the limitations of some traditional mechanical and enzymatic fragmentation methods and improves the library preparation and sequencing for both DNA modification assessment studies and FFPE DNA.
Citation Format: Brittany S. Sexton, Maggie Heider, Louise Williams, Bradley Langhorst, Eileen Dimalanta, Lynne Apone. Novel enzymatic fragmentation for challenging samples and methods [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 58.
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Vaisvila R, Ponnaluri VKC, Sun Z, Langhorst BW, Saleh L, Guan S, Dai N, Campbell MA, Sexton BS, Marks K, Samaranayake M, Samuelson JC, Church HE, Tamanaha E, Corrêa IR, Pradhan S, Dimalanta ET, Evans TC, Williams L, Davis TB. Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res 2021; 31:1280-1289. [PMID: 34140313 PMCID: PMC8256858 DOI: 10.1101/gr.266551.120] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 05/06/2021] [Indexed: 01/15/2023]
Abstract
Bisulfite sequencing detects 5mC and 5hmC at single-base resolution. However, bisulfite treatment damages DNA, which results in fragmentation, DNA loss, and biased sequencing data. To overcome these problems, enzymatic methyl-seq (EM-seq) was developed. This method detects 5mC and 5hmC using two sets of enzymatic reactions. In the first reaction, TET2 and T4-BGT convert 5mC and 5hmC into products that cannot be deaminated by APOBEC3A. In the second reaction, APOBEC3A deaminates unmodified cytosines by converting them to uracils. Therefore, these three enzymes enable the identification of 5mC and 5hmC. EM-seq libraries were compared with bisulfite-converted DNA, and each library type was ligated to Illumina adaptors before conversion. Libraries were made using NA12878 genomic DNA, cell-free DNA, and FFPE DNA over a range of DNA inputs. The 5mC and 5hmC detected in EM-seq libraries were similar to those of bisulfite libraries. However, libraries made using EM-seq outperformed bisulfite-converted libraries in all specific measures examined (coverage, duplication, sensitivity, etc.). EM-seq libraries displayed even GC distribution, better correlations across DNA inputs, increased numbers of CpGs within genomic features, and accuracy of cytosine methylation calls. EM-seq was effective using as little as 100 pg of DNA, and these libraries maintained the described advantages over bisulfite sequencing. EM-seq library construction, using challenging samples and lower DNA inputs, opens new avenues for research and clinical applications.
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Affiliation(s)
| | | | - Zhiyi Sun
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | | | - Lana Saleh
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Shengxi Guan
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Nan Dai
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | | | - Brittany S Sexton
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Katherine Marks
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Mala Samaranayake
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - James C Samuelson
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Heidi E Church
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Esta Tamanaha
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Sriharsa Pradhan
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | | | - Thomas C Evans
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Louise Williams
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
| | - Theodore B Davis
- New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA
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Malkani S, Chin CR, Cekanaviciute E, Mortreux M, Okinula H, Tarbier M, Schreurs AS, Shirazi-Fard Y, Tahimic CGT, Rodriguez DN, Sexton BS, Butler D, Verma A, Bezdan D, Durmaz C, MacKay M, Melnick A, Meydan C, Li S, Garrett-Bakelman F, Fromm B, Afshinnekoo E, Langhorst BW, Dimalanta ET, Cheng-Campbell M, Blaber E, Schisler JC, Vanderburg C, Friedländer MR, McDonald JT, Costes SV, Rutkove S, Grabham P, Mason CE, Beheshti A. Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development. Cell Rep 2020; 33:108448. [PMID: 33242410 PMCID: PMC8441986 DOI: 10.1016/j.celrep.2020.108448] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 12/14/2022] Open
Abstract
We have identified and validated a spaceflight-associated microRNA (miRNA) signature that is shared by rodents and humans in response to simulated, short-duration and long-duration spaceflight. Previous studies have identified miRNAs that regulate rodent responses to spaceflight in low-Earth orbit, and we have confirmed the expression of these proposed spaceflight-associated miRNAs in rodents reacting to simulated spaceflight conditions. Moreover, astronaut samples from the NASA Twins Study confirmed these expression signatures in miRNA sequencing, single-cell RNA sequencing (scRNA-seq), and single-cell assay for transposase accessible chromatin (scATAC-seq) data. Additionally, a subset of these miRNAs (miR-125, miR-16, and let-7a) was found to regulate vascular damage caused by simulated deep space radiation. To demonstrate the physiological relevance of key spaceflight-associated miRNAs, we utilized antagomirs to inhibit their expression and successfully rescue simulated deep-space-radiation-mediated damage in human 3D vascular constructs.
