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Regulatory elements

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Guest Editors: Geoffrey Faulkner and Uwe Ohler

Our understanding of gene regulatory elements and their function is being transformed by  new molecular and computational approaches that provide insights into the 3D structure and chromatin environment involved in enhancer-promoter interactions and their functions. Even further,  the availability of datasets from the ENCODE consortium and others have made it easier to uncover new biological findings attributed to these elements. Other avenues of research are exploring the impact of variation on regulatory function and the evolution of regulatory elements. Genome Biology  highlights these advances in the understanding of gene regulatory elements with a special issue showcasing important work in this area. 


  1. Revealing the gene targets of distal regulatory elements is challenging yet critical for interpreting regulome data. Experiment-derived enhancer-gene links are restricted to a small set of enhancers and/or cel...

    Authors: Tingting Qin, Christopher Lee, Shiting Li, Raymond G. Cavalcante, Peter Orchard, Heming Yao, Hanrui Zhang, Shuze Wang, Snehal Patil, Alan P. Boyle and Maureen A. Sartor
    Citation: Genome Biology 2022 23:105
    Content type: Research Published on:

  2. Circadian (daily) timekeeping is essential to the survival of many organisms. An integral part of all circadian timekeeping systems is negative feedback between an activator and repressor. However, the role of...

    Authors: Jonathan Tyler, Yining Lu, Jay Dunlap and Daniel B. Forger
    Citation: Genome Biology 2022 23:17
    Content type: Research Published on:

  3. Genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are known to preferentially co-locate to active regulatory elements in tissues and cell types relevant to disease aetiology. Further ...

    Authors: Charles E. Breeze, Eric Haugen, Alex Reynolds, Andrew Teschendorff, Jenny van Dongen, Qing Lan, Nathaniel Rothman, Guillaume Bourque, Ian Dunham, Stephan Beck, John Stamatoyannopoulos, Nora Franceschini and Sonja I. Berndt
    Citation: Genome Biology 2022 23:13
    Content type: Research Published on:

  5. Understanding the contributions of transcription factor DNA binding sites to transcriptional enhancers is a significant challenge. We developed Quantitative enhancer-FACS-Seq for highly parallel quantification...

    Authors: Colin T. Waters, Stephen S. Gisselbrecht, Yuliya A. Sytnikova, Tiziana M. Cafarelli, David E. Hill and Martha L. Bulyk
    Citation: Genome Biology 2021 22:348
    Content type: Method Published on:

  6. Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes f...

    Authors: Hieu T. Nim, Louis Dang, Harshini Thiyagarajah, Daniel Bakopoulos, Michael See, Natalie Charitakis, Tennille Sibbritt, Michael P. Eichenlaub, Stuart K. Archer, Nicolas Fossat, Richard E. Burke, Patrick P. L. Tam, Coral G. Warr, Travis K. Johnson and Mirana Ramialison
    Citation: Genome Biology 2021 22:335
    Content type: Research Published on:

  7. Promoters are genomic regions where the transcription machinery binds to initiate the transcription of specific genes. Computational tools for identifying bacterial promoters have been around for decades. Howe...

    Authors: Ruben Chevez-Guardado and Lourdes Peña-Castillo
    Citation: Genome Biology 2021 22:318
    Content type: Method Published on:

  8. Pancreatic ductal adenocarcinoma initiation is most frequently caused by Kras mutations.

    Authors: Angela J. Mathison, Romica Kerketta, Thiago Milech de Assuncao, Elise Leverence, Atefeh Zeighami, Guillermo Urrutia, Timothy J. Stodola, Marina Pasca di Magliano, Juan L. Iovanna, Michael T. Zimmermann, Gwen Lomberk and Raul Urrutia
    Citation: Genome Biology 2021 22:289
    Content type: Research Published on:

  10. Deep learning has proven to be a powerful technique for transcription factor (TF) binding prediction but requires large training datasets. Transfer learning can reduce the amount of data required for deep lear...

    Authors: Gherman Novakovsky, Manu Saraswat, Oriol Fornes, Sara Mostafavi and Wyeth W. Wasserman
    Citation: Genome Biology 2021 22:280
    Content type: Research Published on:

  11. Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions a...

    Authors: Pâmela A. Alexandre, Marina Naval-Sánchez, Moira Menzies, Loan T. Nguyen, Laercio R. Porto-Neto, Marina R. S. Fortes and Antonio Reverter
    Citation: Genome Biology 2021 22:273
    Content type: Research Published on:

  12. Super-enhancers are clusters of enhancer elements that play critical roles in the maintenance of cell identity. Current investigations on super-enhancers are centered on the established ones in static cell typ...

    Authors: Yan Kai, Bin E. Li, Ming Zhu, Grace Y. Li, Fei Chen, Yingli Han, Hye Ji Cha, Stuart H. Orkin, Wenqing Cai, Jialiang Huang and Guo-Cheng Yuan
    Citation: Genome Biology 2021 22:269
    Content type: Research Published on:

  13. Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unk...

