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For: Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z. Nucleosome positioning signals in genomic DNA. Genome Res 2007;17:1170-7. [PMID: 17620451 PMCID: PMC1933512 DOI: 10.1101/gr.6101007] [Citation(s) in RCA: 245] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Number Cited by Other Article(s)
1
Geisberg JV, Moqtaderi Z, Struhl K. Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate. Proc Natl Acad Sci U S A 2024;121:e2405827121. [PMID: 38748572 PMCID: PMC11127049 DOI: 10.1073/pnas.2405827121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024]  Open
2
Struhl K. How is polyadenylation restricted to 3'-untranslated regions? Yeast 2024;41:186-191. [PMID: 38041485 PMCID: PMC11001523 DOI: 10.1002/yea.3915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/30/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]  Open
3
Zhu Y, Vvedenskaya IO, Sze SH, Nickels BE, Kaplan CD. Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels. Nat Struct Mol Biol 2024;31:190-202. [PMID: 38177677 PMCID: PMC10928753 DOI: 10.1038/s41594-023-01171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
4
Back G, Walther D. Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility. NAR Genom Bioinform 2023;5:lqad097. [PMID: 37954573 PMCID: PMC10632188 DOI: 10.1093/nargab/lqad097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023]  Open
5
Yadav M, Zuiddam M, Schiessel H. The role of transcript regions and amino acid choice in nucleosome positioning. NAR Genom Bioinform 2023;5:lqad080. [PMID: 37705829 PMCID: PMC10495542 DOI: 10.1093/nargab/lqad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/19/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023]  Open
6
Han GS, Li Q, Li Y. Nucleosome positioning based on DNA sequence embedding and deep learning. BMC Genomics 2022;23:301. [PMID: 35418074 PMCID: PMC9006412 DOI: 10.1186/s12864-022-08508-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 11/25/2022]  Open
7
Gnan S, Matelot M, Weiman M, Arnaiz O, Guérin F, Sperling L, Bétermier M, Thermes C, Chen CL, Duharcourt S. GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium. Genome Res 2022;32:699-709. [PMID: 35264448 PMCID: PMC8997360 DOI: 10.1101/gr.276125.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/14/2022] [Indexed: 11/24/2022]
8
Chaudhary S, Jabre I, Syed NH. Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana. Genomics 2021;113:3476-3486. [PMID: 34391867 DOI: 10.1016/j.ygeno.2021.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022]
9
Fan K, Moore JE, Zhang XO, Weng Z. Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes. Nucleic Acids Res 2021;49:5705-5725. [PMID: 33978759 PMCID: PMC8191798 DOI: 10.1093/nar/gkab345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/19/2021] [Accepted: 05/01/2021] [Indexed: 12/04/2022]  Open
10
Liu G, Zhao H, Meng H, Xing Y, Cai L. A deformation energy model reveals sequence-dependent property of nucleosome positioning. Chromosoma 2021;130:27-40. [PMID: 33452566 PMCID: PMC7889546 DOI: 10.1007/s00412-020-00750-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 11/18/2022]
11
Markus BM, Waldman BS, Lorenzi HA, Lourido S. High-Resolution Mapping of Transcription Initiation in the Asexual Stages of Toxoplasma gondii. Front Cell Infect Microbiol 2021;10:617998. [PMID: 33553008 PMCID: PMC7854901 DOI: 10.3389/fcimb.2020.617998] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022]  Open
12
Ash1 and Tup1 dependent repression of the Saccharomyces cerevisiae HO promoter requires activator-dependent nucleosome eviction. PLoS Genet 2020;16:e1009133. [PMID: 33382702 PMCID: PMC7806131 DOI: 10.1371/journal.pgen.1009133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/13/2021] [Accepted: 11/25/2020] [Indexed: 11/30/2022]  Open
13
Serizay J, Dong Y, Jänes J, Chesney M, Cerrato C, Ahringer J. Distinctive regulatory architectures of germline-active and somatic genes in C. elegans. Genome Res 2020;30:1752-1765. [PMID: 33093068 PMCID: PMC7706728 DOI: 10.1101/gr.265934.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/08/2020] [Indexed: 01/08/2023]
14
Zhu Y, Ong CS, Huttley GA. Machine Learning Techniques for Classifying the Mutagenic Origins of Point Mutations. Genetics 2020;215:25-40. [PMID: 32193188 PMCID: PMC7198283 DOI: 10.1534/genetics.120.303093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/05/2020] [Indexed: 11/18/2022]  Open
15
Hocher A, Rojec M, Swadling JB, Esin A, Warnecke T. The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog. eLife 2019;8:52542. [PMID: 31710291 PMCID: PMC6877293 DOI: 10.7554/elife.52542] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/10/2019] [Indexed: 02/06/2023]  Open
16
