Skip to main content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Discovery and Annotation of Functional Chromatin Signatures in the Human Genome
Gary Hon, Wei Wang, Bing Ren
PLoS Comput Biol. 2009 Nov; 5(11): e1000566. Published online 2009 Nov 13. doi: 10.1371/journal.pcbi.1000566
PMCID:
PMC2775352
Abstract Article PDF–779K

Is Cited by the Following 98 Articles in this Archive:

The Long Non-Coding RNA ANRIL in Cancers
Aymeric Sanchez, Julien Lhuillier, Guillaume Grosjean, Lilia Ayadi, Sylvain Maenner
Cancers (Basel) 2023 Aug; 15(16): 4160. Published online 2023 Aug 17. doi: 10.3390/cancers15164160
PMCID:
PMC10453084
Abstract Article PDF–1.2M
Epigenetic Modification Factors and microRNAs Network Associated with Differentiation of Embryonic Stem Cells and Induced Pluripotent Stem Cells toward Cardiomyocytes: A Review
Afshin Zare, Aria Salehpour, Arezoo Khoradmehr, Shabnam Bakhshalizadeh, Vahid Najafzadeh, Sahar Almasi-Turk, Mahdi Mahdipour, Reza Shirazi, Amin Tamadon
Life (Basel) 2023 Feb; 13(2): 569. Published online 2023 Feb 17. doi: 10.3390/life13020569
PMCID:
PMC9965891
Abstract Article PDF–1.4M
Histone Marks-Dependent Effect on Alternative Splicing: New Perspectives for Targeted Splicing Modulation in Cancer?
Carol Imbriano, Silvia Belluti
Int J Mol Sci. 2022 Aug; 23(15): 8304. Published online 2022 Jul 27. doi: 10.3390/ijms23158304
PMCID:
PMC9368390
Abstract Article PDF–1.8M
Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias
Gajendra W. Suryawanshi, Hubert Arokium, Sanggu Kim, Wannisa Khamaikawin, Samantha Lin, Saki Shimizu, Koollawat Chupradit, YooJin Lee, Yiming Xie, Xin Guan, Vasantika Suryawanshi, Angela P. Presson, Dong-Sung An, Irvin S. Y. Chen
Stem Cell Res Ther. 2021; 12: 528. Published online 2021 Oct 7. doi: 10.1186/s13287-021-02601-5
PMCID:
PMC8499514
Abstract Article PDF–3.8M
Transcription Factor Reprogramming in the Inner Ear: Turning on Cell Fate Switches to Regenerate Sensory Hair Cells
Amrita A. Iyer, Andrew K. Groves
Front Cell Neurosci. 2021; 15: 660748. Published online 2021 Mar 29. doi: 10.3389/fncel.2021.660748
PMCID:
PMC8039129
Abstract Article PDF–1.5M
Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging
Lei Liu, Changbong Hyeon
Nucleic Acids Res. 2020 Nov 18; 48(20): 11486–11494. Published online 2020 Oct 23. doi: 10.1093/nar/gkaa932
PMCID:
PMC7672452
Abstract Article PDF–1.8M
Epigenome-based splicing prediction using a recurrent neural network
Donghoon Lee, Jing Zhang, Jason Liu, Mark Gerstein
PLoS Comput Biol. 2020 Jun; 16(6): e1008006. Published online 2020 Jun 25. doi: 10.1371/journal.pcbi.1008006
PMCID:
PMC7343189
Abstract Article PDF–2.7M
High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
Marie-Odile Baudement, Axel Cournac, Franck Court, Marie Seveno, Hugues Parrinello, Christelle Reynes, Robert Sabatier, Tristan Bouschet, Zhou Yi, Sephora Sallis, Mathilde Tancelin, Cosette Rebouissou, Guy Cathala, Annick Lesne, Julien Mozziconacci, Laurent Journot, Thierry Forné
Genome Res. 2018 Nov; 28(11): 1733–1746. doi: 10.1101/gr.237073.118
PMCID:
PMC6211644
Abstract Article PDF–10M
Position-specific intron retention is mediated by the histone methyltransferase SDG725
Gang Wei, Kunpeng Liu, Ting Shen, Jinlei Shi, Bing Liu, Miao Han, Maolin Peng, Haihui Fu, Yifan Song, Jun Zhu, Aiwu Dong, Ting Ni
BMC Biol. 2018; 16: 44. Published online 2018 Apr 30. doi: 10.1186/s12915-018-0513-8
PMCID:
PMC5925840
Abstract Article PDF–4.9M
Epigenetic Control of Gene Regulation during Development and Disease: A View from the Retina
Ximena Corso-Díaz, Catherine Jaeger, Vijender Chaitankar, Anand Swaroop
Prog Retin Eye Res. Author manuscript; available in PMC 2019 Jul 1.
