Epigenetic Regulation: A New Frontier for Biomedical Engineers

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., & Mello, C. C. (1998) · Nature · doi:10.1038/35888 · Cited by 15,429

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

WATSON, J. D., & CRICK, F. H. C. (1953) · Nature · doi:10.1038/171737a0 · Cited by 13,584

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14

Lee, R. C., Feinbaum, R. L., & Ambros, V. (1993) · Cell · doi:10.1016/0092-8674(93)90529-y · Cited by 12,948

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898

Circular RNAs are a large class of animal RNAs with regulatory potency

Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., et al. (2013) · Nature · doi:10.1038/nature11928 · Cited by 7,990

Natural RNA circles function as efficient microRNA sponges

Hansen, T. B., Jensen, T. I., Clausen, B. H., Bramsen, J. B., Finsen, B., Damgaard, C. K., & Kjems, J. (2013) · Nature · doi:10.1038/nature11993 · Cited by 7,985

High-Resolution Profiling of Histone Methylations in the Human Genome

Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422

DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development

Okano, M., Bell, D. W., Haber, D. A., & Li, E. (1999) · Cell · doi:10.1016/s0092-8674(00)81656-6 · Cited by 6,143

Regulation of chromatin by histone modifications

Bannister, A. J., & Kouzarides, T. (2011) · Cell Research · doi:10.1038/cr.2011.22 · Cited by 6,012

Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands.

Herman, J. G., Graff, J. R., Myöhänen, S., Nelkin, B. D., & Baylin, S. B. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.18.9821 · Cited by 5,634

Landscape of transcription in human cells

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187

Origins and Mechanisms of miRNAs and siRNAs

Carthew, R. W., & Sontheimer, E. J. (2009) · Cell · doi:10.1016/j.cell.2009.01.035 · Cited by 5,161

Molecular Mechanisms of Long Noncoding RNAs

Wang, K., & Chang, H. Y. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.018 · Cited by 4,462

Capturing Chromosome Conformation

Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C., & Zhang, Y. (2011) · Science · doi:10.1126/science.1210597 · Cited by 3,451

Central Dogma of Molecular Biology

CRICK, F. (1970) · Nature · doi:10.1038/227561a0 · Cited by 3,444

A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands

Frommer, M., McDonald, L. E., Millar, D. S., Collis, C. M., Watt, F., Grigg, G. W., Molloy, P. L., & Paul, C. L. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.5.1827 · Cited by 3,238

CRISPR-Cas systems for editing, regulating and targeting genomes

Sander, J. D., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2842 · Cited by 3,153

A Species of Small Antisense RNA in Posttranscriptional Gene Silencing in Plants

Hamilton, A. J., & Baulcombe, D. C. (1999) · Science · doi:10.1126/science.286.5441.950 · Cited by 3,100

Widespread transcription at neuronal activity-regulated enhancers

Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450

The ENCODE (ENCyclopedia Of DNA Elements) Project

(2004) · Science · doi:10.1126/science.1105136 · Cited by 2,390

Effects of Disturbed Flow on Vascular Endothelium: Pathophysiological Basis and Clinical Perspectives

Chiu, J.-J., & Chien, S. (2011) · Physiological Reviews · doi:10.1152/physrev.00047.2009 · Cited by 2,280

ChIP–seq: advantages and challenges of a maturing technology

Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M. J., Kenzelmann-Broz, D., Khalil, A. M., Zuk, O., Amit, I., Rabani, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.06.040 · Cited by 2,053

Mediator and cohesin connect gene expression and chromatin architecture

Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939

lincRNAs act in the circuitry controlling pluripotency and differentiation

Guttman, M., Donaghey, J., Carey, B. W., Garber, M. G., Grenier, J. K., Munson, G., Young, G., Lucas, A. B., Ach, R. A., Bruhn, L., et al. (2011) · Nature · doi:10.1038/nature10398 · Cited by 1,883

Nanoparticle biointerfacing by platelet membrane cloaking

Hu, C. J., Fang, R. H., Wang, K.-C., Luk, B. T., Thamphiwatana, S., Dehaini, D., Nguyen, P., Angsantikul, P., Wen, C. H., Kroll, A. V., et al. (2015) · Nature · doi:10.1038/nature15373 · Cited by 1,795

Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells

Weber, M., Davies, J. J., Wittig, D., Oakeley, E. J., Haase, M., Lam, W. L., & Schübeler, D. (2005) · Nature Genetics · doi:10.1038/ng1598 · Cited by 1,785

An oestrogen-receptor-α-bound human chromatin interactome

Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Han, X., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Poh, H. M., et al. (2009) · Nature · doi:10.1038/nature08497 · Cited by 1,752

Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene

Bell, A. C., & Felsenfeld, G. (2000) · Nature · doi:10.1038/35013100 · Cited by 1,746

