Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008;40(12):1413–5.
Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S. Increase of functional diversity by alternative splicing. Trends Genet. 2003;19(3):124–8.
Weyn-Vanhentenryck SM, Feng H, Ustianenko D, Duffié R, Yan Q, Jacko M, et al. Precise temporal regulation of alternative splicing during neural development. Nat Commun. 2018;9:2189.
Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biol. 2004;5(10):R74.
Noh SJ, Lee K, Paik H, Hur CG. TISA: Tissue-specific Alternative Splicing in Human and Mouse Genes. DNA Res. 2006;13(5):229–43.
Planells B, Gómez-Redondo I, Pericuesta E, Lonergan P, Gutiérrez-Adán A. Differential isoform expression and alternative splicing in sex determination in mice. BMC Genomics. 2019;20:202.
Gibilisco L, Zhou Q, Mahajan S, Bachtrog D. Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages. PLoS Genet. 2016;12(12):e1006464.
Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen SE, Robinson GE, et al. DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci U S A. 2012;109(13):4968–73.
Wang Y, Wang Z. Systematical identification of splicing regulatory cis-elements and cognate trans-factors. Methods. 2014;65(3):350–8.
Holste D, Ohler U. Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events. PLoS Comput Biol. 2008;4(1):e21.
Kadener S, Fededa JP, Rosbash M, Kornblihtt AR. Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. Proc Natl Acad Sci U S A. 2002;99(12):8185–90.
Esumi S, Kakazu N, Taguchi Y, Hirayama T, Sasaki A, Hirabayashi T, et al. Monoallelic yet combinatorial expression of variable exons of the protocadherin-alpha gene cluster in single neurons. Nat Genet. 2005;37(2):171–6.
Reyes A, Huber W. Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. Nucleic Acids Res. 2018;46(2):582–92.
Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G. Enhancers: five essential questions. Nat Rev Genet. 2013;14(4):288–95.
Lee K, Hsiung CCS, Huang P, Raj A, Blobel GA. Dynamic enhancer–gene body contacts during transcription elongation. Genes Dev. 2015;29(20):2217.
Schoenfelder S, Fraser P. Long-range enhancer-promoter contacts in gene expression control. Nat Rev Genet. 2019;20(8):437–55.
Ong CT, Corces VG. CTCF: An Architectural Protein Bridging Genome Topology and Function. Nat Rev Genet. 2014;15(4):234–6.
Buecker C, Wysocka J. Enhancers as information integration hubs in development: lessons from genomics. Trends Genet. 2012;28(6):276–84.
Gao T, He B, Liu S, Zhu H, Tan K, Qian J. EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types. Bioinformatics. 2016;32(23):3543–51.
Leinonen R, Sugawara H. The Sequence Read Archive. Nucleic Acids Res. 2011;39(Suppl 1):D19-21.
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37(8):907–15.
Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010;465(7295):182–7.
Podsiadło A, Wrzesień M, Paja W, Rudnicki W, Wilczyński B. Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data. BMC Syst Biol. 2013;7(Suppl 6):S16.
Whalen S, Truty RM, Pollard KS. Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. Nat Genet. 2016;48(5):488–96.
Shiau CK, Huang JH, Tsai HK. CATANA: a tool for generating comprehensive annotations of alternative transcript events. Bioinformatics. 2019;35(8):1414–5.
Katz Y, Wang ET, Airoldi EM, Burge CB. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods. 2010;7(12):1009–15.
Venables JP, Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Koh C, et al. Identification of alternative splicing markers for breast cancer. Cancer Res. 2008;68(22):9525–31.
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, et al. A map of the cis-regulatory sequences in the mouse genome. Nature. 2012;488:116–20.
Fishilevich S, Nudel R, Rappaport N, Hadar R, Plaschkes I, Stein TI, et al. GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. Database. 2017;2017:bax028.
Bult CJ, Blake JA, Smith CL, Kadin JA, Richardson JE. the Mouse Genome Database Group. Mouse Genome Database (MGD) 2019. 2019. Nucleic Acids Res. 2019;47(D1):D801-6.
Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics. 2014;30(7):1006–7.
UCSC chain file from hg19 (GRCh37) to mm9 (GRCm37). http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToMm9.over.chain.gz. Accessed 21 Sep 2020.
Manduchi E, Williams SM, Chesi A, Johnson ME, Wells AD, Grant SFA, et al. Leveraging epigenomics and contactomics data to investigate SNP pairs in GWAS. Hum Genet. 2018;137:413–5.
Vilar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, et al. Enhancer evolution across 20 mammalian species. Cell. 2015;160(3):554–66.
Flores MA, Ovcharenko I. Enhancer reprogramming in mammalian genomes. BMC Bioinformatics. 2018;19:316.
Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, et al. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005;15(7):901–13.
Bailey TL. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics. 2011;27(12):1653–9.
Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. Quantifying similarity between motifs. Genome Biol. 2007;8(2):R24.
Fornes O, Castro-Mondragon JA, Khan A, Lee RVD, Zhang X, Richmond PA, et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2020;48(D1):D87-92.
Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, et al. Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes. Cell. 2013;153(2):307–19.
Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-Andre V, Sigova AA, et al. Transcriptional super-enhancers connected to cell identity and disease. Cell. 2013;155(4): https://doi.org/10.1016/j.cell.2013.09.053.
Moorthy SD, Davidson S, Shchuka VM, Singh G, Malek-Gilani N, Langroudi L, et al. Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes. Genome Res. 2017;27(2):246–58.
Khan A, Zhang X. dbSUPER: a database of super-enhancers in mouse and human genome. Nucleic Acids Res. 2016;44(D1):D164–71.
Jiang Y, Qian F, Bai X, Liu Y, Wang Q, Ai B, et al. SEdb: a comprehensive human super-enhancer database. Nucleic Acids Res. 2019;47(D1):D235–43.
Chen C, Zhou D, Gu Y, Wang C, Zhang M, Lin X, et al. SEA version 3.0: a comprehensive extension and update of the Super-Enhancer archive. Nucleic Acids Res. 2020;48(D1):D198-203.
Nakagaki-Silva EE, Gooding C, Llorian M, Jacob AG, Richards F, Buckroyd A, et al. Identification of RBPMS as a mammalian smooth muscle master splicing regulator via proximity of its gene with super-enhancers. eLife. 2019;8:e46327.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.