A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis

Arabidopsis Pol II-Dependent in Vitro Transcription System Reveals Role of Chromatin for Light-Inducible rbcS Gene Transcription

In vitro transcription is an essential tool to study the molecular mechanisms of transcription. For over a decade, we have developed an in vitro transcription system from tobacco (Nicotiana tabacum)-cultured cells (BY-2), and this system supported the basic activities of the three RNA polymerases (Pol I, Pol II, and Pol III). However, it was not suitable to study photosynthetic genes, because BY-2 cells have lost their photosynthetic activity. Therefore, Arabidopsis (Arabidopsis thaliana) in vitro transcription systems were developed from green and etiolated suspension cells. Sufficient in vitro Pol II activity was detected after the minor modification of the nuclear soluble extracts preparation method; removal of vacuoles from protoplasts and L-ascorbic acid supplementation in the extraction buffer were particularly effective. Surprisingly, all four Arabidopsis Rubisco small subunit (rbcS-1A, rbcS-1B, rbcS-2B, and rbcS-3B) gene members were in vitro transcribed from the naked DNA templates without any light-dependent manner. However, clear light-inducible transcriptions were observed using chromatin template of rbcS-1A gene, which was prepared with a human nucleosome assembly protein 1 (hNAP1) and HeLa histones. This suggested that a key determinant of light-dependency through the rbcS gene transcription was a higher order of DNA structure (i.e. chromatin).

lncRNAs in Stress Response

All living organisms sense and respond to harmful changes in their intracellular and extracellular environment through complex signaling pathways that lead to changes in gene expression and cellular function in order to maintain homeostasis. Long non-coding RNAs (lncRNAs), a large and heterogeneous group of functional RNAs, play important roles in cellular response to stressful conditions. lncRNAs constitute a significant fraction of the genes differentially expressed in response to diverse stressful stimuli and, once induced, contribute to the regulation of downstream cellular processes, including feedback regulation of key stress response proteins. While many lncRNAs seem to be induced in response to a specific stress, there is significant overlap between lncRNAs induced in response to different stressful stimuli. In addition to stress-induced RNAs, several constitutively expressed lncRNAs also exert a strong regulatory impact on the stress response. Although our understanding of the contribution of lncRNAs to the cellular stress response is still highly rudimentary, the existing data point to the presence of a complex network of lncRNAs, miRNAs, and proteins in regulation of the cellular response to stress.

The interplay of long non-coding RNAs and MYC in cancer

Long non-coding RNAs (lncRNAs) are a class of RNA molecules that are changing how researchers view eukaryotic gene regulation. Once considered to be non-functional products of low-level aberrant transcription from non-coding regions of the genome, lncRNAs are now viewed as important epigenetic regulators and several lncRNAs have now been demonstrated to be critical players in the development and/or maintenance of cancer. Similarly, the emerging variety of interactions between lncRNAs and MYC, a well-known oncogenic transcription factor linked to most types of cancer, have caught the attention of many biomedical researchers. Investigations exploring the dynamic interactions between lncRNAs and MYC, referred to as the lncRNA-MYC network, have proven to be especially complex. Genome-wide studies have shown that MYC transcriptionally regulates many lncRNA genes. Conversely, recent reports identified lncRNAs that regulate MYC expression both at the transcriptional and post-transcriptional levels. These findings are of particular interest because they suggest roles of lncRNAs as regulators of MYC oncogenic functions and the possibility that targeting lncRNAs could represent a novel avenue to cancer treatment. Here, we briefly review the current understanding of how lncRNAs regulate chromatin structure and gene transcription, and then focus on the new developments in the emerging field exploring the lncRNA-MYC network in cancer.

Viroids, infectious long non-coding RNAs with autonomous replication

Transcriptome deep-sequencing studies performed during the last years confirmed that the vast majority of the RNAs transcribed in higher organisms correspond to several types of non-coding RNAs including long non-coding RNAs (lncRNAs). The study of lncRNAs and the identification of their functions, is still an emerging field in plants but the characterization of some of them indicate that they play an important role in crucial regulatory processes like flowering regulation, and responses to abiotic stress and plant hormones. A second group of lncRNAs present in plants is formed by viroids, exogenous infectious subviral plant pathogens well known since many years. Viroids are composed of circular RNA genomes without protein-coding capacity and subvert enzymatic activities of their hosts to complete its own biological cycle. Different aspects of viroid biology and viroid-host interactions have been elucidated in the last years and some of them are the main topic of this review together with the analysis of the state-of-the-art about the growing field of endogenous lncRNAs in plants.

RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening

Recently, long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in model plants, such as Arabidopsis, rice, and maize. However, the presence of lncRNAs and how they function in fleshy fruit ripening are still largely unknown because fleshy fruit ripening is not present in the above model plants. Tomato is the model system for fruit ripening studies due to its dramatic ripening process. To investigate further the role of lncRNAs in fruit ripening, it is necessary and urgent to discover and identify novel lncRNAs and understand the function of lncRNAs in tomato fruit ripening. Here it is reported that 3679 lncRNAs were discovered from wild-type tomato and ripening mutant fruit. The lncRNAs are transcribed from all tomato chromosomes, 85.1% of which came from intergenic regions. Tomato lncRNAs are shorter and have fewer exons than protein-coding genes, a situation reminiscent of lncRNAs from other model plants. It was also observed that 490 lncRNAs were significantly up-regulated in ripening mutant fruits, and 187 lncRNAs were down-regulated, indicating that lncRNAs could be involved in the regulation of fruit ripening. In line with this, silencing of two novel tomato intergenic lncRNAs, lncRNA1459 and lncRNA1840, resulted in an obvious delay of ripening of wild-type fruit. Overall, the results indicated that lncRNAs might be essential regulators of tomato fruit ripening, which sheds new light on the regulation of fruit ripening.

The roles of cross-talk epigenetic patterns in Arabidopsis thaliana

The epigenetic mechanisms, including histone modifications, DNA cytosine methylation, histone variants and noncoding RNAs (ncRNAs), play a key role in determining transcriptional outcomes. Recently, many studies have demonstrated that the different epigenetic mechanisms interplay with each other rather than work independently. In this article, we outline a framework for how different epigenetic mechanisms work with each other in Arabidopsis thalianaWe build a network of cross-talk between chromatin marks based on six classes of cross-talk interactions. The first pattern details coordinated modifications that act together to enhance or repress gene expression. The second pattern details bivalent modifications that act antagonistically toward gene expression. The third pattern is for unilateral promotion of one modification by the existence of another modification. The fourth pattern is for unilateral inhibition of one modification by another modification. The fifth pattern is for mutual inhibitory patterns. The sixth pattern is for epigenetic modifications that appear independent.We also explore the mutual regulation between chromatin marks and ncRNAs in various ways. These regulations can be divided into six parts: how ncRNA affects the binding of chromatin mark, such as miR2Epi, siR2Epi and lncR2Epi; how chromatin mark regulates ncRNA, such as Epi2miR, Epi2siR and Epi2lncR.A comprehensive network of cross-talk between different epigenetic mechanisms will help in fully understanding the functional roles and biological impacts of epigenetic regulation.

Databases for lncRNAs: a comparative evaluation of emerging tools

The vast majority of the human transcriptome does not code for proteins. Advances in transcriptome arrays and deep sequencing are giving rise to a fast accumulation of large data sets, particularly of long noncoding RNAs (lncRNAs). Although it is clear that individual lncRNAs may play important and diverse biological roles, there is a large gap between the number of existing lncRNAs and their known relation to molecular/cellular function. This and related information have recently been gathered in several databases dedicated to lncRNA research. Here, we review the content of general and more specialized databases on lncRNAs. We evaluate these resources in terms of the quality of annotations, the reporting of validated or predicted molecular associations, and their integration with other resources and computational analysis tools. We illustrate our findings using known and novel cancer-related lncRNAs. Finally, we discuss limitations and highlight potential future directions for these databases to help delineating functions associated with lncRNAs.

Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa

Protein-coding genes are considered to be a dominant component of the eukaryotic transcriptome; however, many studies have shown that intergenic, non-coding transcripts also play an important role. Long intergenic non-coding RNAs (lincRNAs) were found to play a vital role in human and Arabidopsis. However, lincRNAs and their regulatory roles remain poorly characterized in woody plants, especially Populus trichocarpa (P. trichocarpa). A large set of Populus RNA-Seq data were examined with high sequencing depth under control and drought conditions and a total of 2542 lincRNA candidates were identified. In total, 51 lincRNAs and 20 lincRNAs were identified as putative targets and target mimics of known Populus miRNAs, respectively. A total of 504 lincRNAs were found to be drought responsive, eight of which were confirmed by RT-qPCR. These findings provide a comprehensive view of Populus lincRNAs, which will enable in-depth functional analysis.