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Affiliation(s)
- Sherina Malkani
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Christopher R Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Marie Mortreux
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Hazeem Okinula
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ann-Sofie Schreurs
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Yasaman Shirazi-Fard
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Candice G T Tahimic
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | | | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Akanksha Verma
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, Tubingen, Germany
| | - Ceyda Durmaz
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Sheng Li
- The Jackson Laboratories, Farmington, CT, USA
| | - Francine Garrett-Bakelman
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Margareth Cheng-Campbell
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Elizabeth Blaber
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Mountain View, CA 94035, USA
| | - Jonathan C Schisler
- McAllister Heart Institute, Department of Pharmacology, and Department of Pathology and Lab Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles Vanderburg
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - J Tyson McDonald
- Department of Radiation Medicine, Georgetown University School of Medicine, Washington DC 20007, USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Seward Rutkove
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Peter Grabham
- Center for Radiological Research, Columbia University, New York, NY 10032, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Williams L, Ponnaluri VKC, Sexton BS, Saleh L, Marks K, Samaranayake M, Ettwiller L, Guan S, Church HE, Dai N, Tamanaha E, Yigit E, Langhorst B, Sun Z, Evans TC, Vaisvila R, Dimalanta E, Davis TB. Abstract 820: Enzymatic Methyl-Seq: methylome analysis of challenging DNA samples. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
DNA isolated from blood draws (cell-free DNA (cfDNA)) or from archival material like formalin fixed paraffin embedded (FFPE) tissues have advanced the field of cancer genetics. DNA methylation (5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC)) is a key epigenetic factor that plays an important role in cellular processes and it’s misregulation results in diseased states like cancer. Advances in the field of sample preparation from biological matrices and genomics have enabled cancer biomarker identification based on methylation profiling.
Bisulfite sequencing is the standard method to detect methylation and has been employed for both targeted and whole genome methylation analysis. However, the chemical based bisulfite conversion of cytosines to uracils also results in DNA damage which subsequently results in shorter DNA insert sizes as well as introducing bias into the data. Robust biomarker detection relies primarily on the ability to profile methylation accurately. Analysis of DNA methylation from cfDNA and FFPE DNA is challenging as the DNA is typically of low quality and quantity. To overcome the drawbacks of bisulfite sequencing, we developed an enzyme based methylation detection technology, called NEBNext Enzymatic Methyl-Seq (EM-Seq). DNA damage is minimized enabling longer insert sizes, lower duplication rates and minimal GC bias resulting in more accurate quantification of methylation in the sample DNA.
Using EM-Seq, we profiled cfDNA and FFPE DNA from multiple tissue types. Results for these challenging DNA types showed that the EM-Seq libraries had longer inserts, lower duplication rates, higher percentages of mapped reads and less GC bias compared to WGBS libraries. These libraries also identified a higher number of CpG’s and the estimated global methylation levels were in good agreement with the absolute levels quantified using LC/MS. In conclusion, EM-Seq libraries have superior sequencing metrics resulting in robust methylation profiling for these types of challenging DNA samples.
Citation Format: Louise Williams, V K Chaithanya Ponnaluri, Brittany S. Sexton, Lana Saleh, Katherine Marks, Mala Samaranayake, Laurence Ettwiller, Shengxi Guan, Heidi E. Church, Nan Dai, Esta Tamanaha, Erbay Yigit, Bradley Langhorst, Zhiyi Sun, Thomas C. Evans, Romualdas Vaisvila, Eileen Dimalanta, Theodore B. Davis. Enzymatic Methyl-Seq: methylome analysis of challenging DNA samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 820.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Nan Dai
- New England Biolabs, Ipswich, MA
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Sexton BS, Druliner BR, Vera DL, Avey D, Zhu F, Dennis JH. Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response. Oncotarget 2016; 7:6460-75. [PMID: 26771136 PMCID: PMC4872727 DOI: 10.18632/oncotarget.6841] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 12/28/2015] [Indexed: 11/25/2022] Open
Abstract
Nucleosome occupancy is critically important in regulating access to the eukaryotic genome. Few studies in human cells have measured genome-wide nucleosome distributions at high temporal resolution during a response to a common stimulus. We measured nucleosome distributions at high temporal resolution following Kaposi's-sarcoma-associated herpesvirus (KSHV) reactivation using our newly developed mTSS-seq technology, which maps nucleosome distribution at the transcription start sites (TSS) of all human genes. Nucleosomes underwent widespread changes in organization 24 hours after KSHV reactivation and returned to their basal nucleosomal architecture 48 hours after KSHV reactivation. The widespread changes consisted of an indiscriminate remodeling event resulting in the loss of nucleosome rotational phasing signals. Additionally, one in six TSSs in the human genome possessed nucleosomes that are translationally remodeled. 72% of the loci with translationally remodeled nucleosomes have nucleosomes that moved to positions encoded by the underlying DNA sequence. Finally we demonstrated that these widespread alterations in nucleosomal architecture potentiated regulatory factor binding. These descriptions of nucleosomal architecture changes provide a new framework for understanding the role of chromatin in the genomic response, and have allowed us to propose a hierarchical model for chromatin-based regulation of genome response.