Published in final edited form as: Prog Retin Eye Res. 2018 Jul; 65: 1–27. Published online 2018 Mar 12. doi: 10.1016/j.preteyeres.2018.03.002
PMCID:
PMC6054546
Abstract Article PDF–2.3M
Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks
Syed Abbas Bukhari, Michael C. Saul, Christopher H. Seward, Huimin Zhang, Miles Bensky, Noelle James, Sihai Dave Zhao, Sriram Chandrasekaran, Lisa Stubbs, Alison M. Bell
PLoS Genet. 2017 Jul; 13(7): e1006840. Published online 2017 Jul 13. doi: 10.1371/journal.pgen.1006840
PMCID:
PMC5509087
Abstract Article PDF–4.2M
Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain
Qiwen Hu, Eun Ji Kim, Jian Feng, Gregory R. Grant, Elizabeth A. Heller
PLoS Comput Biol. 2017 Jun; 13(6): e1005602. Published online 2017 Jun 13. doi: 10.1371/journal.pcbi.1005602
PMCID:
PMC5487056
Abstract Article PDF–7.3M
Epigenetic Interactions between Alcohol and Cannabinergic Effects: Focus on Histone Modification and DNA Methylation
Tiyash Parira, Alejandra Laverde, Marisela Agudelo
J Alcohol Drug Depend. Author manuscript; available in PMC 2017 Jul 18.
Published in final edited form as: J Alcohol Drug Depend. 2017 Apr; 5(2): 259. Published online 2017 Mar 20. doi: 10.4172/2329-6488.1000259
PMCID:
PMC5515243
Abstract Article PDF–1.9M
Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types
Nan Meng, Raghu Machiraju, Kun Huang
BMC Bioinformatics. 2016; 17(Suppl 17): 534. Published online 2016 Dec 23. doi: 10.1186/s12859-016-1346-5
PMCID:
PMC5259941
Abstract Article PDF–4.3M
Insights into inner ear-specific gene regulation: epigenetics and non-coding RNAs in inner ear development and regeneration
Angelika Doetzlhofer, Karen B. Avraham
Semin Cell Dev Biol. Author manuscript; available in PMC 2018 May 1.
Published in final edited form as: Semin Cell Dev Biol. 2017 May; 65: 69–79. Published online 2016 Nov 9. doi: 10.1016/j.semcdb.2016.11.002
PMCID:
PMC5512292
Abstract Article PDF–522K
Promoter-like epigenetic signatures in exons displaying cell type-specific splicing
Joao Curado, Camilla Iannone, Hagen Tilgner, Juan Valcárcel, Roderic Guigó
Genome Biol. 2015; 16: 236. Published online 2015 Oct 23. doi: 10.1186/s13059-015-0797-8
Correction in:
Genome Biol. 2016; 17: 52.
PMCID:
PMC4619081
Abstract Article PDF–1.6M
Epigenetic program and transcription factor circuitry of dendritic cell development
Qiong Lin, Heike Chauvistré, Ivan G. Costa, Eduardo G. Gusmao, Saskia Mitzka, Sonja Hänzelmann, Bianka Baying, Theresa Klisch, Richard Moriggl, Benoit Hennuy, Hubert Smeets, Kurt Hoffmann, Vladimir Benes, Kristin Seré, Martin Zenke
Nucleic Acids Res. 2015 Nov 16; 43(20): 9680–9693. Published online 2015 Oct 17. doi: 10.1093/nar/gkv1056
PMCID:
PMC4787753
Abstract Article PDF–9.4M
Epigenomics and the structure of the living genome
Nir Friedman, Oliver J. Rando
Genome Res. 2015 Oct; 25(10): 1482–1490. doi: 10.1101/gr.190165.115
PMCID:
PMC4579333
Abstract Article PDF–262K
Architectural and functional commonalities between enhancers and promoters
Tae-Kyung Kim, Ramin Shiekhattar
Cell. Author manuscript; available in PMC 2016 Aug 27.
Published in final edited form as: Cell. 2015 Aug 27; 162(5): 948–959. doi: 10.1016/j.cell.2015.08.008
PMCID:
PMC4556168
Abstract Article PDF–576K
Histone variants and cellular plasticity
Stephen W. Santoro, Catherine Dulac
Trends Genet. Author manuscript; available in PMC 2016 Nov 16.
