A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers
De Santa, Francesca, Barozzi, Iros, Mietton, Flore, Ghisletti, Serena, Polletti, Sara, Tusi, Betsabeh Khoramian, Muller, Heiko, Ragoussis, Jiannis, Wei, Chia-Lin, Natoli, Gioacchino·2010·PLoS Biology
Cited by (934)
Items 601–700 of 934
- Role of mammalian long non-coding RNAs in normal and neuro oncological disordersNeetu Singh · 2021 · Genomics
- Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiationCarlos Guzman, Sascha H. C. Duttke, Yixin Zhu, Camila De Arruda Saldanha, Nicholas L. Downes, Christopher W. Benner, Sven Heinz · 2023 · Nucleic Acids Research
- Higher-Order Chromatin Regulation of Inflammatory Gene ExpressionJin-Wen Xu, Shuang Ling, Jun Liu · 2017 · Mediators of Inflammation
- Roles of super enhancers and enhancer RNAs in skeletal muscle development and diseaseSi Lei, Cheng Li, Yanling She, Shanyao Zhou, Huacai Shi, Rui Chen · 2022 · Cell Cycle
- Enhancer–promoter entanglement explains their transcriptional interdependenceAnil K. Panigrahi, David Michael Lonard, Bert W. O’Malley · 2023 · Proceedings of the National Academy of Sciences
- Control of enhancer and promoter activation in the type I interferon response by the histone demethylase Kdm4d/JMJD2dRohit Chandwani, Terry Fang, Scott B. Dewell, Alexander Tarakhovsky · 2023 · Frontiers in Immunology
- Identification of a ΔNp63-Dependent Basal-Like A Subtype-Specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal AdenocarcinomaXin Wang, Ana P. Kutschat, Joana E. Aggrey-Fynn, Feda H. Hamdan, Rondell Patrell Graham, Alexander Q. Wixom, Yara Souto, Swetlana Ladigan‐Badura, Jennifer A. Yonkus, Amro M. Abdelrahman et al. · 2023 · Molecular Cancer Research
- Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expressionXinhong Liu, Xiangzheng Liu, Yingxue Du, Di Zou, Tian Chen, Yong Li, Xun Lan, Charles J. David, Qianwen Sun, Mo Chen · 2023 · Cell Reports
- An Emerging Role for Enhancer RNAs in Brain DisordersAnkit Patel, Ashutosh A Dharap · 2024 · NeuroMolecular Medicine
- Transcription-controlling regulatory elements of the eukaryotic genomeSergey V. Razin, Alexey A. Gavrilov, Sergey V. Ulianov · 2015 · Molecular Biology
- Functional genomics of the inflammatory response: where are we now?Marta Simonatto, Gioacchino Natoli · 2013 · Briefings in Functional Genomics
- Chromatin architecture underpinning transcription elongationKiwon Lee, Gerd A. Blobel · 2016 · Nucleus
- Anaemia, macrocytosis, vitamin B12 and folate levels in elderly Zimbabweans.Theresa J. Allain, Zvenyika A. R. Gomo, A O Wilson, Buxton Ndemera, Donald J. Adamchak, Jonathan Arthur Matenga · 1997 · PubMed
- Housekeeping and tissue-specific cis-regulatory elements: Recipes for specificity and recipes for activityMarta Russo, Gioacchino Natoli, Serena Ghisletti · 2017 · Transcription
- Cruciform Formable Sequences within Pou5f1 Enhancer Are Indispensable for Mouse ES Cell IntegrityYu Yamamoto, Osamu Miura, Takashi Ohyama · 2021 · International Journal of Molecular Sciences
- Predmoter—cross-species prediction of plant promoter and enhancer regionsFelicitas Kindel, Sebastian ST Triesch, Urte Schlüter, Laura Alexandra Randarevitch, Vanessa Reichel-Deland, Andreas P.M. Weber, Alisandra K. Denton · 2024 · Bioinformatics Advances
- Comprehensive evaluation of diverse massively parallel reporter assays to functionally characterize human enhancers genome-wideJunke Zhang, Alden King-Yung Leung, Yutong Zhu, Li Yao, Avery Willis, Xiuqi Pan, Abdullah Ozer, Zhou Zhou, Keith Siklenka, Alejandro Barrera et al. · 2025 · Genome biology
- Transcriptional plasticity of fibroblasts in heart diseaseRudi Micheletti, Michael Alexanian · 2022 · Biochemical Society Transactions
- Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locusNoa Gil, Rotem Ben‐Tov Perry, Zohar Mukamel, Alex Tuck, Marc Bühler, Igor Ulitsky · 2023 · Cell Reports
- Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigsChao Wang, Choulin Chen, Bowen Lei, Shenghua Qin, Yuanyuan Zhang, Kui Li, Song Zhang, Yuwen Liu · 2024 · Genetics Selection Evolution
- A long noncoding RNA with enhancer-like function in pig zygotic genome activationRenyue Wei, Yaru Yue, Yinhuan Wu, Chenyuan Zhang, Jun‐Xue Jin, Z.H. Liu, Jiaqiang Wang · 2025 · Journal of Molecular Cell Biology
- Embryonic stem cell-specific intragenic enhancer RNA essential for NSUN2-mediated stem cell fate regulationJiin Moon, Hyohi Lee, Myoung‐don Oh, Yeonju Jang, Dahun Um, Tae-Kyung Kim, Seung-Kyoon Kim · 2025 · International Journal of Biological Macromolecules
- Non-Coding Transcriptome Maps across Twenty Tissues of the Korean Black Chicken, Yeonsan OgyeHyosun Hong, Han‐Ha Chai, Kyoungwoo Nam, Dajeong Lim, Kyung‐Tai Lee, Yoon Jung Do, Chang-Yeon Cho, Jin‐Wu Nam · 2018 · International Journal of Molecular Sciences
- Enhancer occlusion transcripts regulate the activity of human enhancer domains via transcriptional interference: a computational perspectiveAmit Pande, Wojciech Makałowski, Jürgen Brosius, Carsten Alexander Raabe · 2020 · Nucleic Acids Research
- The Cohesin Complex and Its Interplay with Non-Coding RNAsMerve Kuru-Schors, Monika Hämmerle, Tony Gutschner · 2021 · Non-Coding RNA
- KAS-Analyzer: a novel computational framework for exploring KAS-seq dataRuitu Lyu, Tong Wu, Gayoung Park, Yu‐Ying He, Mengjie Chen, Chuan He · 2023 · Bioinformatics Advances
- Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissuesPierre de Langen, Fayrouz Hammal, Élise Guéret, Jean-Christophe Mouren, Lionel Spinelli, Benoît Ballester · 2023 · Cell Genomics
- Initiation of Transcription Generates Divergence of Long Noncoding RNAsRiki Kurokawa · 2015 · Springer eBooks
- Non-coding transcription at cis-regulatory elements: Computational and experimental approachesMarta Simonatto, Iros Barozzi, Gioacchino Natoli · 2013 · Methods
- Integrating genomic and epigenomic information: a promising strategy for identifying functional DNA variants of human diseaseSilvio Zaina, Gertrud Lund · 2012 · Clinical Genetics
- Regulation of Eukaryotic Cell Differentiation by Long Non-coding RNAsJuan R. Alvarez‐Dominguez, Wenqian Hu, Harvey F. Lodish · 2013 · Springer eBooks
- ncRNA function in chromatin organizationKeith E. Giles, Jessica L. Woolnough, Blake L. Atwood · 2015 · Elsevier eBooks
- Identification and Functional Characterization of Two Noncoding RNAs Transcribed from Putative Active Enhancers in Hepatocellular CarcinomaYe-Eun Lee, Jiyeon Lee, Yong Sun Lee, Jiyoung Joan Jang, Hyeonju Woo, Hae In Choi, Young Gyu Chai, Tae-Kyung Kim, Tae Soo Kim, Lark Kyun Kim et al. · 2021 · Molecules and Cells
- A NF-κB-Dependent Dual Promoter-Enhancer Initiates the Lipopolysaccharide-Mediated Transcriptional Activation of the Chicken Lysozyme in MacrophagesJames Witham, Lylia Ouboussad, Pascal F. Lefevre · 2013 · PLoS ONE
- Psg22 expression in mouse trophoblast giant cells is associated with gene inversion and co-expression of antisense long non-coding RNAsJohn Mark Williams, Melanie Ball, Andrew Ward, Tom Moore · 2014 · Reproduction
- Uncovering the functions and mechanisms of regulatory elements-associated non-coding RNAsOlivier Fosseprez, Olivier Cuvier · 2024 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- Chromatin-Associated RNAs Regulate Gene Expression and Chromatin StructureBingning Xie, Ann Dean · 2025 · Non-Coding RNA
- Dual promoter–enhancer activities reflect a unified regulatory logicMauricio I. Paramo, Alden King-Yung Leung, Sagar R Shah, J. Zhang, Nathaniel D. Tippens, Jin Hua Liang, Li Yao, Yiyang Jin, Xiuqi Pan, Abdullah Ozer et al. · 2026 · Nature Communications
- Prostate Cancer Epigenetic Plasticity and Enhancer Heterogeneity: Molecular Causes, Consequences and Clinical ImplicationsJeroen Kneppers, Andries Marinus Bergman, Wilbert T. Zwart · 2022 · Advances in experimental medicine and biology
- Enhancer RNA commits osteogenesis via microRNA-3129 expression in human bone marrow-derived mesenchymal stem cellsAnh Phuong Nguyen, Kaoru Yamagata, Shigeru Iwata, Gulzhan Trimova, Tong Zhang, Shan Yu, Mai-Phuong Nguyen, Koshiro Sonomoto, Shingo Nakayamada, Shigeaki Kato et al. · 2022 · Inflammation and Regeneration
- A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cellsJuan González‐Vallinas, Amadís Pagès, Babita Singh, Eduardo Eyras · 2015 · BMC Genomics
- Phytochemicals and Cancer Chemoprevention: Epigenetic Friends or Foe?Katarzyna Szarc vel Szic, Ajay Palagani, Behrouz Hassannia, Linde Sabbe, Karen Heyninck, Guy Haegeman, Wim Vanden · 2011 · InTech eBooks
- Mutations in gene regulatory elements linked to human limb malformationsKarol Nowosad, Ewa Hordyjewska‐Kowalczyk, Przemko Tylżanowski · 2019 · Journal of Medical Genetics
- Enhancing Gonadotrope Gene Expression Through Regulatory lncRNAsTal Refael, Philippa Melamed · 2021 · Endocrinology
- The Phenomenon of Evolutionary “De Novo Generation” of GenesRoman O. Cherezov, Yu. E. Vorontsova, Olga B. Simonova · 2021 · Russian Journal of Developmental Biology
- eRNA co-expression network uncovers TF dependency and convergent cooperativitySeungha Alisa Lee, Katla Kristjánsdóttir, Hojoong Kwak · 2023 · Scientific Reports
- SP8 Transcriptional Regulation of Cyclin D1 During Mouse Early CorticogenesisUgo Borello, Barbara Berarducci, Edwige Delahaye, David J. Price, Colette Dehay · 2018 · Frontiers in Neuroscience
- Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seqXiangying Sun, Zhezhen Wang, Johnathon M. Hall, Carlos Perez-Cervantes, Alexander J. Ruthenburg, Ivan P. G. Moskowitz, Michael Gribskov, Xinan Holly Yang · 2020 · PLoS Computational Biology
- Building integrative functional maps of gene regulationJinrui Xu, Henry Pratt, Jill E. Moore, Mark Gerstein, Zhiping Weng · 2022 · Human Molecular Genetics
- Regulation of stimulus-inducible gene expression in myeloid cellsSimona Saccani, Michèle Trabucchi · 2015 · Seminars in Immunology
- LSD1/KDM1A Maintains Genome-wide Homeostasis of Transcriptional EnhancersSaurabh Agarwal, Patricia Marie Garay, Robert S. Porter, Emily Brookes, Yumie Murata-Nakamura, Todd S. Macfarlan, Bing Ren, Shigeki Iwase · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- Glucocorticoid receptor collaborates with pioneer factors and AP-1 to execute genome-wide regulationErin M. Wissink, Delsy M. Martinez, Kirk Tevebaugh Ehmsen, Keith R. Yamamoto, John T. Lis · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genesWalter Muskovic, Eve Slavich, Ben Maslen, Dominik C. Kaczorowski, Joseph Cursons, Edmund J. Crampin, Maria Kavallaris · 2022 · Genome Research
- Endocrine Disruptors: Genetic, Epigenetic, and Related PathwaysRais Ahmad Ansari, Saleh Alfuraih, Kamran Shekh, Yadollah Omidi, Saleem Javed, Shakil Ahmed Saghir · 2023 · Wiley eBooks
- Facilitators may represent a new class of regulatory elementsMira T. Kassouf, Alexandra Rampasekova, Douglas R. Higgs · 2026 · Current Opinion in Genetics & Development
- Epigenetic regulation of cis-regulatory elements and transcription factors during developmentShagufta Khan, Rakesh K. Mishra, Surabhi Srivastava · 2023 · Elsevier eBooks
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysisMarina Goliasse, Aurore Johary, Adrian E. Platts, Fabian Ortner-Krause, Patrick P. Edger, Jae Young Choi, Michael D. Purugganan, Zoé Joly‐Lopez · 2025 · Genome biology