Jabbari K, Chakraborty M, Wiehe T. DNA sequence-dependent chromatin architecture and nuclear hubs formation. Sci Rep 2019;9:14646. [PMID: 31601866 PMCID: PMC6787200 DOI: 10.1038/s41598-019-51036-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/18/2019] [Indexed: 02/08/2023]  Open
17
He Y, Lu J, Ye Z, Hao S, Wang L, Kohli M, Tindall DJ, Li B, Zhu R, Wang L, Huang H. Androgen receptor splice variants bind to constitutively open chromatin and promote abiraterone-resistant growth of prostate cancer. Nucleic Acids Res 2019;46:1895-1911. [PMID: 29309643 PMCID: PMC5829742 DOI: 10.1093/nar/gkx1306] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/20/2017] [Indexed: 11/13/2022]  Open
18
Datta S, Patel M, Patel D, Singh U. Distinct DNA Sequence Preference for Histone Occupancy in Primary and Transformed Cells. Cancer Inform 2019;18:1176935119843835. [PMID: 31037026 PMCID: PMC6475841 DOI: 10.1177/1176935119843835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 03/24/2019] [Indexed: 11/15/2022]  Open
19
The Role of Nucleosomes in Epigenetic Gene Regulation. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]  Open
20
Malkowska M, Zubek J, Plewczynski D, Wyrwicz LS. ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning. PeerJ 2018;6:e5742. [PMID: 30519505 PMCID: PMC6275119 DOI: 10.7717/peerj.5742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/13/2018] [Indexed: 02/01/2023]  Open
21
Lu M, Liu S. Nucleosome positioning based on generalized relative entropy. Soft comput 2018. [DOI: 10.1007/s00500-018-3602-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
22
Li W, Thanos D, Provata A. Quantifying local randomness in human DNA and RNA sequences using Erdös motifs. J Theor Biol 2018;461:41-50. [PMID: 30336158 DOI: 10.1016/j.jtbi.2018.09.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/14/2018] [Accepted: 09/25/2018] [Indexed: 10/28/2022]
23
Tahir M, Hayat M, Khan SA. iNuc-ext-PseTNC: an efficient ensemble model for identification of nucleosome positioning by extending the concept of Chou's PseAAC to pseudo-tri-nucleotide composition. Mol Genet Genomics 2018;294:199-210. [PMID: 30291426 DOI: 10.1007/s00438-018-1498-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
24
Zhao H, Zhang F, Guo M, Xing Y, Liu G, Zhao X, Cai L. The affinity of DNA sequences containing R5Y5 motif and TA repeats with 10.5-bp periodicity to histone octamer in vitro. J Biomol Struct Dyn 2018;37:1935-1943. [PMID: 30044196 DOI: 10.1080/07391102.2018.1477621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
25
Liu G, Liu GJ, Tan JX, Lin H. DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions. Genomics 2018;111:1167-1175. [PMID: 30055231 DOI: 10.1016/j.ygeno.2018.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/07/2018] [Accepted: 07/15/2018] [Indexed: 12/15/2022]
26
Ma W, Yang L, Rohs R, Noble WS. DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding. Bioinformatics 2018;33:3003-3010. [PMID: 28541376 PMCID: PMC5870879 DOI: 10.1093/bioinformatics/btx336] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/23/2017] [Indexed: 01/07/2023]  Open
27
The implication of DNA bending energy for nucleosome positioning and sliding. Sci Rep 2018;8:8853. [PMID: 29891930 PMCID: PMC5995830 DOI: 10.1038/s41598-018-27247-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 05/24/2018] [Indexed: 11/24/2022]  Open
28
Brunet FG, Audit B, Drillon G, Argoul F, Volff JN, Arneodo A. Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates. Biophys J 2018;114:2308-2316. [PMID: 29580552 PMCID: PMC6028776 DOI: 10.1016/j.bpj.2018.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/07/2018] [Accepted: 02/20/2018] [Indexed: 12/15/2022]  Open
29
Jia C, Yang Q, Zou Q. NucPosPred: Predicting species-specific genomic nucleosome positioning via four different modes of general PseKNC. J Theor Biol 2018;450:15-21. [PMID: 29678692 DOI: 10.1016/j.jtbi.2018.04.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 11/20/2022]
30
Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin. Cells 2018;7:cells7030017. [PMID: 29498679 PMCID: PMC5870349 DOI: 10.3390/cells7030017] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 02/07/2023]  Open
31
High-Resolution Genome-Wide Mapping of Nucleosome Positioning and Occupancy Level Using Paired-End Sequencing Technology. Methods Mol Biol 2018;1528:229-243. [PMID: 27854025 DOI: 10.1007/978-1-4939-6630-1_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
32
Nanan KK, Ocheltree C, Sturgill D, Mandler MD, Prigge M, Varma G, Oberdoerffer S. Independence between pre-mRNA splicing and DNA methylation in an isogenic minigene resource. Nucleic Acids Res 2017;45:12780-12797. [PMID: 29244186 PMCID: PMC5727405 DOI: 10.1093/nar/gkx900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 09/13/2017] [Accepted: 09/25/2017] [Indexed: 12/27/2022]  Open
33
Angarica VE, Del Sol A. Bioinformatics Tools for Genome-Wide Epigenetic Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017;978:489-512. [PMID: 28523562 DOI: 10.1007/978-3-319-53889-1_25] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