    Authors: Anna Ullastres, Miriam Merenciano and Josefa González
    Citation: Genome Biology 2021 22:265
    Content type: Research Published on:

  14. We develop a novel computational method, NucHMM, to identify functional nucleosome states associated with cell type-specific combinatorial histone marks and nucleosome organization features such as phasing, sp...

    Authors: Kun Fang, Tianbao Li, Yufei Huang and Victor X. Jin
    Citation: Genome Biology 2021 22:250
    Content type: Method Published on:

  15. The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studi...

    Authors: Beisi Xu, Hong Wang, Shaela Wright, Judith Hyle, Yang Zhang, Ying Shao, Mingming Niu, Yiping Fan, Wojciech Rosikiewicz, Mohamed Nadhir Djekidel, Junmin Peng, Rui Lu and Chunliang Li
    Citation: Genome Biology 2021 22:244
    Content type: Research Published on:

  16. A specific 3-dimensional intrachromosomal architecture of core stem cell factor genes is required to reprogram a somatic cell into pluripotency. As little is known about the epigenetic readers that orchestrate...

    Authors: Zhonghua Du, Xue Wen, Yichen Wang, Lin Jia, Shilin Zhang, Yudi Liu, Lei Zhou, Hui Li, Wang Yang, Cong Wang, Jingcheng Chen, Yajing Hao, Daniela Salgado Figueroa, Huiling Chen, Dan Li, Naifei Chen…
    Citation: Genome Biology 2021 22:233
    Content type: Research Published on:

    The Author Correction to this article has been published in Genome Biology 2021 22:272

  18. Transposable elements are increasingly recognized as a source of cis-regulatory variation. Previous studies have revealed that transposons are often bound by transcription factors and some have been co-opted into...

    Authors: Julius Judd, Hayley Sanderson and Cédric Feschotte
    Citation: Genome Biology 2021 22:193
    Content type: Research Published on:

  19. Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still unde...

    Authors: Mayra Furlan-Magaril, Masami Ando-Kuri, Rodrigo G. Arzate-Mejía, Jörg Morf, Jonathan Cairns, Abraham Román-Figueroa, Luis Tenorio-Hernández, A. César Poot-Hernández, Simon Andrews, Csilla Várnai, Boo Virk, Steven W. Wingett and Peter Fraser
    Citation: Genome Biology 2021 22:162
    Content type: Research Published on:

  20. Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there ...

    Authors: Chia-Chi Flora Huang, Shreyas Lingadahalli, Tunc Morova, Dogancan Ozturan, Eugene Hu, Ivan Pak Lok Yu, Simon Linder, Marlous Hoogstraat, Suzan Stelloo, Funda Sar, Henk van der Poel, Umut Berkay Altintas, Mohammadali Saffarzadeh, Stephane Le Bihan, Brian McConeghy, Bengul Gokbayrak…
    Citation: Genome Biology 2021 22:149
    Content type: Research Published on:

  21. Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio cDNA sequencing of normal hu...

    Authors: Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner and Seth W. Cheetham
    Citation: Genome Biology 2021 22:146
    Content type: Short Report Published on:

  22. Cellular senescence is a permanent state of replicative arrest defined by a specific pattern of gene expression. The epigenome in senescent cells is sculptured in order to sustain the new transcriptional requi...

    Authors: Eros Di Giorgio, Harikrishnareddy Paluvai, Emiliano Dalla, Liliana Ranzino, Alessandra Renzini, Viviana Moresi, Martina Minisini, Raffaella Picco and Claudio Brancolini
    Citation: Genome Biology 2021 22:129
    Content type: Research Published on:

  24. The binding of transcription factors (TF) to genomic targets is critical in the regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely implicated in TF recruitment, but many qu...

    Authors: Jochen Spiegel, Sergio Martínez Cuesta, Santosh Adhikari, Robert Hänsel-Hertsch, David Tannahill and Shankar Balasubramanian
    Citation: Genome Biology 2021 22:117
    Content type: Research Published on:

  25. Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs ar...

    Authors: Anil Panigrahi and Bert W. O’Malley
    Citation: Genome Biology 2021 22:108
    Content type: Review Published on:

  26. Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address ...

    Authors: Gareth B. Gillard, Lars Grønvold, Line L. Røsæg, Matilde Mengkrog Holen, Øystein Monsen, Ben F. Koop, Eric B. Rondeau, Manu Kumar Gundappa, John Mendoza, Daniel J. Macqueen, Rori V. Rohlfs, Simen R. Sandve and Torgeir R. Hvidsten
    Citation: Genome Biology 2021 22:103
    Content type: Research Published on:

  27. Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3′ untranslated regions (3′UTRs). We have recently shown...

    Authors: Oliver Daniel Schwich, Nicole Blümel, Mario Keller, Marius Wegener, Samarth Thonta Setty, Melinda Elaine Brunstein, Ina Poser, Igor Ruiz De Los Mozos, Beatrix Suess, Christian Münch, François McNicoll, Kathi Zarnack and Michaela Müller-McNicoll
    Citation: Genome Biology 2021 22:82
    Content type: Research Published on: