Intragenic Enhancers Act as Alternative Promoters

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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TopHat: discovering splice junctions with RNA-Seq

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

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Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

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The Transcriptional Landscape of the Mammalian Genome

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Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclassesPreprint

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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

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Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

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Histone modifications at human enhancers reflect global cell-type-specific gene expression

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RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Jana Hertel, A., Jörg Hackermüller, A., Hofacker, I. L., et al. (2007) · Science · doi:10.1126/science.1138341 · Cited by 2,519 · see citing works

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 · see citing works

A unique chromatin signature uncovers early developmental enhancers in humans

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Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

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The NIH Roadmap Epigenomics Mapping Consortium

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

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Divergent transcription from active promoters

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RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

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The Antisense Transcriptomes of Human Cells

He, Y., Vogelstein, B., Velculescu, V. E., Papadopoulos, N., & Kinzler, K. W. (2008) · Science · doi:10.1126/science.1163853 · Cited by 531 · see citing works

A major positive regulatory region located far upstream of the human alpha-globin gene locus.Preprint

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Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arraysPreprint

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Gene Regulation in the Third Dimension

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Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression

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A global view of genomic information – moving beyond the gene and the master regulator

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Globin gene activation during haemopoiesis is driven by protein complexes nucleated by GATA‐1 and GATA‐2

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Enhancers: The abundance and function of regulatory sequences beyond promoters

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Divergent transcription: A new feature of active promoters

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Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

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Establishment of normal, terminally differentiating mouse erythroid progenitors: molecular characterization by cDNA arrays

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Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

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Chromosome looping at the human α-globin locus is mediated via the major upstream regulatory element (HS −40)

Vernimmen, D., Marques-Kranc, F., Sharpe, J. A., Sloane-Stanley, J. A., Wood, W. G., Wallace, H. A. C., Smith, A. J. H., & Higgs, D. R. (2009) · Blood · doi:10.1182/blood-2009-03-213439 · Cited by 89 · see citing works

Long-range regulation of ?? globin gene expression during erythropoiesis

Higgs, D. R., & Wood, W. G. (2008) · Current Opinion in Hematology · doi:10.1097/moh.0b013e3282f734c4 · Cited by 73 · see citing works

Tissue-specific histone modification and transcription factor binding in α globin gene expression

Gobbi, M. D., Anguita, E., Hughes, J. R., Sloane-Stanley, J. A., Sharpe, J. A., Koch, C. M., Dunham, I., Gibbons, R. J., Wood, W. G., & Higgs, D. R. (2007) · Blood · doi:10.1182/blood-2007-06-097964 · Cited by 71 · see citing works

Bystander gene activation by a locus control region

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The complex transcription regulatory landscape of our genome: control in three dimensions

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Deletion of the mouse α-globin regulatory element (HS −26) has an unexpectedly mild phenotype

Anguita, E., Sharpe, J. A., Sloane-Stanley, J. A., Tufarelli, C., Higgs, D. R., & Wood, W. G. (2002) · Blood · doi:10.1182/blood-2002-05-1409 · Cited by 58 · see citing works

The evolutionary conserved gene C16orf35 encodes a nucleo-cytoplasmic protein that interacts with p73

Lunardi, A., Chiacchiera, F., D’Este, E., Carotti, M., Ferro, M. D., Minin, G. D., Sal, G. D., & Collavin, L. (2009) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2009.08.027 · Cited by 14 · see citing works

An atlas of active enhancers across human cell types and tissues

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The functions and unique features of long intergenic non-coding RNA

Ransohoff, J. D., Wei, Y., & Khavari, P. A. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.104 · Cited by 1,337 · see citing works

The selection and function of cell type-specific enhancers

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BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

Canver, M. C., Smith, E. C., Sher, F., Pinello, L., Sanjana, N. E., Shalem, O., Chen, D. D., Schupp, P. G., Vinjamur, D. S., Garcia, S. P., et al. (2015) · Nature · doi:10.1038/nature15521 · Cited by 886 · see citing works

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

Li, W., Notani, D., & Rosenfeld, M. G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.4 · Cited by 710 · see citing works

An Erythroid Enhancer of <i>BCL11A</i> Subject to Genetic Variation Determines Fetal Hemoglobin Level

Bauer, D. E., Kamran, S. C., Lessard, S., Xu, J., Fujiwara, Y., Lin, C., Shao, Z., Canver, M. C., Smith, E. C., Pinello, L., et al. (2013) · Science · doi:10.1126/science.1242088 · Cited by 653 · see citing works

Integrative annotation of chromatin elements from ENCODE data

Hoffman, M. M., Ernst, J., Wilder, S. P., Kundaje, A. B., Harris, R. S., Libbrecht, M., Giardine, B. M., Ellenbogen, P. M., Bilmes, J. A., Birney, E., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1284 · Cited by 521 · see citing works

