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Non-coding RNA

There is increasing evidence that non-coding RNAs play a major role in epigenetic regulation. This article collection focuses on understanding the mechanisms of non-coding RNA, describing insights into the biogenesis and activity of non-coding RNAs, their interaction with chromatin, and novel methods for analysis and manipulation of RNA-mediated regulation. We welcome further research submissions on these topics. Please submit your manuscript through our website and indicate in your covering letter that you would like it to be considered for the series, or alternatively, send a pre-submission enquiry to editorial@epigeneticsandchromatin.com.

  1. Content type: Research

    A Xist RNA decorated Barr body is the structural hallmark of the compacted inactive X territory in female mammals. Using super-resolution three-dimensional structured illumination microscopy (3D-SIM) and quant...

    Authors: Daniel Smeets, Yolanda Markaki, Volker J Schmid, Felix Kraus, Anna Tattermusch, Andrea Cerase, Michael Sterr, Susanne Fiedler, Justin Demmerle, Jens Popken, Heinrich Leonhardt, Neil Brockdorff, Thomas Cremer, Lothar Schermelleh and Marion Cremer

    Citation: Epigenetics & Chromatin 2014 7:8

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  2. Content type: Research

    Regulation of chromatin structure involves deposition of selective histone variants into nucleosome arrays. Numerous histone H3 variants become differentially expressed by individual nanochromosomes in the cou...

    Authors: Sakeh Forcob, Aneta Bulic, Franziska Jönsson, Hans J Lipps and Jan Postberg

    Citation: Epigenetics & Chromatin 2014 7:4

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  3. Content type: Research

    The establishment of facultative heterochromatin by X-chromosome inactivation requires the long non-coding RNA XIST/Xist. However, the molecular mechanism by which the RNA achieves chromosome-wide gene silenci...

    Authors: Jakub Minks, Sarah EL Baldry, Christine Yang, Allison M Cotton and Carolyn J Brown

    Citation: Epigenetics & Chromatin 2013 6:23

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  4. Content type: Review

    The packaging of eukaryotic DNA into nucleosomal arrays permits cells to tightly regulate and fine-tune gene expression. The ordered disassembly and reassembly of these nucleosomes allows RNA polymerase II (RN...

    Authors: Swaminathan Venkatesh, Jerry L Workman and Michaela Smolle

    Citation: Epigenetics & Chromatin 2013 6:16

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  5. Content type: Methods

    DNA methylation ensures genome integrity and regulates gene expression indiverse eukaryotes. In Arabidopsis, methylation occurs in threesequence contexts: CG, CHG and CHH. The initial establishment of DNAmethylat...

    Authors: Thanh Theresa Dinh, Michael O’Leary, So Youn Won, Shengben Li, Lorena Arroyo, Xigang Liu, Andrew Defries, Binglian Zheng, Sean R Cutler and Xuemei Chen

    Citation: Silence 2013 4:1

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  6. Content type: Research

    In fission yeast, centromeric heterochromatin is necessary for the fidelity of chromosome segregation. Propagation of heterochromatin in dividing cells requires RNA interference (RNAi) and transcription of cen...

    Authors: Michael Thorsen, Heidi Hansen, Michela Venturi, Steen Holmberg and Genevieve Thon

    Citation: Epigenetics & Chromatin 2012 5:19

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  7. Content type: Research

    The processing of a microRNA results in an intermediate duplex of two potential mature products that derive from the two arms (5′ and 3′) of the precursor hairpin. It is often suggested that one of the sequenc...

    Authors: Antonio Marco, Jamie I MacPherson, Matthew Ronshaugen and Sam Griffiths-Jones

    Citation: Silence 2012 3:8

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  8. Content type: Methods

    Cytosine methylation is an important chromatin modification that maintains genome integrity and regulates gene expression through transcriptional gene silencing. Major players in de novo methylation guided by siR...

    Authors: So Youn Won, Shengben Li, Binglian Zheng, Yuanyuan Zhao, Dongming Li, Xin Zhao, Huilan Yi, Lei Gao, Thanh Theresa Dinh and Xuemei Chen

    Citation: Silence 2012 3:6

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  9. Content type: Review

    To reduce the losses caused by plant pathogens, plant biologists have adopted numerous methods to engineer resistant plants. Among them, RNA silencing-based resistance has been a powerful tool that has been us...

    Authors: Cheng-Guo Duan, Chun-Han Wang and Hui-Shan Guo

    Citation: Silence 2012 3:5

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  10. Content type: Short report

    The use of nucleic acid-modifying enzymes has driven the rapid advancement in molecular biology. Understanding their function is important for modifying or improving their activity. However, functional analysi...