- Emerging Role of Enhancer RNAs as Potential Diagnostic and Prognostic Biomarkers in CancerSomayeh Panahi-Moghadam, Shokoufeh Hassani, Shirin Farivar, Faezeh Vakhshiteh · 2022 · Non-Coding RNA
- Non-coding RNAsMarta Elżbieta Kasprzyk, Marta Kazimierska, Weronika Sura, Agnieszka Dzikiewicz‐Krawczyk, Marta Podralska · 2023 · Elsevier eBooks
- Mutant FOXO1 controls an oncogenic network via enhancer accessibilityHillary M. Layden, Jacob D. Ellis, Monica L. Bomber, Luke N. Bartlett, Scott W. Hiebert, Kristy R. Stengel · 2024 · Cell Genomics
- Embryonic Stem Cells: A Perfect Tool for Studying Mammalian Transcriptional EnhancersSridhar Rao · 2012 · Journal of Stem Cell Research & Therapy
- The Estrogen-Regulated Transcriptome: Rapid, Robust, Extensive, and TransientYasmin M. Vasquez, W. Lee Kraus · 2018 · Cancer drug discovery and develogment/Cancer drug discovery and development
- Prognostic signatures and potential pathogenesis of eRNAs‐related genes in colon adenocarcinomaHao Rong, Yanguo Li, Shiyun Hu, Liuying Gao, Tianfei Yi, Yangyang Xie, Ping Cai, Jianjiong Li, Xiaoyu Dai, Meng Ye et al. · 2021 · Molecular Carcinogenesis
- PINTing for p53Ramin Shiekhattar · 2013 · Genome biology
- Exploiting the hypoxia sensitive non-coding genome for organ-specific physiologic reprogrammingCorinne Bischof, Jaya Krishnan · 2016 · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research
- An Epigenetic Spin to ALS and FTDMark Ebbert, Rebecca J. Lank, Véronique Belzil · 2018 · Advances in neurobiology
- The Genome in a Three-Dimensional Context: Deciphering the Contribution of Noncoding Mutations at Enhancers to Blood CancerLlorenç Rovirosa, Alberto Ramos-Morales, Biola M. Javierre · 2020 · Frontiers in Immunology
- Androgen ReceptorPäivi Sutinen, Marjo Malinen, Jorma J. Palvimo · 2017 · Endocrinology
- Dysregulation of Long Non-coding RNAs in Human DiseaseNian-Wei Lin, Tariq M. Rana · 2013 · Springer eBooks
- Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seqLaura V. Glaser, Mara Steiger, Alisa Fuchs, Alena van Bömmel, Edda Einfeldt, Ho-Ryun Chung, Martin Vingron, Sebastiaan H. Meijsing · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- Genomic codes governing enhancer RNA fateChi Wai Yip, Callum Parr, Hazuki Takahashi, Kayoko Yasuzawa, Matthew N. Z. Valentine, Hiromi Nishiyori-Sueki, Camilla Ugolini, Valeria Ranzani, Mitsuyoshi Murata, Masaki Kato et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Multiple human enhancer RNAs contain long translated open reading framesPavel A. Vlasov, Koichi Ogami, Elizabeth Valenzuela, Risa Karakida Kawaguchi, Marko Jovanovic, James L. Manley · 2025 · Genes & Development
- The untold story between enhancers and skeletal muscle developmentYongsheng Zhang, Dan Lü, Yu-wen LIU, Guoqiang Yi, Zhonglin Tang · 2020 · Journal of Integrative Agriculture
- A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAsDinesh Babu Uthaya Kumar, Marina Yurieva, Jessica D. S. Grassmann, Lina Kozhaya, Caleb D. McBride, Derya Unutmaz, Adam Williams · 2023 · Frontiers in Molecular Biosciences
- Current progress and future perspective of super-enhancers: a viable and effective bridge between the transcriptional apparatus and diseaseRan Wang, Aiying Li, Zongran Pang · 2025 · Frontiers in Genetics
- From Junk DNA to Genomic Treasure: Impacts of Transposable Element DNA , RNA , and Protein in Mammalian Development and DiseaseTen D. Li, Katelyn Toohill, Andrew J. Modzelewski · 2025 · Wiley Interdisciplinary Reviews - RNA
- Enhancer regulation in cancer: from epigenetics to m6A RNA modificationArathy Vasukutty, Poshan Yugal Bhattarai, Hong Seok Choi · 2025 · Archives of Pharmacal Research