34
Meng H, Li H, Zheng Y, Yang Z, Jia Y, Bo S. Evolutionary analysis of nucleosome positioning sequences based on New Symmetric Relative Entropy. Genomics 2017;110:154-161. [PMID: 28917635 DOI: 10.1016/j.ygeno.2017.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/06/2017] [Accepted: 09/12/2017] [Indexed: 10/18/2022]
35
Application of Synthetic Tumor-Specific Promoters Responsive to the Tumor Microenvironment. Methods Mol Biol 2017. [PMID: 28801910 DOI: 10.1007/978-1-4939-7223-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
36
How does chromatin package DNA within nucleus and regulate gene expression? Int J Biol Macromol 2017;101:862-881. [PMID: 28366861 DOI: 10.1016/j.ijbiomac.2017.03.165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023]
37
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] [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
38
Yang D, Ioshikhes I. Drosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns. J Comput Biol 2016;24:289-298. [PMID: 27992255 DOI: 10.1089/cmb.2016.0173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
39
Lu Y, Gan Y, Guan J, Zhou S. An integrative analysis of nucleosome occupancy and positioning using diverse sequence dependent properties. Neurocomputing 2016. [DOI: 10.1016/j.neucom.2015.11.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
40
Awazu A. Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition. Bioinformatics 2016;33:42-48. [PMID: 27563027 PMCID: PMC5860184 DOI: 10.1093/bioinformatics/btw562] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/02/2016] [Accepted: 08/19/2016] [Indexed: 11/13/2022]  Open
41
Drillon G, Audit B, Argoul F, Arneodo A. Evidence of selection for an accessible nucleosomal array in human. BMC Genomics 2016;17:526. [PMID: 27472913 PMCID: PMC4966569 DOI: 10.1186/s12864-016-2880-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/04/2016] [Indexed: 11/13/2022]  Open
42
Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples. Sci Rep 2016;6:26101. [PMID: 27189082 PMCID: PMC4870644 DOI: 10.1038/srep26101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 04/27/2016] [Indexed: 11/08/2022]  Open
43
MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat Commun 2016;7:11485. [PMID: 27151365 PMCID: PMC4859066 DOI: 10.1038/ncomms11485] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/31/2016] [Indexed: 01/01/2023]  Open
44
Wight A, Yang D, Ioshikhes I, Makrigiannis AP. Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors. PLoS Comput Biol 2016;12:e1004894. [PMID: 27124577 PMCID: PMC4849748 DOI: 10.1371/journal.pcbi.1004894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/31/2016] [Indexed: 12/28/2022]  Open
45
Liu G, Xing Y, Zhao H, Wang J, Shang Y, Cai L. A deformation energy-based model for predicting nucleosome dyads and occupancy. Sci Rep 2016;6:24133. [PMID: 27053067 PMCID: PMC4823781 DOI: 10.1038/srep24133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/21/2016] [Indexed: 12/14/2022]  Open
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Rube HT, Lee W, Hejna M, Chen H, Yasui DH, Hess JF, LaSalle JM, Song JS, Gong Q. Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nat Commun 2016;7:11025. [PMID: 27008915 PMCID: PMC4820824 DOI: 10.1038/ncomms11025] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/15/2016] [Indexed: 01/24/2023]  Open
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Chen W, Feng P, Ding H, Lin H, Chou KC. Using deformation energy to analyze nucleosome positioning in genomes. Genomics 2016;107:69-75. [DOI: 10.1016/j.ygeno.2015.12.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/06/2015] [Accepted: 12/22/2015] [Indexed: 12/28/2022]
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Utro F, Di Benedetto V, Corona DF, Giancarlo R. The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes. Bioinformatics 2015;32:835-42. [DOI: 10.1093/bioinformatics/btv679] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/09/2015] [Indexed: 11/14/2022]  Open
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Flickinger R. AT-rich repetitive DNA sequences, transcription frequency and germ layer determination. Mech Dev 2015;138 Pt 3:227-32. [PMID: 26506258 DOI: 10.1016/j.mod.2015.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/19/2015] [Accepted: 10/21/2015] [Indexed: 01/30/2023]
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Yazdi PG, Pedersen BA, Taylor JF, Khattab OS, Chen YH, Chen Y, Jacobsen SE, Wang PH. Nucleosome Organization in Human Embryonic Stem Cells. PLoS One 2015;10:e0136314. [PMID: 26305225 PMCID: PMC4549264 DOI: 10.1371/journal.pone.0136314] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/02/2015] [Indexed: 12/18/2022]  Open
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