Genomic views of distant-acting enhancers

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216

The sequence of the human genome

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RNA-Seq: a revolutionary tool for transcriptomics

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Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187

High-Resolution Profiling of Histone Methylations in the Human Genome

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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

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Finishing the euchromatic sequence of the human genome

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

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Capturing Chromosome Conformation

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Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells

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Distant Activation of Transcription: Mechanisms of Enhancer Action

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Chromosome 8q24-Associated Cancers and MYC

Grisanzio, C., & Freedman, M. L. (2010) · Genes & Cancer · doi:10.1177/1947601910381380 · Cited by 130

Leveraging Cross-Species Transcription Factor Binding Site Patterns: From Diabetes Risk Loci to Disease Mechanisms

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Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

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Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk

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Deciphering the transcriptional cis-regulatory code

Yáñez-Cuna, J. O., Kvon, E. Z., & Stark, A. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.09.007 · Cited by 126

Inflammation-Induced NFATc1–STAT3 Transcription Complex Promotes Pancreatic Cancer Initiation by Kras G12D

Baumgart, S., Chen, N., Siveke, J. T., König, A. O., Zhang, J., Singh, S. K., Wolf, E., Bartkuhn, M., Esposito, I., Heßmann, E., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0593 · Cited by 122

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

He, Q., Bardet, A. F., Patton, B., Purvis, J., Johnston, J. J., Paulson, A., Gogol, M., Stark, A., & Zeitlinger, J. (2011) · Nature Genetics · doi:10.1038/ng.808 · Cited by 128

A predictive modeling approach for cell line-specific long-range regulatory interactions

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Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines

Fernández, M., & Miranda‐Saavedra, D. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks149 · Cited by 121

In silico prediction of high-resolution Hi-C interaction matrices

Zhang, S., Chasman, D. A., Knaack, S., & Roy, S. (2019) · Nature Communications · doi:10.1038/s41467-019-13423-8 · Cited by 119

Cell-Type-Specific Control of Enhancer Activity by H3K9 Trimethylation

Zhu, Y., van Essen, D., & Saccani, S. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.011 · Cited by 123

Helper T-cell differentiation and plasticity: insights from epigenetics

Hirahara, K., Vahedi, G., Ghoreschi, K., Yang, X., Nakayamada, S., Kanno, Y., O’Shea, J. J., & Laurence, A. D. J. (2011) · Immunology · doi:10.1111/j.1365-2567.2011.03483.x · Cited by 119

Chromatin signatures of active enhancers

Spicuglia, S., & Vanhille, L. (2012) · Nucleus · doi:10.4161/nucl.19232 · Cited by 127

Systems genetics analysis of gene-by-environment interactions in human cells

Romanoski, C. E., Lee, S., Kim, M. J., Ingram-Drake, L., Plaisier, C. L., Yordanova, R., Tilford, C., Guan, B., He, A., Gargalovic, P. S., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.02.002 · Cited by 111

Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks

Sandhu, K. S., Li, G., Poh, H. M., Quek, Y. L. K., Sia, Y. Y., Peh, S. Q., Mulawadi, F. H., Lim, J., Šikić, M., Menghi, F., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.09.022 · Cited by 113

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene

Gheldof, N., Smith, E. M., Tabuchi, T. M., Koch, C. M., Dunham, I., Stamatoyannopoulos, J. A., & Dekker, J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq175 · Cited by 114

Transcriptional Control of Inflammatory ResponsesPreprint

Smale, S. T., & Natoli, G. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016261 · Cited by 112

Getting the genome in shape: the formation of loops, domains and compartments

Bouwman, B. A. M., & de Laat, W. L. (2015) · Genome biology · doi:10.1186/s13059-015-0730-1 · Cited by 115

A genome-wide map of human genetic interactions inferred from radiation hybrid genotypesPreprint

Lin, A., Wang, R. T., Ahn, S., Park, C. C., & Smith, D. (2010) · Genome Research · doi:10.1101/gr.104216.109 · Cited by 112

Chromatin and epigenetic features of long-range gene regulation

Harmston, N., & Lenhard, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt499 · Cited by 113

Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene

Davison, L. J., Wallace, C., Cooper, J. D., Cope, N. F., Wilson, N. K., Smyth, D. J., Howson, J. M. M., Saleh, N. M., Aljeffery, A., Angus, K. L., et al. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr468 · Cited by 107

Zic2 Is an Enhancer-Binding Factor Required for Embryonic Stem Cell Specification

Luo, Z., Gao, X., Lin, C., Smith, E. R., Marshall, S. A., Swanson, S. K., Florens, L. A., Washburn, M. P., & Shilatifard, A. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.01.007 · Cited by 110

Enhancers, enhancers – from their discovery to today’s universe of transcription enhancers

Schaffner, W. (2015) · Biological Chemistry · doi:10.1515/hsz-2014-0303 · Cited by 105