Principles and challenges of genome-wide DNA methylation analysis

Laird, P. W. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2732 · Cited by 1,611

Expanded identification and characterization of mammalian circular RNAs

Guo, J. U., Agarwal, V., Guo, H., & Bartel, D. P. (2014) · Genome biology · doi:10.1186/s13059-014-0409-z · Cited by 1,591

Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders

Falkenberg, K. J., & Johnstone, R. W. (2014) · Nature Reviews Drug Discovery · doi:10.1038/nrd4360 · Cited by 1,564

5-Azacytidine and 5-aza-2′-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy

Christman, J. K. (2002) · Oncogene · doi:10.1038/sj.onc.1205699 · Cited by 1,561

Role of Endothelial Shear Stress in the Natural History of Coronary Atherosclerosis and Vascular Remodeling

Chatzizisis, Y. S., Coskun, A. U., Jonas, M., Edelman, E. R., Feldman, C. L., & Stone, P. H. (2007) · Journal of the American College of Cardiology · doi:10.1016/j.jacc.2007.02.059 · Cited by 1,483

Nanoparticles as drug delivery systems

Wilczewska, A. Z., Niemirowicz, K., Markiewicz, K. H., & Car, H. (2012) · Pharmacological Reports · doi:10.1016/s1734-1140(12)70901-5 · Cited by 1,445

Molecular Interplay of the Noncoding RNA ANRIL and Methylated Histone H3 Lysine 27 by Polycomb CBX7 in Transcriptional Silencing of INK4a

Yap, K. L., Li, S., Muñoz-Cabello, A. M., Raguz, S., Zeng, L., Mujtaba, S., Gil, J., Walsh, M. J., & Zhou, M.-M. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.03.021 · Cited by 1,391

X inactivation, differentiation, and DNA methylation

Riggs, A. D. (2008) · Cytogenetics and Cell Genetics · doi:10.1159/000130315 · Cited by 1,343

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

Chu, C., Qu, K., Zhong, F. L., Artandi, S. E., & Chang, H. Y. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.027 · Cited by 1,293

Epigenetic Regulation by Long Noncoding RNAs

Lee, J. T. (2012) · Science · doi:10.1126/science.1231776 · Cited by 1,281

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis

Meissner, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki901 · Cited by 1,261

How Are Alkynes Scrambled?

Bunz, U. H. F. (2005) · Science · doi:10.1126/science.1111098 · Cited by 1,244

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elementsPreprint

Dostie, J., Richmond, T., Arnaout, R., Selzer, R. R., Lee, W. L., Honan, T., Rubio, E. D., Krumm, A., Lamb, J., Nusbaum, C., et al. (2006) · Genome Research · doi:10.1101/gr.5571506 · Cited by 1,237

Cohesin mediates transcriptional insulation by CCCTC-binding factor

Wendt, K. S., Yoshida, K., Itoh, T., Bando, M., Koch, B., Schirghuber, E., Tsutsumi, S., Nagae, G., Ishihara, K., Mishiro, T., et al. (2008) · Nature · doi:10.1038/nature06634 · Cited by 1,193

ALTERATION OF NUCLEOSOME STRUCTURE AS A MECHANISM OF TRANSCRIPTIONAL REGULATION

Workman, J. L., & Kingston, R. E. (1998) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.67.1.545 · Cited by 1,159

CLIP Identifies Nova-Regulated RNA Networks in the Brain

Ule, J., Jensen, K. B., Ruggiu, M., Mele, A., Ule, A., & Darnell, R. B. (2003) · Science · doi:10.1126/science.1090095 · Cited by 1,120

The protein CTCF is required for the enhancer blocking activity of vertebrate insulators

Bell, A. C., West, A. G., & Felsenfeld, G. (1999) · Cell · doi:10.1016/s0092-8674(00)81967-4 · Cited by 1,101

Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions

Wu, H., & Zhang, Y. (2014) · Cell · doi:10.1016/j.cell.2013.12.019 · Cited by 1,065

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

Li, W., Notani, D., Ma, Q., Tanasa, B., Nunez, E., Chen, A. Y., Merkurjev, D., Zhang, J., Ohgi, K., Song, X., et al. (2013) · Nature · doi:10.1038/nature12210 · Cited by 1,049

Amount and distribution of 5-methylcytosine in human DNA from different types of tissues or cells

Ehrlich, M., Gama-Sosa, M. A., Huang, L.-H., Midgett, R. M., Kuo, K. C., McCune, R. A., & Gehrke, C. W. (1982) · Nucleic Acids Research · doi:10.1093/nar/10.8.2709 · Cited by 1,039

A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements

Yang, A. S. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh032 · Cited by 1,033

