Special Issue "Gene Silencing"
A special issue of Genes (ISSN 2073-4425).
Deadline for manuscript submissions: closed (15 May 2013)
Dr. Célia Baroux
Institute of Plant Biology, Basel-Zürich Plant Science Center, University of Zürich, Zollikerstr. 107, CH-8008 Zürich, Switzerland
Interests: epigenetics; cytogenetics; chromatin dynamics; plant development
The development of multicellular organisms and the operation of complex cellular function requires not only perfect orchestration of gene expression but also a precise spatial and temporal control of gene silencing. Gene silencing mechanisms are diverse and exquisitely refined. These mechanisms operate at the transcriptional and post-transcriptional levels, or during meiosis; they use a variety of cellular components such as cis-DNA elements, chromatin modifications, small and non-coding RNAs and specific protein factors responsible for the initiation, operation and readout of silencing.
Common scenarios of gene silencing are found in plants, insects, worms and mammals. Yet each organism reveal specific adaptations and regulations. Those are important to elucidate, not only for philosophical purposes (with the meaning of studying and understanding general and fundamental problems) but also for medical or biotechnological applications.
This Special issue of "Genes" welcomes reviews and original papers covering recent research in gene silencing at the mechanistic and regulation levels in different organisms, but also research bridging gene silencing and cellular function, development or biotechnological applications.
Dr. Célia Baroux
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed Open Access quarterly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 500 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.
- gene silencing
- genomic Imprinting
- transposon silencing
- transgene silencing
- position effect
- RNA-directed DNA methylation
- RNA interference
- nonsense mediated decay
- meiotic silencing of unpaired DNA
Genes 2013, 4(2), 226-243; doi:10.3390/genes4020226
Received: 28 March 2013; in revised form: 9 April 2013 / Accepted: 23 April 2013 / Published: 29 April 2013| Download PDF Full-text (447 KB) | View HTML Full-text | Download XML Full-text | Supplementary Files
Communication: RNAi-Mediated Gene Silencing in a Gonad Organ Culture to Study Sex Determination Mechanisms in Sea Turtle
Genes 2013, 4(2), 293-305; doi:10.3390/genes4020293
Received: 31 January 2013; in revised form: 15 May 2013 / Accepted: 20 May 2013 / Published: 7 June 2013| Download PDF Full-text (1024 KB) | View HTML Full-text | Download XML Full-text
Genes 2013, 4(3), 358-374; doi:10.3390/genes4030358
Received: 14 May 2013; in revised form: 2 July 2013 / Accepted: 11 July 2013 / Published: 19 July 2013| Download PDF Full-text (1396 KB) | View HTML Full-text | Download XML Full-text
Genes 2013, 4(3), 435-456; doi:10.3390/genes4030435
Received: 15 May 2013; in revised form: 17 August 2013 / Accepted: 22 August 2013 / Published: 5 September 2013| Download PDF Full-text (576 KB) | View HTML Full-text | Download XML Full-text
Genes 2013, 4(3), 457-484; doi:10.3390/genes4030457
Received: 20 May 2013; in revised form: 11 July 2013 / Accepted: 13 August 2013 / Published: 10 September 2013| Download PDF Full-text (942 KB) | View HTML Full-text | Download XML Full-text
Genes 2013, 4(4), 583-595; doi:10.3390/genes4040583
Received: 21 May 2013; in revised form: 11 October 2013 / Accepted: 17 October 2013 / Published: 25 October 2013| Download PDF Full-text (181 KB) | View HTML Full-text | Download XML Full-text
Genes 2013, 4(4), 620-645; doi:10.3390/genes4040620
Received: 17 May 2013; in revised form: 14 August 2013 / Accepted: 8 October 2013 / Published: 7 November 2013| Download PDF Full-text (613 KB) | View HTML Full-text | Download XML Full-text
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Type of Paper: Review
Title: siRNA: The Excalibur against Acute Brain Injuries
Authors: Andrew M. Fukuda 1, and Jerome Badaut 1,2, *
Affiliations: 1 Department of Physiology, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA; E-Mail: firstname.lastname@example.org (A.M.F.)
2 Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, 92354, USA; E-Mail: email@example.com (J.B.); Tel.: +1-909-558-8242; Fax: +1-909-558-0479
Abstract: Ever since the discovery of small interference RNA a little over a decade ago, its potential as a therapeutic agent for many diseases has been sought after by many. In this review, we discuss the promising possibility of siRNA to be used as a drug to treat acute brain injuries such as traumatic brain injury and stroke. We will first give the principles of RNA interference as an effective mechanism to decrease protein expression. Then, recent works that have been published in vitro and in vivo for brain diseases will be discussed, highlighting especially those concerned with in vivo acute brain injury models. Lastly, we will discuss the future of siRNA while addressing the current obstacles it must overcome to be used effectively against brain diseases in the clinic.