Identification of altered cis-regulatory elements in human disease

Mathelier, A., Shi, W., & Wasserman, W. W. (2015) · Trends in Genetics · doi:10.1016/j.tig.2014.12.003 · Cited by 107

Regulation of angiotensin II actions by enhancers and super-enhancers in vascular smooth muscle cells

Das, S., Senapati, P., Chen, Z., Reddy, M. A., Ganguly, R., Lanting, L. L., Mandi, V., Bansal, A., Leung, A., Zhang, S., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01629-7 · Cited by 105

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

Petrovic, J., Zhou, Y., Fasolino, M., Goldman, N., Schwartz, G. W., Mumbach, M. R., Nguyen, S. C., Rome, K., Sela, Y., Zapataro, Z., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.01.006 · Cited by 107

PEDLA: predicting enhancers with a deep learning-based algorithmic framework

Liu, F., Li, H., Ren, C., Bo, X., & Shu, W. (2016) · Scientific Reports · doi:10.1038/srep28517 · Cited by 101

Expression and mutation analyses implicate ARHGAP29 as the etiologic gene for the cleft lip with or without cleft palate locus identified by genome‐wide association on chromosome 1p22

Leslie, E. J., Mansilla, M. A., Biggs, L. C., Schuette, K., Bullard, S. A., Cooper, M. E., Dunnwald, M., Lidral, A. C., Marazita, M. L., Beaty, T. H., et al. (2012) · Birth Defects Research Part A Clinical and Molecular Teratology · doi:10.1002/bdra.23076 · Cited by 103

The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages

Daniel, B., Nagy, G., Hah, N., Horvath, A., Czimmerer, Z., Poliska, S., Gyuris, T., Keirsse, J., Gysemans, C., Van Ginderachter, J. A., et al. (2014) · Genes & Development · doi:10.1101/gad.242685.114 · Cited by 97

Expression of ABO blood-group genes is dependent upon an erythroid cell–specific regulatory element that is deleted in persons with the Bm phenotype

Sano, R., Nakajima, T., Takahashi, K., Kubo, R., Kominato, Y., Tsukada, J., Takeshita, H., Yasuda, T., Ito, K., Maruhashi, T., et al. (2012) · Blood · doi:10.1182/blood-2011-10-387167 · Cited by 97

Affinity-optimizing enhancer variants disrupt development

Lim, F., Solvason, J. J., Ryan, G. E., Le, S. H., Jindal, G. A., Steffen, P., Jandu, S. K., & Farley, E. K. (2024) · Nature · doi:10.1038/s41586-023-06922-8 · Cited by 102

Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations

Lee, D. S. M., Ghanem, L. R., & Barash, Y. (2020) · Nature Communications · doi:10.1038/s41467-020-14404-y · Cited by 96

Enhancer and super-enhancer dynamics in repair after ischemic acute kidney injury

Wilflingseder, J., Willi, M., Lee, H., Olauson, H., Jankowski, J., Ichimura, T., Erben, R. G., Valerius, M. T., Hennighausen, L. G., & Bonventre, J. V. (2020) · Nature Communications · doi:10.1038/s41467-020-17205-5 · Cited by 96

Progress and challenges in bioinformatics approaches for enhancer identification

Kleftogiannis, D., Kalnis, P., & Bajić, V. B. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv101 · Cited by 92

Retinoic Acid and Histone Deacetylases Regulate Epigenetic Changes in Embryonic Stem Cells

Urvalek, A. M., & Gudas, L. J. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.556555 · Cited by 92

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes

Yao, L., Berman, B. P., & Farnham, P. (2015) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2015.1087961 · Cited by 93

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

Murtha, M. J., Keskin, Z. T., Tang, Z., Strino, F., Chen, X. X., Wang, Y., Xi, X., Basilico, C., Brown, S. M., Bonneau, R., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2885 · Cited by 94

Massive turnover of functional sequence in human and other mammalian genomesPreprint

Meader, S., Ponting, C. P., & Lunter, G. A. (2010) · Genome Research · doi:10.1101/gr.108795.110 · Cited by 92

Genome-Wide Tissue-Specific Occupancy of the Hox Protein Ultrabithorax and Hox Cofactor Homothorax in Drosophila

Slattery, M. G., Ma, L., Nègre, N., White, K. P., & Mann, R. S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0014686 · Cited by 89

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

Lee, H. J., Lowdon, R. F., Maricque, B. B., Zhang, B., Stevens, M. W., Li, D., Johnson, S. L., & Wang, T. (2015) · Nature Communications · doi:10.1038/ncomms7315 · Cited by 92

Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation

Hoffmann, A. D., Yang, X. H., Burnicka-Turek, O., Bosman, J. D., Ren, X., Steimle, J. D., Vokes, S. A., McMahon, A. P., Kalinichenko, V. V., & Moskowitz, I. P. G. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004604 · Cited by 88