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatinPreprint

Giresi, P. G., Kim, J., McDaniell, R. M., Iyer, V. R., & Lieb, J. D. (2006) · Genome Research · doi:10.17615/8cez-3e87 · Cited by 993

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

De Santa, F., Barozzi, I., Mietton, F., Ghisletti, S., Polletti, S., Tusi, B. K., Muller, H., Ragoussis, J., Wei, C.-L., & Natoli, G. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000384 · Cited by 934

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

Klattenhoff, C., Scheuermann, J. C., Surface, L. E., Bradley, R. K., Fields, P., Steinhauser, M. L., Ding, H., Butty, V. L., Sosa, L. T., Haas, S. F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.01.003 · Cited by 927

Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry

Ehrich, M., Nelson, M. R., Stanssens, P. E., Zabeau, M., Liloglou, T., Xinarianos, G., Cantor, C. R., Field, J. K., & van den Boom, D. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507816102 · Cited by 815

Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4

Gilchrist, M., Thórsson, V., Li, B., Rust, A. G., Korb, M., Kennedy, K., Hai, T., Bolouri, H., & Aderem, A. A. (2006) · Nature · doi:10.1038/nature04768 · Cited by 810

PIWI-Interacting RNA: Its Biogenesis and Functions

Iwasaki, Y. W., Siomi, M. C., & Siomi, H. (2015) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060614-034258 · Cited by 796

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

Rhee, H. S., & Pugh, B. F. (2011) · Cell · doi:10.1016/j.cell.2011.11.013 · Cited by 779

Long Noncoding RNAs in Cardiovascular Diseases

Uchida, S., & Dimmeler, S. (2015) · Circulation Research · doi:10.1161/circresaha.116.302521 · Cited by 746

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

Luger, K., Dechassa, M. L., & Tremethick, D. J. (2012) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3382 · Cited by 738

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

Harris, R. A., Wang, T., Coarfa, C., Nagarajan, R. P., Hong, C., Downey, S. L., Johnson, B., Fouse, S. D., Delaney, A. D., Zhao, Y., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1682 · Cited by 723

Determinants of nucleosome positioning

Struhl, K., & Segal, E. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2506 · Cited by 696

Rapid spontaneous accessibility of nucleosomal DNA

Gu, L.-Q., Levitus, M., Bustamante, C., & Widom, J. (2005) · Nature Structural &Molecular Biology · doi:10.1038/nsmb869 · Cited by 692

Circulating Long Noncoding RNA, LIPCAR, Predicts Survival in Patients With Heart Failure

Kumarswamy, R., Bauters, C., Volkmann, I. R., Maury, F., Fetisch, J., Holzmann, A., Lemesle, G., de Groote, P., Pinet, F., & Thum, T. (2014) · Circulation Research · doi:10.1161/circresaha.114.303915 · Cited by 627

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

Harismendy, O., Notani, D., Song, X., Rahim, N. G., Tanasă, B., Heintzman, N. D., Ren, B., Fu, X., Topol, E. J., Rosenfeld, M. G., et al. (2011) · Nature · doi:10.1038/nature09753 · Cited by 619

Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units

Song, F., Chen, P., Sun, D., Wang, M., Dong, L., Liang, D., Xu, R.-M., Zhu, P., & Li, G. (2014) · Science · doi:10.1126/science.1251413 · Cited by 617

NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis

Brown, J. D., Lin, C. Y., Duan, Q., Griffin, G., Federation, A. J., Paranal, R. M., Bair, S., Newton, G., Lichtman, A. H., Kung, A. L., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.024 · Cited by 614

The Dnmt1 DNA-(cytosine-C5)-methyltransferase Methylates DNA Processively with High Preference for Hemimethylated Target Sites

Hermann, A., Goyal, R., & Jeltsch, A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m403427200 · Cited by 593

lncRNAdb: a reference database for long noncoding RNAs

Amaral, P., Clark, M. B., Gascoigne, D. K., Dinger, M. E., & Mattick, J. S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1138 · Cited by 591

Prenatal Tobacco Smoke Exposure Affects Global and Gene-specific DNA Methylation

Breton, C. V., Byun, H., Wenten, M., Pan, F., Yang, A. S., & Gilliland, F. D. (2009) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.200901-0135oc · Cited by 591

Chromatin remodelling: the industrial revolution of DNA around histones

Saha, A., Wittmeyer, J., & Cairns, B. R. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1945 · Cited by 590

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

Hesselberth, J. R., Chen, X., Zhang, Z., Sabo, P. J., Sandstrom, R., Reynolds, A. P., Thurman, R. E., Neph, S., Kuehn, M. S., Noble, W. S., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1313 · Cited by 559

Mapping Human Epigenomes

Rivera, C. M., & Ren, B. (2013) · Cell · doi:10.1016/j.cell.2013.09.011 · Cited by 550