Type of Paper: Review
Title: miRNA Regulation of Early Vertebrate Development
Authors: Chunyao Wei and James G. Patton
Affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; E-Mail: james.g.patton@Vanderbilt.Edu
Abstract: miRNAs are a class of small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. By specific binding to recognition elements in the 3’ untranslated regions (UTRs) of target mRNAs, miRNAs inhibit gene expression in a sequence-dependent manner via destabilizing target mRNAs and/or blocking translation. During early vertebrate development, gene expression is precisely regulated and coordinated to specify proliferation, differentiation and cell fate. miRNA expression patterns are relatively simple at the earliest stages of embryogenesis and in stem cells but become increasingly complex as development proceeds. Fully differentiated cells express hundreds of miRNAs and each miRNA is capable of regulating multiple mRNAs consistent with a critical role for miRNAs in determining and maintaining cell fate. In this review, we will briefly outline miRNA biogenesis and then summarize the current understanding of miRNA regulation of early vertebrate development. Comprehensive understanding of the function of miRNAs during embryogenesis will provide fundamental insight into the regulation of gene expression pathways during normal development and disease.
Type of Paper: Review
Title: Gene Silencing in Crustaceans: From Basic Research to Biotechnologies
Authors: Amir Sagi, Rivka Manor and Tomer Ventura
Affiliation: Department of life Sciences and the National Institute for Biotechnology in the Negev, Ben Gurion University, P.O. Box 653, Beer Sheva 84105, Israel; E-Mail: firstname.lastname@example.org
Abstract: In crustaceans the approach of gene silencing is gaining momentum, for both research and development, through the injection of double-stranded RNA (dsRNA). Gene silencing has proven instrumental in a growing number of crustacean species which contributed to our understanding of the functionality of novel crustacean genes of importance to metabolism, reproduction and growth. Genes encoding to eyestalk neuropeptides, structural exoskeletal proteins and receptors were successfully silenced. Also, extensive study was done in crustaceans on silencing of viral transcripts. Finally, the first case of a practical use of gene silencing in the entire aquaculture industry has been achieved through manipulation of a crustacean insulin-like androgenic gland hormone.
Type of Paper: Review
Title: RNA interference—Possible Therapy for Neurodegenerative Disorders?
Author: Troels Tolstrup Nielsen 1,2
Affiliations: 1 Memory Disorders Research Group, Department of Neurology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; E-Mail: email@example.com
2 Section of Neurogenetics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
Abstract: Since the first reports that double-stranded RNAs can efficiently silence gene expression in C. elegans, the technology of RNA interference (RNAi) has been intensively exploited as an experimental tool to study gene function. With the subsequent discovery that RNAi could also be utilized in mammalian cells the technology of RNAi was expanded from being a valuable experimental tool to being a possible method for gene-specific therapeutic regulation, and much effort has been put into developing the technique. Here I will review the current literature of how RNAi has developed over the years and how the technique is exploited in a pre-clinical and clinical perspective with special emphasis on neurodegenerative disorders.
Type of Paper: Article
Title: High SINE RNA Expression Correlates with Post-transcriptional Downregulation of BRCA1
Author: Maureen Peterson 1, Vicki L Chandler 2,3 and Giovanni Bosco 1
Affiliations: 1. Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover New Hampshire; E-Mail: Maureen.Peterson@dartmouth.edu
2. Department of Plant Sciences
3. Bio5 Institute; University of Arizona, Tucson Arizona
Abstract: Short Interspersed Nuclear Elements (SINEs) are non-autonomous retrotransposons that comprise a large fraction of the human genome. SINEs are demethylated in human disease, but whether SINEs become transcriptionally induced and how the resulting transcripts may affect the expression of protein coding genes is unknown. Here, we show that downregulation of the mRNA of the tumor suppressor gene BRCA1 is associated with increased transcription of SINEs and production of sense and antisense SINE small RNAs. We find that BRCA1 mRNA is post-transcriptionally down-regulated in a Dicer and Drosha dependent manner and that expression of a SINE inverted repeat with sequence identity to a BRCA1 intron is sufficient for downregulation of BRCA1 mRNA. These observations suggest that transcriptional activation of SINEs could contribute to a novel mechanism of RNA mediated post-transcriptional silencing of human genes.
Last update: 21 February 2013