How to make stripes: deciphering the transition from non-periodic to periodic patterns in Drosophila segmentation

Schroeder, M. D., Greer, C., & Gaul, U. (2011) · Development · doi:10.1242/dev.062141 · Cited by 88

A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS

Richardson, K., Lai, C., Parnell, L. D., Lee, Y., & Ordovás, J. M. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-504 · Cited by 88

Normal Levels of Sox9 Expression in the Developing Mouse Testis Depend on the TES/TESCO Enhancer, but This Does Not Act Alone

Gonen, N., Quinn, A., O’Neill, H. C., Koopman, P. A., & Lovell-Badge, R. H. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006520 · Cited by 85

Common genetic variants in the PSCA gene influence gene expression and bladder cancer risk

Fu, Y., Kohaar, I., Rothman, N., Earl, J., Figueroa, J. D., Ye, Y., Malats, N., Tang, W., Liu, L., García‐Closas, M., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1202189109 · Cited by 86

Increased enhancer–promoter interactions during developmental enhancer activation in mammals

Chen, Z., Snetkova, V., Bower, G., Jacinto, S. H., Clock, B., Dizehchi, A., Barozzi, I., Mannion, B. J., Alcaina‐Caro, A., López-Ríos, J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01681-2 · Cited by 98

STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells

Peng, T., Zhai, Y., Atlasi, Y., ter Huurne, M., Marks, H., Stunnenberg, H. G., & Megchelenbrink, W. (2020) · Genome Biology · doi:10.1186/s13059-020-02156-3 · Cited by 83

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

Park, S. G., Hannenhalli, S. S., & Choi, S. S. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-526 · Cited by 83

A comprehensively molecular haplotype-resolved genome of a European individualPreprint

Suk, E.-K., McEwen, G. K., Duitama, J., Nowick, K., Schulz, S., Palczewski, S., Schreiber, S., Holloway, D. T., McLaughlin, S., Peckham, H. E., et al. (2011) · Genome Research · doi:10.1101/gr.125047.111 · Cited by 83

Function-based identification of mammalian enhancers using site-specific integration

Dickel, D. E., Zhu, Y., Nord, A. S., Wylie, J. N., Akiyama, J. A., Afzal, V., Plajzer-Frick, I., Kirkpatrick, A. M., Göttgens, B., Bruneau, B. G., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2886 · Cited by 87

Elevated 5-hydroxymethylcytosine in the Engrailed-2 (EN-2) promoter is associated with increased gene expression and decreased MeCP2 binding in autism cerebellum

James, S. J., Shpyleva, S., Melnyk, S., Pavliv, O., & Pogribny, I. P. (2014) · Translational Psychiatry · doi:10.1038/tp.2014.87 · Cited by 79

The mystery of extreme non-coding conservation

Harmston, N., Barešić, A., & Lenhard, B. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0021 · Cited by 80

CRISPR-Based Epigenome Editing: Mechanisms and Applications

Fadul, S. M., Arshad, A., & Mehmood, R. (2023) · Epigenomics · doi:10.2217/epi-2023-0281 · Cited by 80

Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals

Acemel, R. D., Maeso, I., & Gómez-Skármeta, J. L. (2017) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.265 · Cited by 82

Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds

Doyle, J. L., Berry, D. P., Veerkamp, R. F., Carthy, T. R., Evans, R. D., Walsh, S. W., & Purfield, D. C. (2020) · Genetics Selection Evolution · doi:10.1186/s12711-020-0523-1 · Cited by 76

Mutations in ACTRT1 and its enhancer RNA elements lead to aberrant activation of Hedgehog signaling in inherited and sporadic basal cell carcinomas

Bal, É., Park, H.-S., Belaid, Z., Kayserili, H., Naville, M., Madrange, M., Chiticariu, E., Hadj-Rabia, S., Cagnard, N., Kuonen, F., et al. (2017) · Nature Medicine · doi:10.1038/nm.4368 · Cited by 75

Genes Expressed in Specific Areas of the Human Fetal Cerebral Cortex Display Distinct Patterns of Evolution

Lambert, N., Lambot, M.-A., Bilheu, A., Albert, V., Englert, Y., Libert, F., Noel, J.-C., Sotiriou, C., Holloway, A. K., Pollard, K. S., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017753 · Cited by 73

Cdkn2a Is an Atherosclerosis Modifier Locus That Regulates Monocyte/Macrophage Proliferation

Kuo, C.-L., Murphy, A. J., Sayers, S., Li, R., Yvan-Charvet, L., Davis, J. Z., Krishnamurthy, J., Liu, Y., Puig, O., Sharpless, N. E., et al. (2011) · Arteriosclerosis, Thrombosis, and Vascular Biology · doi:10.1161/atvbaha.111.234492 · Cited by 73