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

Quek, X. C., Thomson, D. W., Mååg, J. L. V., Bartoniček, N., Signal, B., Clark, M. B., Gloss, B., & Dinger, M. E. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku988 · Cited by 535

Sensitive and quantitative universal Pyrosequencing™ methylation analysis of CpG sites

Colella, S., Shen, L., Baggerly, K., Issa, J. J., & Krahe, R. (2003) · BioTechniques · doi:10.2144/03351md01 · Cited by 514

LincRNA-p21 Regulates Neointima Formation, Vascular Smooth Muscle Cell Proliferation, Apoptosis, and Atherosclerosis by Enhancing p53 Activity

Wu, G., Cai, J., Han, Y., Chen, J., Huang, Z., Chen, C., Cai, Y., Huang, H., Yang, Y., Liu, Y., et al. (2014) · Circulation · doi:10.1161/circulationaha.114.011675 · Cited by 486

Phase 1/2 study of the combination of 5-aza-2′-deoxycytidine with valproic acid in patients with leukemia

Garcia‐Manero, G., Kantarjian, H. M., Sánchez‐González, B., Yang, H., Rosner, G. L., Verstovšek, S., Rytting, M., Wierda, W. G., Ravandi, F., Koller, C. A., et al. (2006) · Blood · doi:10.1182/blood-2006-03-009142 · Cited by 470

Loss of imprinting of IGF2 is linked to reduced expression and abnormal methylation of H19 in Wilms' tumour

Steenman, M., Rainier, S. R., Dobry, C. J., Grundy, P., Horon, I. L., & Feinberg, A. P. (1994) · Nature Genetics · doi:10.1038/ng0794-433 · Cited by 461

ANRIL Expression Is Associated With Atherosclerosis Risk at Chromosome 9p21

Holdt, L. M., Beutner, F., Scholz, M. R., Gielen, S., Gäbel, G., Bergert, H., Schuler, G. C., Thiery, J., & Teupser, D. (2010) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.109.196832 · Cited by 461

Deep RNA Sequencing Reveals Dynamic Regulation of Myocardial Noncoding RNAs in Failing Human Heart and Remodeling With Mechanical Circulatory Support

Yang, K., Yamada, K. A., Patel, A., Topkara, V. K., George, I., Cheema, F. H., Ewald, G. A., Mann, D. L., & Nerbonne, J. M. (2014) · Circulation · doi:10.1161/circulationaha.113.003863 · Cited by 453

Parental-origin-specific epigenetic modification of the mouse H19 gene

Ferguson‐Smith, A. C., Sasaki, H., Cattanach, B. M., & Surani, M. A. (1993) · Nature · doi:10.1038/362751a0 · Cited by 434

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia

Trimarchi, T., Bilal, E., Ntziachristos, P., Fabbri, G., Dalla‐Favera, R., Tsirigos, A., & Aifantis, I. (2014) · Cell · doi:10.1016/j.cell.2014.05.049 · Cited by 426

Functional implications of genome topology

Cavalli, G., & Misteli, T. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2474 · Cited by 415

Monoallelic expression of the human H19 gene

Zhang, Y., & Tycko, B. (1992) · Nature Genetics · doi:10.1038/ng0492-40 · Cited by 414

Epigenetics and cardiovascular disease

Ordovás, J. M., & Smith, C. E. (2010) · Nature Reviews Cardiology · doi:10.1038/nrcardio.2010.104 · Cited by 413

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

Brinkman, A. B., Gu, H., Bartels, S. J. J., Zhang, Y., Matarese, F., Simmer, F., Marks, H., Bock, C., Gnirke, A., Meissner, A., et al. (2012) · Genome Research · doi:10.1101/gr.133728.111 · Cited by 413

Epigenetic histone H3 lysine 9 methylation in metabolic memory and inflammatory phenotype of vascular smooth muscle cells in diabetes

Villeneuve, L. M., Reddy, M. A., Lanting, L. L., Wang, M., Li, M., & Natarajan, R. D. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803623105 · Cited by 411

Increased Homocysteine and S-Adenosylhomocysteine Concentrations and DNA Hypomethylation in Vascular Disease

Castro, R., Rivera, I. A., Struys, E. A., Jansen, E. E. W., Ravasco, P., Camilo, M., Blom, H. J., Jakobs, C., & de Almeida, I. T. (2003) · Clinical Chemistry · doi:10.1373/49.8.1292 · Cited by 409

Alu Elements in ANRIL Non-Coding RNA at Chromosome 9p21 Modulate Atherogenic Cell Functions through Trans-Regulation of Gene Networks

Holdt, L. M., Hoffmann, S., Sass, K., Langenberger, D., Scholz, M., Krohn, K., Finstermeier, K., Stahringer, A., Wilfert, W., Beutner, F., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003588 · Cited by 397