    Authors: Karim Sorefan, Helio Pais, Adam E Hall, Ana Kozomara, Sam Griffiths-Jones, Vincent Moulton and Tamas Dalmay

    Citation: Silence 2012 3:4

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  11. Content type: Research

    MicroRNA (miRNA) target genes tend to have relatively long and conserved 3' untranslated regions (UTRs), but to what degree these characteristics contribute to miRNA targeting is poorly understood. Different h...

    Authors: Takaya Saito and Pål Sætrom

    Citation: Silence 2012 3:3

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  12. Content type: Review

    MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in many developmental and cellular processes. Moreover, there is now ample evidence that perturbations in the lev...

    Authors: Jan Stenvang, Andreas Petri, Morten Lindow, Susanna Obad and Sakari Kauppinen

    Citation: Silence 2012 3:1

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  13. Content type: Research

    Gene regulation in eukaryotes is a complex process entailing the establishment of transcriptionally silent chromatin domains interspersed with regions of active transcription. Imprinted domains consist of clus...

    Authors: Lisa Korostowski, Anjali Raval, Gillian Breuer and Nora Engel

    Citation: Epigenetics & Chromatin 2011 4:21

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  14. Content type: Research

    MicroRNAs, post-transcriptional regulators of eukaryotic gene expression, are implicated in host defense against pathogens. Viruses and bacteria have evolved strategies that suppress microRNA functions, result...

    Authors: Cédric Belair, Jessica Baud, Sandrine Chabas, Cynthia M Sharma, Jörg Vogel, Cathy Staedel and Fabien Darfeuille

    Citation: Silence 2011 2:7

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  15. Content type: Research

    Expression of Xist, the master regulator of X chromosome inactivation, is extinguished in pluripotent cells, a process that has been linked to programmed X chromosome reactivation. The key pluripotency transcript...

    Authors: Tatyana B Nesterova, Claire E Senner, Janina Schneider, Tilly Alcayna-Stevens, Anna Tattermusch, Myriam Hemberger and Neil Brockdorff

    Citation: Epigenetics & Chromatin 2011 4:17

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  16. Content type: Meeting report

    The study of miRNAs and other noncoding RNAs has revolutionised our understanding of gene expression regulation during cancer development and progression, creating one of the fastest-growing research fields in...

    Authors: Ohad Yogev and Dimitris Lagos

    Citation: Silence 2011 2:6

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  17. Content type: Research

    RNA interference (RNAi) screens have been used to identify novel components of signal-transduction pathways in a variety of organisms. We performed a small interfering (si)RNA screen for novel members of the t...

    Authors: Nikolaus Schultz, Dina R Marenstein, Dino A De Angelis, Wei-Qing Wang, Sven Nelander, Anders Jacobsen, Debora S Marks, Joan Massagué and Chris Sander

    Citation: Silence 2011 2:3

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  18. Content type: Review

    Prior to the advent of new, deep sequencing methods, small RNA (sRNA) discovery was dependent on Sanger sequencing, which was time-consuming and limited knowledge to only the most abundant sRNA. The innovation...

    Authors: Kevin P McCormick, Matthew R Willmann and Blake C Meyers

    Citation: Silence 2011 2:2

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  19. Content type: Research

    A current challenge of microRNA (miRNA) research is the identification of biologically relevant miRNA:target gene relationships. In plants, high miRNA:target gene complementarity has enabled accurate target pr...

    Authors: Robert S Allen, Junyan Li, Maria M Alonso-Peral, Rosemary G White, Frank Gubler and Anthony A Millar

    Citation: Silence 2010 1:18

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  20. Content type: Research

    Micro (mi)RNAs comprise a large family of small non-coding RNAs that are thought to regulate a large fraction of protein-coding genes. Generally, miRNAs downregulate messenger (m)RNA expression by binding to t...

    Authors: Limor Leibovich, Yael Mandel-Gutfreund and Zohar Yakhini

    Citation: Silence 2010 1:17

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  21. Content type: Methodology

    While increasing numbers of small interfering RNA (siRNA) therapeutics enter into clinical trials, the quantification of siRNA from clinical samples for pharmacokinetic studies remains a challenge. This challe...

    Authors: Yosef Landesman, Nenad Svrzikapa, Armand Cognetta III, Xuemei Zhang, Brian R Bettencourt, Satya Kuchimanchi, Keri Dufault, Sarfraz Shaikh, Maple Gioia, Akin Akinc, Renta Hutabarat and Rachel Meyers

    Citation: Silence 2010 1:16

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  22. Content type: Review

    Fire and Mello initiated the current explosion of interest in RNA interference (RNAi) biology with their seminal work in Caenorhabditis elegans. These observations were closely followed by the demonstration of RN...