Published in final edited form as: Trends Genet. 2015 Sep; 31(9): 516–527. Published online 2015 Aug 20. doi: 10.1016/j.tig.2015.07.005
PMCID:
PMC5111554
Abstract Article PDF–1.0M
Connecting the dots: chromatin and alternative splicing in EMT
Jessica A. Warns, James R. Davie, Archana Dhasarathy
Biochem Cell Biol. Author manuscript; available in PMC 2016 Feb 1.
Published in final edited form as: Biochem Cell Biol. 2016 Feb; 94(1): 12–25. Published online 2015 Jul 7. doi: 10.1139/bcb-2015-0053
PMCID:
PMC4704998
Abstract Article PDF–540K
A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins
Eneritz Agirre, Nicolás Bellora, Mariano Alló, Amadís Pagès, Paola Bertucci, Alberto R Kornblihtt, Eduardo Eyras
BMC Biol. 2015; 13: 31. Published online 2015 May 2. doi: 10.1186/s12915-015-0141-5
PMCID:
PMC4446157
Abstract Article PDF–2.6M
High-Resolution Chromatin Dynamics during a Yeast Stress Response
Assaf Weiner, Tsung-Han S. Hsieh, Alon Appleboim, Hsiuyi V. Chen, Ayelet Rahat, Ido Amit, Oliver J. Rando, Nir Friedman
Mol Cell. 2015 Apr 16; 58(2): 371–386. doi: 10.1016/j.molcel.2015.02.002
PMCID:
PMC4405355
Abstract Article
Co‐transcriptional mRNP formation is coordinated within a molecular mRNP packaging station in S. cerevisiae
Dominik M. Meinel, Katja Sträßer
Bioessays. 2015 Jun; 37(6): 666–677. Published online 2015 Mar 20. doi: 10.1002/bies.201400220
PMCID:
PMC5054900
Abstract Article PDF–1.9M
A diverse epigenetic landscape at human exons with implication for expression
Meromit Singer, Idit Kosti, Lior Pachter, Yael Mandel-Gutfreund
Nucleic Acids Res. 2015 Apr 20; 43(7): 3498–3508. Published online 2015 Mar 12. doi: 10.1093/nar/gkv153
PMCID:
PMC4402514
Abstract Article PDF–2.0M
Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data
Qian Wu, Kyoung-Jae Won, Hongzhe Li
Cancer Inform. 2015; 14(Suppl 1): 11–22. Published online 2015 Jan 27. doi: 10.4137/CIN.S13972
PMCID:
PMC4310510
Abstract Article PDF–2.2M
Sustained Reprogramming of the Estrogen Response After Chronic Exposure to Endocrine Disruptors
Andrea R. Patterson, Xiaokui Mo, Ali Shapiro, Karen E. Wernke, Trevor K. Archer, Craig J. Burd
Mol Endocrinol. 2015 Mar; 29(3): 384–395. Published online 2015 Jan 16. doi: 10.1210/me.2014-1237
PMCID:
PMC4347288
Abstract Article
Identification by high-throughput imaging of the histone methyltransferase EHMT2 as an epigenetic regulator of VEGFA alternative splicing
Maayan Salton, Ty C. Voss, Tom Misteli
Nucleic Acids Res. 2014 Dec 16; 42(22): 13662–13673. Published online 2014 Nov 20. doi: 10.1093/nar/gku1226
PMCID:
PMC4267647
Abstract Article PDF–3.4M
Computational schemes for the prediction and annotation of enhancers from epigenomic assays
John W. Whitaker, Tung T. Nguyen, Yun Zhu, Andre Wildberg, Wei Wang
Methods. Author manuscript; available in PMC 2016 Mar 4.
Published in final edited form as: Methods. 2015 Jan 15; 72: 86–94. Published online 2014 Oct 15. doi: 10.1016/j.ymeth.2014.10.008
PMCID:
PMC4778972
Abstract Article PDF–774K
Bisphenol A Disrupts Transcription and Decreases Viability in Aging Vascular Endothelial Cells
Edna Ribeiro-Varandas, H. Sofia Pereira, Sara Monteiro, Elsa Neves, Luísa Brito, Ricardo Boavida Ferreira, Wanda Viegas, Margarida Delgado
Int J Mol Sci. 2014 Sep; 15(9): 15791–15805. Published online 2014 Sep 9. doi: 10.3390/ijms150915791
PMCID:
PMC4200871
Abstract Article PDF–377K