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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. 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

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  2. 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

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  3. 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

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  4. 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

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  5. 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

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  6. 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

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

  7. 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

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  8. 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

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  9. 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

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  10. 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

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  11. 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

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  12. 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

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  13. 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

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  14. 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

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  15. 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

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