    Authors: Akshay K Vaishnaw, Jared Gollob, Christina Gamba-Vitalo, Renta Hutabarat, Dinah Sah, Rachel Meyers, Tony de Fougerolles and John Maraganore

    Citation: Silence 2010 1:14

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  23. Content type: Meeting report

    Earlier this year plant scientists met in Santa Fe, New Mexico at the Keystone Symposium "RNA Silencing Mechanisms in Plants". Sessions included small RNA biogenesis and signalling, development and stress resp...

    Authors: Rebecca A Mosher, Mathew G Lewsey and Padubidri V Shivaprasad

    Citation: Silence 2010 1:13

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  24. Content type: Research

    X chromosome inactivation, the mechanism used by mammals to equalise dosage of X-linked genes in XX females relative to XY males, is triggered by chromosome-wide localisation of a cis-acting non-coding RNA, Xist....

    Authors: Y Amy Tang, Derek Huntley, Giovanni Montana, Andrea Cerase, Tatyana B Nesterova and Neil Brockdorff

    Citation: Epigenetics & Chromatin 2010 3:10

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  25. Content type: Commentary

    Micro(mi)RNAs regulate gene expression by what are believed to be related but separate mechanistic processes. The relative contribution that each process plays, their mechanistic overlap, and the degree by whi...

    Authors: Shuo Gu and Mark A Kay

    Citation: Silence 2010 1:11

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  26. Content type: Research

    Micro(mi)RNAs regulate gene expression through translational attenuation and messenger (m)RNA degradation, and are associated with differentiation, homeostasis and disease. Natural miRNA target recognition is ...

    Authors: Barbara Robertson, Andrew B Dalby, Jon Karpilow, Anastasia Khvorova, Devin Leake and Annaleen Vermeulen

    Citation: Silence 2010 1:10

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  27. Content type: Short report

    Breast milk is a complex liquid that provides nutrition to the infant and facilitates the maturation of the infant's immune system. Recent studies indicated that microRNA (miRNA) exists in human body fluid. Be...

    Authors: Nobuyoshi Kosaka, Hirohisa Izumi, Kazunori Sekine and Takahiro Ochiya

    Citation: Silence 2010 1:7

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  28. Content type: Research

    MicroRNAs are a class of small noncoding RNAs that are abnormally expressed in different cancer cells. Molecular signature of miRNAs in different malignancies suggests that these are not only actively involved...

    Authors: Sanghamitra Bandyopadhyay, Ramkrishna Mitra, Ujjwal Maulik and Michael Q Zhang

    Citation: Silence 2010 1:6

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  29. Content type: Review

    This potent ability of small interfering (si)RNAs to inhibit the expression of complementary RNA transcripts is being exploited as a new class of therapeutics for a variety of diseases. However, the efficient ...

    Authors: Jiehua Zhou and John J Rossi

    Citation: Silence 2010 1:4

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  30. Content type: Research

    Drosha is a nuclear RNase III enzyme that initiates processing of regulatory microRNA. Together with partner protein DiGeorge syndrome critical region 8 (DGCR8), it forms the Microprocessor complex, which clea...

    Authors: Geoffrey A Mueller, Matthew T Miller, Eugene F DeRose, Mahua Ghosh, Robert E London and Traci M Tanaka Hall

    Citation: Silence 2010 1:2

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  31. Content type: Review

    Argonaute is the principal protein component of the mechanisms of RNA silencing, providing anchor sites for the small guide RNA strand and the 'slicer' activity for cleavage of target mRNAs or short passenger ...

    Authors: James S Parker

    Citation: Silence 2010 1:3

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  32. Content type: Research

    Delimiting distinct chromatin domains is essential for temporal and spatial regulation of gene expression. Within the X-inactivation centre region (Xic), the Xist locus, which triggers X-inactivation, is juxtapos...

    Authors: Pablo Navarro, Sophie Chantalat, Mario Foglio, Corinne Chureau, Sébastien Vigneau, Philippe Clerc, Philip Avner and Claire Rougeulle

    Citation: Epigenetics & Chromatin 2009 2:8

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  33. Content type: Research

    X chromosome inactivation is the mechanism used in mammals to achieve dosage compensation of X-linked genes in XX females relative to XY males. Chromosome silencing is triggered in cis by expression of the non-co...

    Authors: Tatyana B Nesterova, Bilyana C Popova, Bradley S Cobb, Sara Norton, Claire E Senner, Y Amy Tang, Thomas Spruce, Tristan A Rodriguez, Takashi Sado, Matthias Merkenschlager and Neil Brockdorff

    Citation: Epigenetics & Chromatin 2008 1:2

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