Robust 4C-seq data analysis to screen for regulatory DNA interactions

van de Werken, H. J. G., Landan, G., Holwerda, S. J. B., Hoichman, M., Klous, P., Chachik, R., Splinter, E., Valdes‐Quezada, C., Öz, Y., Bouwman, B. A. M., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2173 · Cited by 391

Localization of the X inactivation centre on the human X chromosome in Xq13

Brown, C. J., Lafrenière, R. G., Powers, V. E. C., Sebastio, G., Ballabio, A., Pettigrew, A. L., Ledbetter, D. H., Levy, E. R., Craig, I., & Willard, H. F. (1991) · Nature · doi:10.1038/349082a0 · Cited by 387

Profiling genome-wide DNA methylation

Yong, W.-S., Hsu, F.-M., & Chen, P.-Y. (2016) · Epigenetics & Chromatin · doi:10.1186/s13072-016-0075-3 · Cited by 374

Inhibition of Histone Deacetylation Blocks Cardiac Hypertrophy Induced by Angiotensin II Infusion and Aortic Banding

Kee, H. J., Sohn, I. S., Nam, K. I., Park, J., Qian, Y., Yin, Z., Ahn, Y., Jeong, M., Bang, Y., Kim, N., et al. (2005) · Circulation · doi:10.1161/circulationaha.105.559724 · Cited by 368

SUMO Promotes HDAC-Mediated Transcriptional Repression

Yang, S., & Sharrocks, A. D. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00060-7 · Cited by 358

An update on LNCipedia: a database for annotated human lncRNA sequences

Volders, P., Verheggen, K., Menschaert, G., Vandepoele, K., Martens, L., Vandesompele, J., & Mestdagh, P. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1060 · Cited by 355

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

Meyer, C. A., & Liu, X. S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3788 · Cited by 342

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

Aran, D., Sivan Sabato, A., & Hellman, A. (2013) · Genome biology · doi:10.1186/gb-2013-14-3-r21 · Cited by 342

Genetic variants at the 9p21 locus contribute to atherosclerosis through modulation of ANRIL and CDKN2A/B

Congrains, A., Kamide, K., Oguro, R., Yasuda, O., Miyata, K., Yamamoto, E., Kawai, T., Kusunoki, H., Yamamoto, H., Takeya, Y., et al. (2011) · Atherosclerosis · doi:10.1016/j.atherosclerosis.2011.11.017 · Cited by 335

Cardiac hypertrophy and histone deacetylase–dependent transcriptional repression mediated by the atypical homeodomain protein Hop

Kook, H., Lepore, J. J., Gitler, A. D., Lu, M. M., Yung, W. W.-M., Mackay, J. P., Zhou, R., Ferrari, V. A., Gruber, P. J., & Epstein, J. A. (2003) · Journal of Clinical Investigation · doi:10.1172/jci19137 · Cited by 332

Coordinated regulation of transcriptional repression by the RBP2 H3K4 demethylase and Polycomb-Repressive Complex 2Preprint

Pasini, D., Hansen, K. H., Christensen, J. F., Agger, K., Cloos, P. A., & Helin, K. (2008) · Genes & Development · doi:10.1101/gad.470008 · Cited by 322

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

Zhang, Z., Wippo, C. J., Wal, M., Ward, E., Korber, P., & Pugh, B. F. (2011) · Science · doi:10.1126/science.1200508 · Cited by 318

Epigenetic lesions at the H19 locus in Wilms' tumour patients

Moulton, T. A., Crenshaw, T., Hao, Y., Moosikasuwan, J., Lin, N., Dembitzer, F. R., Hensle, T., Weiss, L. M., McMorrow, L. E., Loew, T. H., et al. (1994) · Nature Genetics · doi:10.1038/ng0794-440 · Cited by 316

LUMA (LUminometric Methylation Assay)—A high throughput method to the analysis of genomic DNA methylation

Karimi, M., Johansson, S., Stach, D., Corcoran, M., Grandér, D., Schalling, M., Bakalkin, G. Y., Lyko, F., Larsson, C., & Ekström, T. J. (2006) · Experimental Cell Research · doi:10.1016/j.yexcr.2006.03.006 · Cited by 313

Flow-dependent epigenetic DNA methylation regulates endothelial gene expression and atherosclerosis

Dunn, J., Qiu, H., Kim, S., Jjingo, D., Hoffman, R., Kim, C. W., Jang, I.-H., Son, D. J., Kim, D., Pan, C., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci74792 · Cited by 308

Methylation of the hypoxanthine phosphoribosyltransferase locus on the human X chromosome: implications for X-chromosome inactivation.

Wolf, S. F., Jolly, D. J., Lunnen, K. D., Friedmann, T., & Migeon, B. R. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.9.2806 · Cited by 298

Dnmt3a and Dnmt1 functionally cooperate during de novo methylation of DNA

Fatemi, M., Hermann, A., Gowher, H., & Jeltsch, A. (2002) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2002.03198.x · Cited by 285

The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA

Fatemi, M., Hermann, A., Pradhan, S., & Jeltsch, A. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4709 · Cited by 275

Histone Deacetylase 1 Phosphorylation Promotes Enzymatic Activity and Complex Formation

Pflum, M. K. H., Tong, J. K., Lane, W. S., & Schreiber, S. L. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m105590200 · Cited by 265

Endocardial Brg1 Represses ADAMTS1 to Maintain the Microenvironment for Myocardial Morphogenesis

Stankunas, K., Hang, C. T., Tsun, Z.-Y., Chen, H., Lee, N. V., Wu, J. I., Shang, C., Bayle, J. H., Shou, W., Iruela‐Arispe, M. L., et al. (2008) · Developmental Cell · doi:10.1016/j.devcel.2007.11.018 · Cited by 262

Evaluating the Role of Epigenetic Histone Modifications in the Metabolic Memory of Type 1 Diabetes

Miao, F., Chen, Z., GENUTH, S. M., Paterson, A. D., Zhang, L., Wu, X., Li, S. M., Cleary, P. A., Riggs, A. D., Harlan, D. M., et al. (2014) · Diabetes · doi:10.2337/db13-1251 · Cited by 255

Xist has properties of the X-chromosome inactivation centre

Herzing, L. B. K., Romer, J. T., Horn, J. M., & Ashworth, A. (1997) · Nature · doi:10.1038/386272a0 · Cited by 253

microRNA: A Master Regulator of Cellular Processes for Bioengineering Systems

Sun, W., Li, Y.-S. J., Huang, H., Shyy, J. Y.-J., & Chien, S. (2010) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-070909-105314 · Cited by 242

The Expression of Endothelial Nitric-oxide Synthase Is Controlled by a Cell-specific Histone Code

Fish, J. E., Matouk, C. C., Rachlis, A., Lin, S., Tai, S. C., D'Abreo, C., & Marsden, P. A. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m502115200 · Cited by 235

The histone trimethyllysine demethylase JMJD2A promotes cardiac hypertrophy in response to hypertrophic stimuli in mice

Zhang, Q.-J., Chen, H., Wang, L., Liu, D., Hill, J. A., & Liu, Z. (2011) · Journal of Clinical Investigation · doi:10.1172/jci46277 · Cited by 227

Endothelial Kruppel-like factor 4 protects against atherothrombosis in mice

Zhou, G., Hamik, A., Nayak, L. V., Tian, H., Shi, H., Lu, Y., Sharma, N., Liao, X., Hale, A. T., Boerboom, L., et al. (2012) · Journal of Clinical Investigation · doi:10.1172/jci66056 · Cited by 217

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

Jäger, R., Migliorini, G., Henrion, M., Kandaswamy, R., Speedy, H. E., Heindl, A., Whiffin, N., Carnicer, M. J., Broome, L. R., Dryden, N. H., et al. (2015) · Nature Communications · doi:10.1038/ncomms7178 · Cited by 216

Role of Nucleosomal Occupancy in the Epigenetic Silencing of the MLH1 CpG Island

Lin, J., Jeong, S., Liang, G., Takai, D., Fatemi, M., Tsai, Y., Egger, G., Gal‐Yam, E. N., & Jones, P. A. (2007) · Cancer Cell · doi:10.1016/j.ccr.2007.10.014 · Cited by 210

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNAPreprint

Statham, A. L., Robinson, M. D., Song, J. Z., Coolen, M. W., Stirzaker, C., & Clark, S. J. (2012) · Genome Research · doi:10.1101/gr.132076.111 · Cited by 208

Hemodynamic Disturbed Flow Induces Differential DNA Methylation of Endothelial Kruppel-Like Factor 4 Promoter In Vitro and In Vivo

Jiang, Y., Jiménez, J. M., Ou, K., McCormick, M. E., Zhang, L.-D., & Davies, P. F. (2014) · Circulation Research · doi:10.1161/circresaha.115.303883 · Cited by 196

Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification

Quinn, J. J., Ilik, İ., Qu, K., Georgiev, P., Chu, C., Akhtar, A., & Chang, H. Y. (2014) · Nature Biotechnology · doi:10.1038/nbt.2943 · Cited by 177

Evaluation of a potential epigenetic biomarker by quantitative methyl‐single nucleotide polymorphism analysis

Uhlmann, K., Brinckmann, A., Toliat, M. R., Ritter, H., & Nürnberg, P. (2002) · Electrophoresis · doi:10.1002/elps.200290023 · Cited by 171