RNA regulatory networks in animals and plants: a long noncoding RNA perspective

A recent highlight of genomics research has been the discovery of many families of transcripts which have function but do not code for proteins. An important group is long noncoding RNAs (lncRNAs), which are typically longer than 200 nt, and whose members originate from thousands of loci across genomes. We review progress in understanding the biogenesis and regulatory mechanisms of lncRNAs. We describe diverse computational and high throughput technologies for identifying and studying lncRNAs. We discuss the current knowledge of functional elements embedded in lncRNAs as well as insights into the lncRNA-based regulatory network in animals. We also describe genome-wide studies of large amount of lncRNAs in plants, as well as knowledge of selected plant lncRNAs with a focus on biotic/abiotic stress-responsive lncRNAs.

Arabidopsis non-coding RNA regulation in abiotic stress responses

Plant growth and productivity are largely affected by environmental stresses. Therefore, plants have evolved unique adaptation mechanisms to abiotic stresses through fine-tuned adjustment of gene expression and metabolism. Recent advanced technologies, such as genome-wide transcriptome analysis, have revealed that a vast amount of non-coding RNAs (ncRNAs) apart from the well-known housekeeping ncRNAs such as rRNAs, tRNAs, small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) are expressed under abiotic stress conditions. These various types of ncRNAs are involved in chromatin regulation, modulation of RNA stability and translational repression during abiotic stress response. In this review, we summarize recent progress that has been made on ncRNA research in plant abiotic stress response.

Long noncoding RNAs: new regulators in plant development

Plant long noncoding RNAs (lncRNAs) play important roles in a wide range of biological processes, especially in plant reproductive development and response to stresses. They are transcribed by RNA polymerase II (Pol II), Pol III and Pol V, and exert their functions by a variety of regulation pathways. In this review, we summarized the current knowledge of lncRNAs discoveries in plant, including their identification, functions and regulation pathways as well as production and mediators, with an emphasizing on the novel regulation mechanisms in plant development.

Identification of RNA polymerase III-transcribed genes in eukaryotic genomes

The RNA polymerase (Pol) III transcription system is devoted to the production of short, generally abundant noncoding (nc) RNAs in all eukaryotic cells. Previously thought to be restricted to a few housekeeping genes easily detectable in genome sequences, the set of known Pol III-transcribed genes (class III genes) has been expanding in the last ten years, and the issue of their detection, annotation and actual expression has been stimulated and revived by the results of recent high-resolution genome-wide location analyses of the mammalian Pol III machinery, together with those of Pol III-centered computational studies and of ncRNA-focused transcriptomic approaches. In this article, we provide an outline of distinctive features of Pol III-transcribed genes that have allowed and currently allow for their detection in genome sequences, we critically review the currently practiced strategies for the identification of novel class III genes and transcripts, and we discuss emerging themes in Pol III transcription regulation which might orient future transcriptomic studies. This article is part of a Special Issue entitled: Transcription by Odd Pols.

Long non-coding RNAs coordinate cellular responses to stress

Following the initial discovery of the heat shock RNA omega (hsrω) gene of Drosophila melanogaster to be non-coding (nc) and also inducible by cell stress, other stress-inducible long non-coding RNAs (lncRNA) have been described in diverse organisms. In view of the rapid sequence divergence of lncRNAs, present knowledge of stress trasncriptome is limited and fragmented. Several known stress-related lncRNAs, associated with specific nuclear speckled domains or nucleolus, provide structural base for sequestering diverse RNA-processing/regulatory proteins. Others have roles in transcriptional or translational inhibition during stress or in signaling pathways; functions of several other lncRNAs are not yet known. Most stress-related lncRNAs act primarily by modulating activity of the proteins to which they bind or by sequestering specific sets of proteins away from the active pool. A common emerging theme is that a given lncRNA targets one or more protein/s with key role/s in the cascade of events triggered by the stress and therefore has a widespread integrative effect. Since proteins associate with RNA through short sequence motifs, the overall base sequence of functionally similar ncRNAs is often not conserved except for specific motifs. The rapid evolvability of ncRNA sequences provides elegant modules for adaptability to changing environment as binding of one or the other protein to ncRNA can alter its structure and functions in distinct ways. Thus the stress-related lncRNAs act as hubs in the cellular networks to coordinate activities of the members within and between different networks to maintain cellular homeostasis for survival or to trigger cell death.