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Affiliation(s)
- Brittany S Sexton
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA
| | - Brooke R Druliner
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA.,Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel L Vera
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA.,The Center for Genomics and Personalized Medicine The Florida State University, Tallahassee, Florida, USA
| | - Denis Avey
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA
| | - Fanxiu Zhu
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA
| | - Jonathan H Dennis
- Department of Biological Science, The Florida State University, Tallahassee, Florida, USA
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Abstract
In the eukaryotic nucleus, DNA is packaged into chromatin. The fundamental subunit of chromatin is the nucleosome, DNA is wrapped 1.6 times around a histone octamer core. Nuclear processes in eukaryotes are impacted by whether regulatory DNA is occupied by nucleosomes. We used microarrays to measure nucleosome occupancy in human cells post-Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation at hundreds of immunity-related loci. The detailed analysis of these technologies can be found in recent publications from our lab [1,3]. We found that nucleosome redistributions displayed chromosome specific nucleosome occupancy. This resource can be used to map nucleosome distributions in a variety of biological contexts.
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Affiliation(s)
- Brittany S Sexton
- Department of Biological Science, The Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Brooke R Druliner
- Department of Biological Science, The Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Denis Avey
- Department of Biological Science, The Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Fanxiu Zhu
- Department of Biological Science, The Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Jonathan H Dennis
- Department of Biological Science, The Florida State University, Tallahassee, Florida 32306-4295, USA
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Sexton BS, Avey D, Druliner BR, Fincher JA, Vera DL, Grau DJ, Borowsky ML, Gupta S, Girimurugan SB, Chicken E, Zhang J, Noble WS, Zhu F, Kingston RE, Dennis JH. The spring-loaded genome: nucleosome redistributions are widespread, transient, and DNA-directed. Genome Res 2013; 24:251-9. [PMID: 24310001 PMCID: PMC3912415 DOI: 10.1101/gr.160150.113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleosome occupancy plays a key role in regulating access to eukaryotic genomes. Although various chromatin regulatory complexes are known to regulate nucleosome occupancy, the role of DNA sequence in this regulation remains unclear, particularly in mammals. To address this problem, we measured nucleosome distribution at high temporal resolution in human cells at hundreds of genes during the reactivation of Kaposi's sarcoma–associated herpesvirus (KSHV). We show that nucleosome redistribution peaks at 24 h post-KSHV reactivation and that the nucleosomal redistributions are widespread and transient. To clarify the role of DNA sequence in these nucleosomal redistributions, we compared the genes with altered nucleosome distribution to a sequence-based computer model and in vitro–assembled nucleosomes. We demonstrate that both the predicted model and the assembled nucleosome distributions are concordant with the majority of nucleosome redistributions at 24 h post-KSHV reactivation. We suggest a model in which loci are held in an unfavorable chromatin architecture and “spring” to a transient intermediate state directed by DNA sequence information. We propose that DNA sequence plays a more considerable role in the regulation of nucleosome positions than was previously appreciated. The surprising findings that nucleosome redistributions are widespread, transient, and DNA-directed shift the current perspective regarding regulation of nucleosome distribution in humans.
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Affiliation(s)
- Brittany S Sexton
- Department of Biological Science, The Florida State University, Tallahassee, Florida 32306-4295, USA
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Abstract
The development and progression of lung adenocarcinoma, one of the most common cancers, is driven by the interplay of genetic and epigenetic changes and the role of chromatin structure in malignant transformation remains poorly understood. We used systematic nucleosome distribution and chromatin accessibility microarray mapping platforms to analyze the genome-wide chromatin structure from normal tissues and from primary lung adenocarcinoma of different grades and stages. We identified chromatin-based patterns across different patients with lung adenocarcinoma of different cancer grade and stage. Low-grade cancers had nucleosome distributions very different compared with the corresponding normal tissue but had nearly identical chromatin accessibility. Conversely, nucleosome distributions of high-grade cancers showed few differences. Substantial disruptions in chromosomal accessibility were seen in a patient with a high-grade and high-stage tumor. These data imply that chromatin structure changes during the progression of lung adenocarcinoma. We have therefore developed a model in which low-grade lung adenocarcinomas are linked to changes in nucleosome distributions, whereas higher-grade tumors are linked to large-scale chromosomal changes. These results provide a foundation for the development of a comprehensive framework linking the general and locus-specific roles of chromatin structure to lung cancer progression. We propose that this strategy has the potential to identify a new class of chromatin-based diagnostic, prognostic and therapeutic markers in cancer progression.
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Affiliation(s)
- Brooke R Druliner
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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