Using transgenic reporter assays to functionally characterize enhancers in animals

Kvon, E. Z. (2015) · Genomics · doi:10.1016/j.ygeno.2015.06.007 · Cited by 73

STARR‐seq and UMI‐STARR‐seq: Assessing Enhancer Activities for Genome‐Wide‐, High‐, and Low‐Complexity Candidate Libraries

Neumayr, C., Pagani, M., Stark, A., & Arnold, C. D. (2019) · Current Protocols in Molecular Biology · doi:10.1002/cpmb.105 · Cited by 73

Primate optogenetics: Progress and prognosis

El-Shamayleh, Y., & Horwitz, G. D. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1902284116 · Cited by 78

Marked Diversity of Unique Cortical Enhancers Enables Neuron-Specific Tools by Enhancer-Driven Gene Expression

Blankvoort, S., Witter, M. P., Noonan, J., Cotney, J., & Kentros, C. (2018) · Current Biology · doi:10.1016/j.cub.2018.05.015 · Cited by 72

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish

Hiller, M., Agarwal, S., Notwell, J. H., Parikh, R., Guturu, H., Wenger, A. M., & Bejerano, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt557 · Cited by 72

Human skin color is influenced by an intergenic DNA polymorphism regulating transcription of the nearby BNC2 pigmentation gene

Visser, M., Palstra, R.-J. T. S., & Kayser, M. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu289 · Cited by 76

Molecular insights into genome-wide association studies of chronic kidney disease-defining traits

Xu, X., Eales, J., Akbarov, A., Guo, H., Becker, L. K., Talavera, D., Ashraf, F., Nawaz, J., Pramanik, S., Bowes, J., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07260-4 · Cited by 73

The regulation of Sox9 expression in the gonad

Gonen, N., & Lovell-Badge, R. H. (2019) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2019.01.004 · Cited by 75

Genetic variants in urinary bladder cancer: collective power of the “wimp SNPs”

Golka, K., Selinski, S., Lehmann, M., Blaszkewicz, M., Marchan, R., Ickstadt, K., Schwender, H. R., Bolt, H. M., & Hengstler, J. G. (2011) · Archives of Toxicology · doi:10.1007/s00204-011-0676-3 · Cited by 71

The FaceBase Consortium: A comprehensive program to facilitate craniofacial research

Hochheiser, H., Aronow, B. J., Artinger, K., Beaty, T. H., Brinkley, J. F., Chai, Y., Clouthier, D. E., Cunningham, M. L., Dixon, M. J., Donahue, L. R., et al. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2011.02.033 · Cited by 71

miRNAs Regulation and Its Role as Biomarkers in Endometriosis

Marí‐Alexandre, J., Sánchez-Izquierdo, D., Gilabert–Estellés, J., Barceló‐Molina, M., Braza‐Boïls, A., & Sandoval, J. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17010093 · Cited by 71

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features

Chen, C., Morris, Q., & Mitchell, J. A. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-152 · Cited by 75

Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement

Rose, A. B., Emami, S., Bradnam, K. R., & Korf, I. F. (2011) · Frontiers in Plant Science · doi:10.3389/fpls.2011.00098 · Cited by 70

The Conserved Sonic Hedgehog Limb Enhancer Consists of Discrete Functional Elements that Regulate Precise Spatial Expression

Lettice, L. A., Devenney, P., De Angelis, C., & Hill, R. E. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.07.037 · Cited by 70

29 Mammalian Genomes Reveal Novel Exaptations of Mobile Elements for Likely Regulatory Functions in the Human Genome

Lowe, C. B., & Haussler, D. H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043128 · Cited by 77

Global Quantitative Mapping of Enhancers in Rice by STARR-Seq

Sun, J., He, N., Niu, L., Huang, Y., Shen, W., Zhang, Y., Li, L., & Hou, C. (2019) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2018.11.003 · Cited by 69

A Unique Epigenomic Landscape Defines Human Erythropoiesis

Schulz, V., Yan, H., Lezon-Geyda, K., An, X., Hale, J., Hillyer, C. D., Mohandas, N., & Gallagher, P. G. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.08.020 · Cited by 73

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytesPreprint

Gorkin, D. U., Lee, D., Reed, X., Fletez-Brant, C., Bessling, S. L., Loftus, S. K., Beer, M., Pavan, W. J., & McCallion, A. S. (2012) · Genome Research · doi:10.1101/gr.139360.112 · Cited by 72

Evolution of Gene Regulation in Humans

Reilly, S. K., & Noonan, J. P. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090314-045935 · Cited by 66

Long-range regulatory interactions at the 4q25 atrial fibrillation risk locus involve PITX2c and ENPEP

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Bat accelerated regions identify a bat forelimb specific enhancer in the HoxD locus

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