Genome‐wide histone methylation profile for heart failure

Kaneda, R., Takada, S., Yamashita, Y., Choi, Y. L., Nonaka‐Sarukawa, M., Soda, M., Misawa, Y., Isomura, T., Shimada, K., & Mano, H. (2008) · Genes to Cells · doi:10.1111/j.1365-2443.2008.01252.x · Cited by 165

Exploiting the Epigenome to Control Cancer-Promoting Gene-Expression Programs

Brien, G. L., Valerio, D. G., & Armstrong, S. A. (2016) · Cancer Cell · doi:10.1016/j.ccell.2016.03.007 · Cited by 155

A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo

Li, K., Blum, Y., Verma, A., Liu, Z., Pramanik, K., Leigh, N. R., Chun, C. Z., Samant, G. V., Zhao, B., Garnaas, M., et al. (2009) · Blood · doi:10.1182/blood-2009-09-242180 · Cited by 152

Role of histone deacetylases in transcription factor regulation and cell cycle modulation in endothelial cells in response to disturbed flow

Lee, D.-Y., Lee, C.-I., Lin, T., Lim, S. H., Zhou, J., Tseng, Y.-C., Chien, S., & Chiu, J. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1121214109 · Cited by 150

ATP-dependent chromatin remodeling shapes the DNA replication landscape

Vincent, J. A., Kwong, T. J., & Tsukiyama, T. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1419 · Cited by 149

The SWI/SNF Complex Creates Loop Domains in DNA and Polynucleosome Arrays and Can Disrupt DNA-Histone Contacts within These Domains

Bazett‐Jones, D. P., Côté, J., Landel, C. C., Peterson, C. L., & Workman, J. L. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.2.1470 · Cited by 146

Clinical trial on 5-AZA-2′-deoxycytidine in patients with acute leukemia

Momparler, R. L., Rivard, G. E., & Gyger, M. (1985) · Pharmacology & Therapeutics · doi:10.1016/0163-7258(85)90052-x · Cited by 143

Nucleosome structural studies

Tan, S., & Davey, C. A. (2010) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2010.11.006 · Cited by 141

Tracing dynamic changes of DNA methylation at single cell resolution

Stelzer, Y., Shivalila, C. S., Soldner, F., Markoulaki, S., & Jaenisch, R. (2015) · Cell · doi:10.1016/j.cell.2015.08.046 · Cited by 141

Real-time imaging of histone H4 hyperacetylation in living cells

Sasaki, K., Ito, T., Nishino, N., Khochbin, S., & Yoshida, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902150106 · Cited by 137

Enhanced top-down characterization of histone post-translational modifications

Tian, Z., Tolić, N., Zhao, R., Moore, R., Hengel, S. M., Robinson, E. W., Stenoien, D. L., Wu, S., Smith, R. D., & Paša‐Tolić, L. (2012) · Genome biology · doi:10.1186/gb-2012-13-10-r86 · Cited by 126

Histone Acetylation Modifiers in the Pathogenesis of Alzheimer’s Disease

Lu, X., Wang, L., Yu, C., Yu, D., & Yu, G. (2015) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2015.00226 · Cited by 124

Dynamics of Nucleosomes Assessed with Time-Lapse High-Speed Atomic Force Microscopy

Miyagi, A., Ando, T., & Lyubchenko, Y. L. (2011) · Biochemistry · doi:10.1021/bi200946z · Cited by 124

The chromatin-remodeling enzyme BRG1 plays an essential role in primitive erythropoiesis and vascular development

Griffin, C. T., Brennan, J. A., & Magnuson, T. (2007) · Development · doi:10.1242/dev.010090 · Cited by 122

Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo

Geisberg, J. V. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh148 · Cited by 107

CpG methylation regulates the Igf2/H19 insulator

Holmgren, C., Kanduri, C., Dell, G. C., Ward, A., Mukhopadhya, R., Kanduri, M., Lobanenkov, V. V., & OHLSSON, R. I. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00314-1 · Cited by 92

Epigenetic Mechanism in Regulation of Endothelial Function by Disturbed Flow: Induction of DNA Hypermethylation by DNMT1

Zhou, J., Li, Y.-S. J., Wang, K.-C., & Chien, S. (2014) · Cellular and Molecular Bioengineering · doi:10.1007/s12195-014-0325-z · Cited by 90

A High-Resolution Imaging Approach to Investigate Chromatin Architecture in Complex Tissues

Linhoff, M. W., Garg†, S. K., & Mandel, G. (2015) · Cell · doi:10.1016/j.cell.2015.09.002 · Cited by 83

Transcriptional Profiling Uncovers a Network of Cholesterol-Responsive Atherosclerosis Target Genes