- The effect of transcription on enhancer activity in Drosophila melanogasterMaksim Erokhin, A. I. Davydova, Д. В. Ломаев, Pavel G Georgiev, Darya Chetverina · 2016 · Russian Journal of Genetics
- Enhancer RNA IRS2e is essential for IRS2 expression and the oncogenic properties in oral squamous cell carcinomaLingyan Yan, Jiayun Wang, Jihua Guo, Rong Jia · 2023 · Carcinogenesis
- Genome-wide analysis of transcription-coupled repair reveals novel transcription events in Caenorhabditis elegansCansu Köse, Laura A. Lindsey‐Boltz, Aziz Sancar, Yuchao Jiang · 2024 · PLoS Genetics
- Feedback regulation of retinaldehyde reductase DHRS3 , a critical determinant of retinoic acid homeostasisParisa Varshosaz, Catherine O'Connor, Alexander R. Moise · 2024 · FEBS Letters
- Possible role of human ribonuclease dicer in the regulation of R loopsKlaudia Wójcik, Paulina Krzemińska, Anna Kurzyńska‐Kokorniak · 2025 · FEBS Open Bio
- A Super Enhancer-Derived Enhancer RNA Acts Together with CTCF/Cohesin in Trans to Regulate ErythropoiesisBingning Xie, Ann Dean · 2025 · Genes
- Shaping the nebulous enhancer in the era of high-throughput assays and genome editingEdwin Yu-Kiu Ho, Qin Cao, Mengting Gu, Ricky Wai-Lun Chan, Qiong Wu, Mark Gerstein, Kevin Yuk-Lap Yip · 2019 · Briefings in Bioinformatics
- The Yin and Yang of enhancer‐like RNAsRamin Shiekhattar · 2013 · The EMBO Journal
- Revisiting models of enhancer–promoter communication in gene regulationGilad Barshad, Charles G. Danko · 2025 · Genome Research
- The epipliancy journey: Tumor initiation at the mercy of identity crisis and epigenetic driftRahma Benhassoun, Anne‐Pierre Morel, Victoria Jacquot, Alain Puisieux, Maria Ouzounova · 2025 · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer
- Role of eRNAs in Cardiovascular DiseasesYuqing Li, Chao Song, Jian Cui, Xiangyu Fei, Xiaoyong Lei, Huifang Tang · 2025 · Current Cardiology Reviews
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq)Mackenzie Meyer, Oluwadamilola Olanrewaju, Patricia Montilla‐Perez, Anna L. McDonald, Eva M. Rickard, Francesca Telese, Christopher W. Benner, Marina I. Savenkova, Sascha H. C. Duttke · 2026 · Nature Protocols
- Transcriptional interference revisitedMartin Fischer, Steve Hoffmann · 2026 · Nature Genetics
- Epigenetic Regulation of Macrophage PolarizationAkhil Maheshwari, Srijan Singh · 2025 · Newborn
- Enhancer Elements in Plants: Genomic Context and Biological FunctionsHongwoo Lee, Dong Hyeon Kang, Pil Joon Seo · 2025 · Journal of Plant Biology
- JUND plays a genome-wide role in the quiescent to contractile switch in the pregnant human myometriumNawrah Khader, Anna Dorogin, Oksana P. Shynlova, Jennifer A. Mitchell · 2025 · PLoS Genetics
- Nucleosomal packaging of eukaryotic DNA and regulation of transcriptionArkadiy K. Golov, Sergey V. Razin, Alexey A. Gavrilov · 2014 · Biopolymers and Cell
- Exploring the role of eRNA in regulating gene expressionHeli Tan, Tuoqi Liu, Tianshou Zhou · 2021 · Mathematical Biosciences & Engineering
- Connectome and regulatory hubs of CAGE highly active enhancersMewen Briend, Anne Rufiange, Louis-Hippolyte Minvielle Moncla, Samuel Mathieu, Yohan Bossé, Patrick Mathieu · 2023 · Scientific Reports
- Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafishLe A. Trinh, Vanessa Chong-Morrison, Tatjana Sauka‐Spengler · 2018 · Methods
- Chromatin Regulation by Long Non-coding RNAsDaniel C. Factor, Paul J. Tesar, Ahmad Mohammad Khalil · 2013 · Springer eBooks
- Molecular analysis of RNA induced by enhancer in Drosophila cells carrying reporter genetic constructsDaria M. Fedoseeva, Olga V. Kretova, Nickolai A. Tchurikov · 2010 · Doklady Biochemistry and Biophysics
- RNA-mediated regulation of chromatin structuresYoungtae Kwon, Yun Doo Chung · 2020 · Genes & Genomics