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461 · see citing works

Transcriptional regulatory functions of nuclear long noncoding RNAs

Vance, K. W., & Ponting, C. P. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.06.001 · Cited by 423 · see citing works

Noncoding Transcription at Enhancers: General Principles and Functional Models

Natoli, G., & Andrau, J. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155459 · Cited by 395 · see citing works

Genetic dissection of the α-globin super-enhancer in vivo

Hay, D., Hughes, J. R., Babbs, C., Davies, J. O. J., Graham, B. J., Hanssen, L. L. P., Kassouf, M. T., Oudelaar, A. M., Sharpe, J. A., Suciu, M. C., et al. (2016) · Nature Genetics · doi:10.1038/ng.3605 · Cited by 385 · see citing works

The Diversity of Long Noncoding RNAs and Their Generation

Wu, H., Yang, L. C., & Chen, L. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.05.004 · Cited by 378 · see citing works

Enhancer RNAs are an important regulatory layer of the epigenome

Sartorelli, V., & Lauberth, S. M. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0446-0 · Cited by 367 · see citing works

Architectural and Functional Commonalities between Enhancers and Promoters

Kim, T.-K., & Shiekhattar, R. (2015) · Cell · doi:10.1016/j.cell.2015.08.008 · Cited by 331 · see citing works

Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19

Hua, J. T., Ahmed, M., Guo, H., Zhang, Y., Chen, S., Soares, F., Lu, J., Zhou, S., Wang, M., Li, H., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.014 · Cited by 317 · see citing works

Seventy-five genetic loci influencing the human red blood cell

van der Harst, P., Zhang, W., Leach, I. M., Rendon, A., Verweij, N., Sehmi, J., Paul, D. S., Elling, U., Allayee, H., Li, X., et al. (2012) · Nature · doi:10.1038/nature11677 · Cited by 306 · see citing works

The relationship between genome structure and function

Oudelaar, A. M., & Higgs, D. R. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00303-x · Cited by 304 · see citing works

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

Schlackow, M., Nojima, T., Gomes, T., Dhir, A., Carmo‐Fonseca, M., & Proudfoot, N. J. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.11.029 · Cited by 295 · see citing works

Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications

Kapusta, A., & Feschotte, C. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.08.004 · Cited by 291 · see citing works

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

Mikhaylichenko, O., Bondarenko, V., Harnett, D., Schor, I. E., Males, M., Viales, R. R., & Furlong, E. E. M. (2018) · Genes &amp; Development · doi:10.1101/gad.308619.117 · Cited by 293 · see citing works

Dealing with Pervasive Transcription

Jensen, T. H., Jacquier, A., & Libri, D. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.10.032 · Cited by 284 · see citing works

Genome-wide characterization of mammalian promoters with distal enhancer functions

Dao, L. T. M., Galindo-Albarrán, A. O., Castro-Mondragon, J. A., Andrieu-Soler, C., Medina-Rivera, A., Souaid, C., Charbonnier, G., Griffon, A., Vanhille, L., Stephen, T., et al. (2017) · Nature Genetics · doi:10.1038/ng.3884 · Cited by 281 · see citing works

Core circadian clock genes regulate leukemia stem cells in AML

Puram, R. V., Kowalczyk, M. S., de Boer, C. G., Schneider, R. K., Miller, P. G., McConkey, M., Tothova, Z., Tejero, H., Heckl, D., Järås, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.03.015 · Cited by 274 · see citing works

Long Noncoding RNAs in Cardiovascular Pathology, Diagnosis, and Therapy

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Integrative analysis of haplotype-resolved epigenomes across human tissues

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Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

Hanssen, L. L. P., Kassouf, M. T., Oudelaar, A. M., Biggs, D., Preece, C., Downes, D. J., Gosden, M., Sharpe, J. A., Sloane-Stanley, J. A., Hughes, J. R., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3573 · Cited by 219 · see citing works

A unified architecture of transcriptional regulatory elements

Andersson, R., Sandelin, A., & Danko, C. G. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.05.007 · Cited by 211 · see citing works

Set3 HDAC Mediates Effects of Overlapping Noncoding Transcription on Gene Induction Kinetics

Kim, T. S., Xu, Z., Clauder‐Münster, S., Steinmetz, L. M., & Buratowski, S. (2012) · Cell · doi:10.1016/j.cell.2012.08.016 · Cited by 201 · see citing works

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

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Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

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Defining genome architecture at base-pair resolution

Peng, H., Badat, M., Hanssen, L. L. P., Hentges, L. D., Crump, N. T., Downes, D. J., Jeziorska, D. M., Oudelaar, A. M., Schweßinger, R., Taylor, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03639-4 · Cited by 176 · see citing works

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar, V. R., Mishra, T., Luan, J. Y., Yao, Y., Kossenkov, A. V., Anderson, S. M., Dunagin, M. C., Pimkin, M., Gore, M., Sun, D. K., et al. (2014) · Blood · doi:10.1182/blood-2013-12-544494 · Cited by 184 · see citing works

Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex

Shen, H., Xu, W., Guo, R., Rong, B., Gu, L., Wang, Z., He, C., Zheng, L., Hu, X., Hu, Z., et al. (2016) · Cell · doi:10.1016/j.cell.2016.02.064 · Cited by 184 · see citing works

Reduced dosage of ERF causes complex craniosynostosis in humans and mice and links ERK1/2 signaling to regulation of osteogenesis

Twigg, S. R. F., Vorgia, E., McGowan, S. J., Peraki, I., Fenwick, A. L., Sharma, V., Allégra, M., Ζαραγκούλιας, Α., Akha, E. S., Knight, S. J. L., et al. (2013) · Nature Genetics · doi:10.1038/ng.2539 · Cited by 173 · see citing works

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

Andersson, R., Refsing Andersen, P., Valen, E., Core, L. J., Bornholdt, J., Boyd, M., Heick Jensen, T., & Sandelin, A. (2014) · Nature Communications · doi:10.1038/ncomms6336 · Cited by 171 · see citing works

Divergent Transcription: A Driving Force for New Gene Origination?

Wu, X., & Sharp, P. A. (2013) · Cell · doi:10.1016/j.cell.2013.10.048 · Cited by 171 · see citing works

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

Marques, A. C., Hughes, J. R., Graham, B., Kowalczyk, M. S., Higgs, D. R., & Ponting, C. P. (2013) · Genome biology · doi:10.1186/gb-2013-14-11-r131 · Cited by 169 · see citing works

R-Loops Promote Antisense Transcription across the Mammalian Genome

Tan‐Wong, S. M., Dhir, S., & Proudfoot, N. J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.10.002 · Cited by 164 · see citing works

The Hierarchy of Transcriptional Activation: From Enhancer to Promoter

Vernimmen, D., & Bickmore, W. A. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.10.004 · Cited by 155 · see citing works

Occupancy maps of 208 chromatin-associated proteins in one human cell type

Partridge, E. C., Chhetri, S. B., Prokop, J. W., Ramaker, R. C., Jansen, C. S., Goh, S.-T., Mackiewicz, M., Newberry, K. M., Brandsmeier, L. A., Meadows, S. K., et al. (2020) · Nature · doi:10.1038/s41586-020-2023-4 · Cited by 154 · see citing works

Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis

Wu, H., Whitfield, T. W., Gordon, J. A. R., Dobson, J. R., Tai, P. W. L., van Wijnen, A. J., Stein, J. L., Stein, G. S., & Lian, J. B. (2014) · Genome biology · doi:10.1186/gb-2014-15-3-r52 · Cited by 146 · see citing works

An in-depth map of polyadenylation sites in cancer

Lin, Y., Li, Z., Ozsolak, F., Kim, S. W., Arango-Argoty, G., Liu, T. T., Tenenbaum, S. A., Bailey, T. L., Monaghan, A. P., Milos, P. M., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks637 · Cited by 140 · see citing works

Balancing of Histone H3K4 Methylation States by the Kdm5c/SMCX Histone Demethylase Modulates Promoter and Enhancer Function

Outchkourov, N. S., Muiño, J. M., Kaufmann, K., van IJcken, W. F. J., Koerkamp, M. J. A. G., van Leenen, D., de Graaf, P., Holstege, F. C. P., Grosveld, F. G., & Timmers, H. T. M. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.02.030 · Cited by 136 · see citing works

Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease

Ounzain, S., Pezzuto, I., Micheletti, R., Burdet, F., Sheta, R., Nemir, M., Gonzales, C., Sarre, A., Alexanian, M., Blow, M. J., et al. (2014) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2014.08.009 · Cited by 137 · see citing works

DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer

Stone, A. M., Zotenko, E., Locke, W. J., Korbie, D. J., Millar, E. K. A., Pidsley, R., Stirzaker, C., Graham, P., Trau, M., Musgrove, E. A., et al. (2015) · Nature Communications · doi:10.1038/ncomms8758 · Cited by 136 · see citing works

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin foldingPreprint

Andrey, G., Schöpflin, R., Jerković, I., Heinrich, V., Ibrahim, D. M., Paliou, C., Hochradel, M., Timmermann, B., Haas, S. A., Vingron, M., et al. (2016) · Genome Research · doi:10.1101/gr.213066.116 · Cited by 122 · see citing works

Promoter or enhancer, what’s the difference? Deconstruction of established distinctions and presentation of a unifying model

Andersson, R. (2015) · BioEssays · doi:10.1002/bies.201400162 · Cited by 127 · see citing works

Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons

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A novel isoform of TET1 that lacks a CXXC domain is overexpressed in cancer

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Myeloid receptor CD36 is required for early phagocytosis of myocardial infarcts and induction of Nr4a1‐dependent mechanisms of cardiac repair

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