Papers by Luis María Vaschetto
CRISPR-/Cas9 Based Genome Editing for Treating Genetic Disorders and Diseases
CRISPR-/Cas9 Based Genome Editing for Treating Genetic Disorders and Diseases
Miniature Inverted-repeat Transposable Elements (MITEs) and their effects on the regulation of major genes in cereal grass genomes
Molecular Breeding, 2016
Various chemical modifications to non-coding DNA sequences can alter the regulation of gene expre... more Various chemical modifications to non-coding DNA sequences can alter the regulation of gene expression. Although the mechanisms governing these pathways are still unclear, and non-coding regions were previously referred to as junk DNA, the evidence accumulated to date shows that these unknown processes are becoming more understandable and, in addition, that these sequences (Transposable Elements, repeat sequences) play critical roles in gene regulation. Consequently, this study aims to understand how Miniature Inverted-repeat Transposable Elements (MITEs) and chromatin remodeling complexes are involved in regulating the gene expression of Rht-1 and tb1, key developmental loci from bread wheat (Triticum aestivum) and maize (Zea mays), respectively. At present, the transcription regulation functions of MITEs in crop genomes are rather undefined, therefore it becomes important to focus on these issues in order to improve current molecular breeding methods. Moreover, this study will att...
In a recent past, Transposable Elements (TEs) were referred as selfish genetic components only ca... more In a recent past, Transposable Elements (TEs) were referred as selfish genetic components only capable of copying themselves with the aim to increase the odds that will be inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into genome host comprise an important evolutionary mechanism capable to produce diverse chromosome rearrangements and thus increase the adaptive fitness. According to as insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility to setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular typ...
RNA activation: A diamond in the rough for genome engineers
Journal of cellular biochemistry, Jan 21, 2017
The ability to develop efficient and versatile technologies for manipulating gene expression is a... more The ability to develop efficient and versatile technologies for manipulating gene expression is a fundamental issue both in biotechnology and therapeutics. The endogenous RNA interference (RNAi) pathway which mediates gene silencing was discovered at the end of the 20th century and it is nowadays considered as an essential strategy for knockdown of specific genes and for studying gene function. Remarkably, during the past decade, a RNA-induced mechanism of gene activation has also been reported. Likewise RNAi, the RNA activation (RNAa) process is also mediated by sequence-specific double-stranded RNA (dsRNA) molecules, and interesting resemblances between both RNA-based transcriptional mechanisms have been described. Small activating RNAs (saRNAs) and related molecules have been used for targeting of genes in species that are as different as nematodes and humans, and similar dsRNA-induced activation phenomena have also been observed in plants. The aim of this letter is to highlight ...
Exploring an Emerging Issue: Crop Epigenetics
Plant Molecular Biology Reporter, 2014
High genetic diversity in the harvestman Geraeocormobius sylvarum (Arachnida, Opiliones, Gonyleptidae) from subtropical forests in north-eastern Argentina revealed by mitochondrial DNA sequences
Journal of Zoological Systematics and Evolutionary Research, 2015
RNA activation: A diamond in the rough for genome engineers
Journal of cellular biochemistry, Jan 21, 2017
The ability to develop efficient and versatile technologies for manipulating gene expression is a... more The ability to develop efficient and versatile technologies for manipulating gene expression is a fundamental issue both in biotechnology and therapeutics. The endogenous RNA interference (RNAi) pathway which mediates gene silencing was discovered at the end of the 20th century and it is nowadays considered as an essential strategy for knockdown of specific genes and for studying gene function. Remarkably, during the past decade, a RNA-induced mechanism of gene activation has also been reported. Likewise RNAi, the RNA activation (RNAa) process is also mediated by sequence-specific double-stranded RNA (dsRNA) molecules, and interesting resemblances between both RNA-based transcriptional mechanisms have been described. Small activating RNAs (saRNAs) and related molecules have been used for targeting of genes in species that are as different as nematodes and humans, and similar dsRNA-induced activation phenomena have also been observed in plants. The aim of this letter is to highlight ...
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), also known as COVID-19, encodes... more The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), also known as COVID-19, encodes for a spike protein that is responsible for both attachment and membrane fusion, thereby being critical in the pathogenicity of this virus. Here, I report that a putative miRNA localized in the spike gene of SARS-CoV-2 matches to the forward strand of hsa-miR-8055, a miRNA expressed during T-cell response to antigen, and also binds with perfect complementarity to its seed region
The critical role of epigenetic regulation in developmental programming of higher organisms
The Emergence of Non-coding RNAs as Versatile and Efficient Therapeutic Tools
Cereal Circular RNAs (circRNAs): An Overview of the Computational Resources for Identification and Analysis
Circular RNAs (circRNAs) are a widespread class of endogenous noncoding RNAs and they have been s... more Circular RNAs (circRNAs) are a widespread class of endogenous noncoding RNAs and they have been studied in the past few years, implying important biological functions in all kingdoms of life. Recently, circRNAs have been identified in many plant species, including cereal crops, showing differential expression during stress response and developmental programs, which suggests their role in these process. In the following years, it is expected that insights into the functional roles of circRNAs can be used by cereal scientists and molecular breeders with the aim to develop new strategies for crop improvement. Here, we briefly outline the current knowledge about circRNAs in plants and we also outline available computational resources for their validation and analysis in cereal species.