Skogsberg, J., Lundström, J., Kovacs, A., Nilsson, R., Noori, P., Maleki, S., Köhler, M., Hamsten, A., Tegner, J. N., & Björkegren, J. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000036 · Cited by 79

Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo

Jiang, Y.-Z., Manduchi, E., Stoeckert, C. J., & Davies, P. F. (2015) · BMC Genomics · doi:10.1186/s12864-015-1656-4 · Cited by 63

Histone deacetylases as therapeutic targets — From cancer to cardiac disease

Abend, A., & Kehat, I. (2014) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2014.11.003 · Cited by 58

Cracking the chromatin code: Precise rule of nucleosome positioning

Trifonov, E. N. (2011) · Physics of Life Reviews · doi:10.1016/j.plrev.2011.01.004 · Cited by 55

A preoccupied position on nucleosomes

Pugh, B. F. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb0810-923 · Cited by 45

ReCoGnizing methylated DNA.

Wade, P. A., & Wolffe, A. P. (2001) · Nature Structural Biology · doi:10.1038/89593 · Cited by 37

A Global Clustering Algorithm to Identify Long Intergenic Non-Coding RNA - with Applications in Mouse Macrophages

Garmire, L. X., Garmire, D. G., Huang, W. J. M., Yao, J., Glass, C. K., & Subramaniam, S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024051 · Cited by 27

Additive Effect of ANRIL and BRAP Polymorphisms on Ankle-Brachial Index in a Taiwanese Population

Tsai, P., Liao, Y., Lin, T., Hsi, E., Yang, Y., & Juo, S. H. (2011) · Circulation Journal · doi:10.1253/circj.cj-11-0925 · Cited by 27

Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability

Das, A., Morley, M. P., Moravec, C. S., Tang, W. H. W., Hakonarson, H. H., Ashley, E. A., Brandimarto, J., Hu, R., Li, M., Li, H., et al. (2015) · Nature Communications · doi:10.1038/ncomms9555 · Cited by 25

Preparation of a Monoclonal Antibody Specific for 5-Methyl-2'-deoxycytidine and Its Application for the Detection of DNA Methylation Levels in Human Peripheral Blood Cells.

Mizugaki, M., Itoh, K., YAMAGUCHI, T., Ishiwata, S., Hishinuma, T., 野崎, 征., & Ishida, N. (1996) · Biological and Pharmaceutical Bulletin · doi:10.1248/bpb.19.1537 · Cited by 15

Brain Lateralization: A Comparative Perspective.

Güntürkün, O., Ströckens, F., & Ocklenburg, S. (2020) · Physiological Reviews · doi:10.1152/physrev.00006.2019 · Cited by 412

Alveolar Epithelial Type II Cells as Drivers of Lung Fibrosis in Idiopathic Pulmonary Fibrosis

Parimon, T., Yao, C., Stripp, B. R., Noble, P. W., & Chen, P. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21072269 · Cited by 397

Idiopathic Pulmonary Fibrosis: An Update on Pathogenesis

Mei, Q., Liu, Z., Zuo, H., Yang, Z., & Qu, J. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2021.797292 · Cited by 360

Vascular mechanotransduction

Davis, M. J., Earley, S., Li, Y.-S., & Chien, S. (2023) · Physiological Reviews · doi:10.1152/physrev.00053.2021 · Cited by 273

Phosphoenolpyruvate carboxykinase in cell metabolism: Roles and mechanisms beyond gluconeogenesis

Yu, S., Meng, S., Xiang, M., & Ma, H. (2021) · Molecular Metabolism · doi:10.1016/j.molmet.2021.101257 · Cited by 277

Epitranscriptional Regulation: From the Perspectives of Cardiovascular Bioengineering

Chen, Z., He, M., Li, J. Y.-S., Shyy, J. Y.-J., & Chien, S. (2023) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-081922-021233 · Cited by 3

Epigenomic Reprogramming in Cardiovascular Disease

Zhou, Y., Liu, J., & Li, Q. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814513-5.00010-6 · Cited by 5

Epigenomes in Cardiovascular Disease

Rosa‐Garrido, M., Chapski, D. J., & Vondriska, T. M. (2018) · Circulation Research · doi:10.1161/circresaha.118.311597 · Cited by 73

Role of epigenetics in cardiovascular diseases: An out and out check

Wasim, R., Mahmood, T., Siddiqui, M. H., Singh, A. N., Ahmad, A., & Ahsan, F. (2023) · Intelligent Pharmacy · doi:10.1016/j.ipha.2023.09.001 · Cited by 2

Epigenetic Regulations in Mammalian Cells: Roles and Profiling Techniques

Kim, U., & Lee, D.-S. (2023) · Molecules and Cells · doi:10.14348/molcells.2023.0013 · Cited by 27