Wednesday, July 27, 2016

MicroRNAs: Important Epigenetic Regulators in Osteoarthritis

Author(s):

Tomasz Trzeciak and Malwina Czarny-RatajczakPages 481-484 (4)

Abstract:


Multiple mechanisms are implicated in the development of primary osteoarthritis (OA), in which genetic and epigenetic factors appear to interact with environmental factors and age to initiate the disease and stimulate its progression. Changes in expression of microRNAs (miRs) contribute to development of osteoarthritis. Numerous miRs are involved in cartilage development, homeostasis and degradation through targeting genes expressed in this tissue. An important regulator of gene expression in human cartilage is miR-140, which directly targets a gene coding aggrecanase ADAMTS-5, that cleaves aggrecan in cartilage. This miR is considered a biological marker for cartilage and its level significantly decreases in OA cartilage. On the other hand, increased expression of miR-146a in early OA inhibits two other cartilage-degrading enzymes: MMP13 and ADAMTS4, and may provide a useful tool in developing treatments for OA. The COL2A1 gene, encoding collagen type II, which is the most abundant structural protein of the cartilage, is silenced by miR-34a and activated by miR-675. Every year, new targets of cartilage miRs are validated experimentally and this opens new possibilities for new therapies that control joint destruction and stimulate cartilage repair. At the same time development of next-generation sequencing technologies allows to identify new miRs involved in cartilage biology.

Keywords:

Gene expression profiling, MicroRNAs, Cartilage, Osteoarthritis.

Affiliation:

Tulane University, School of Medicine, Department of Medicine, Center for Aging, 1430 Tulane Ave., SL-12, New Orleans, LA 70112, USA.


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Changing Faces of Transcriptional Regulation Reflected by Zic3

Author(s):

Cecilia Lanny Winata, Igor Kondrychyn and Vladimir KorzhPages 117-127 (11)

Abstract:


The advent of genomics in the study of developmental mechanisms has brought a trove of information on gene datasets and regulation during development, where the Zic family of zinc-finger proteins plays an important role. Genomic analysis of the modes of action of Zic3 in pluripotent cells demonstrated its requirement for maintenance of stem cells pluripotency upon binding to the proximal regulatory regions (promoters) of genes associated with cell pluripotency (Nanog, Sox2, Oct4, etc.) as well as cell cycle, proliferation, oncogenesis and early embryogenesis. In contrast, during gastrulation and neurulation Zic3 acts by binding the distal regulatory regions (enhancers, etc) associated with control of gene transcription in the Nodal and Wnt signaling pathways, including genes that act to break body symmetry. This illustrates a general role of Zic3 as a transcriptional regulator that acts not only alone, but in many instances in conjunction with other transcription factors. The latter is done by binding to adjacent sites in the context of multi-transcription factor complexes associated with regulatory elements.

Keywords:

Enhancer, Gastrulation, Left-right asymmetry, Neurogenesis, Promoter, Stem cells, Transcription, Zebrafish.

Affiliation:

International Institute of Molecular and Cell Biology, Warsaw, Poland.

Graphical Abstract:



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    RNA Silencing in Plants: Mechanisms, Technologies and Applications in Horticultural Crops

    Author(s):

    Qigao Guo, Qing Liu, Neil A. Smith, Guolu Liang and Ming-Bo WangPages 1-14 (14)

    Abstract:


    Understanding the fundamental nature of a molecular process or a biological pathway is often a catalyst for the development of new technologies in biology. Indeed, studies from late 1990s to early 2000s have uncovered multiple overlapping but functionally distinct RNA silencing pathways in plants, including the posttranscriptional microRNA and small interfering RNA pathways and the transcriptional RNA-directed DNA methylation pathway. These findings have in turn been exploited for developing artificial RNA silencing technologies such as hairpin RNA, artificial microRNA, intrinsic direct repeat, 3’ UTR inverted repeat, artificial trans-acting siRNA, and virus-induced gene silencing technologies. Some of theseRNA silencing technologies, such as the hairpin RNA technology, have already been widely used for genetic improvement of crop plants in agriculture. For horticultural plants, RNA silencing technologies have been used to increase disease and pest resistance, alter plant architecture and flowering time, improve commercial traits of fruits and flowers, enhance nutritional values, remove toxic compounds and allergens, and develop high-value industrial products. In this article we aim to provide an overview of the RNA silencing pathways in plants, summarize the existing RNA silencing technologies, and review the current progress in applying these technologies for the improvement of agricultural crops particularly horticultural crops.

    Keywords:

    Double-stranded RNA, Hairpin RNA, miRNA, Plants, RNA silencing, siRNA, Virus

    Affiliation:

    1College of Horticulture & Landscape Architecture, Southwest University, Chongqing, 400716, China., 2Commonwealth Scientific and Industrial Research Organisation Agriculture, Clunies Ross Street, Canberra ACT 2601, Australia.


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    Genome-assisted Breeding For Drought Resistance

    Author(s):

    Awais Khan, Valpuri Sovero and Dorcus GemenetPages 330-342 (13)

    Abstract:


    Drought stress caused by unpredictable precipitation poses a major threat to food production worldwide, and its impact is only expected to increase with the further onset of climate change. Understanding the effect of drought stress on crops and plants' response is critical for developing improved varieties with stable high yield to fill a growing food gap from an increasing population depending on decreasing land and water resources. When a plant encounters drought stress, it may use multiple response types, depending on environmental conditions, drought stress intensity and duration, and the physiological stage of the plant. Drought stress responses can be divided into four broad types: drought escape, drought avoidance, drought tolerance, and drought recovery, each characterized by interacting mechanisms, which may together be referred to as drought resistance mechanisms. The complex nature of drought resistance requires a multi-pronged approach to breed new varieties with stable and enhanced yield under drought stress conditions. High throughput genomics and phenomics allow marker-assisted selection (MAS) and genomic selection (GS), which offer rapid and targeted improvement of populations and identification of parents for rapid genetic gains and improved drought-resistant varieties. Using these approaches together with appropriate genetic diversity, databases, analytical tools, and well-characterized drought stress scenarios, weather and soil data, new varieties with improved drought resistance corresponding to grower preferences can be introduced into target regions rapidly.

    Keywords:

    Drought stress, Genomics, Phenomics, Breeding, Marker-assisted selection, Physiological processes.

    Affiliation:

    International Potato Center (CIP), Avenida La Molina 1895, Lima 12, Peru.

    Graphical Abstract:



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    Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques

    Author(s):

    Yoshihiko Onda and Keiichi MochidaPages 358-367 (10)

    Abstract:


    Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called nextgeneration sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome- wide association study.

    Keywords:

    Genetic diversity, NGS technology, Genotyping, QTL analysis, GWAS, Crop improvement.

    Affiliation:

    Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.

    Graphical Abstract:



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