Recently, the conjunction of disciplines such as developmental biology and proteomics enabled the... more Recently, the conjunction of disciplines such as developmental biology and proteomics enabled the dissection of diverse cellular processes, by analysis of their transcriptional regulatory pathways. In particular, it has been shown that transcription factor interactions play critical roles in the development of many complex traits and control cellular phenotypic plasticity , whereas protein phosphorylation modifications regulate protein activity at the posttranslational level. The present work posits that protein-protein interactions by functional motifs, as well as the phosphorylation state in these sites, are fundamental plant biological phenotype determinants, whose elucidation and understanding will allow manipulation of complex traits, thereby contributing to the design of novel methodologies for molecular breeders and plant physiologists.
Recently generated high‐throughput sequencing data sets have shed light on the important regulato... more Recently generated high‐throughput sequencing data sets have shed light on the important regulatory roles of noncoding RNA (ncRNA) molecules in the development of higher organisms. Nowadays it is well‐known that regulatory ncRNAs can bind complementary RNA or DNA sequences and recruit chromatin remodelers to selectively modulate gene expression. Consequently, genome sequencing and transcriptomics technologies are now being used to reveal hidden associations among ncRNAs and distinct biological mechanisms. This is the case for the diamondback moth Plutella xylostella, a worldwide pest known to infest cruciferous crops and to display resistance to most insecticides, including Bacillus thuringiensis (Bt) based biopesticides. In P. xylostella, it is thought that ncRNAs could play important roles in both development and insecticide resistance. This review will highlight recent insights into the roles of ncRNAs in P. xylostella and related lepidopterans, and will outline genetic engineering technologies which might be used to design efficient ncRNA‐based pest control strategies.
The Role of Sequence Duplication in Transcriptional Regulation and Genome Evolution
Sequence duplication is nowadays recognized as an important mechanism that underlies the evolutio... more Sequence duplication is nowadays recognized as an important mechanism that underlies the evolution of eukaryote genomes, being indeed one of the most powerful strategies for the generation of adaptive diversity by modulating transcriptional activity. The evolutionary novelties simultaneously associated with sequence duplication and differential gene expression can be collectively referred to as duplication-mediated transcriptional regulation. In the last years, evidence has emerged supporting the idea that sequence duplication and functionalization represent important evolutionary strategies acting at genome level, and both coding and non-coding sequences have been found to be targets of such events. Moreover, it has been proposed that deleterious effects of sequence duplication might be potentially silenced by endogenous cell machinery (i.e., RNA interference, epigenetic repressive marks, etc). Along these lines our aim is to highlight the role of sequence duplication on transcriptional activity and the importance of both in genome evolution.
Miniature Inverted-repeat Transposable Elements (MITEs) and their effects on the regulation of ma... more Miniature Inverted-repeat Transposable Elements (MITEs) and their effects on the regulation of major genes in cereal grass genomes
The ability to develop efficient and versatile technologies for manipulating gene expression is a... more The ability to develop efficient and versatile technologies for manipulating gene expression is a fundamental issue both in biotechnology and therapeutics. The endogenous RNA interference (RNAi) pathway which mediates gene silencing was discovered at the end of the 20th century and it is nowadays considered as an essential strategy for knockdown of specific genes and for studying gene function. Remarkably, during the past decade, a RNA-induced mechanism of gene activation has also been reported. Likewise RNAi, the RNA activation (RNAa) process is also mediated by sequence-specific double-stranded RNA (dsRNA) molecules, and interesting resemblances between both RNA-based transcriptional mechanisms have been described. Small activating RNAs (saRNAs) and related molecules have been used for targeting of genes in species that are as different as nematodes and humans, and similar dsRNA-induced activation phenomena have also been observed in plants. The aim of this letter is to highlight recent molecular insights into yet unexplored RNAa mechanism and its potential for manipulating transcriptional activity.
Transfection of small non-coding RNAs (sncRNAs) molecules has become a routine technique widely u... more Transfection of small non-coding RNAs (sncRNAs) molecules has become a routine technique widely used for silencing gene expression by triggering post-transcriptional and transcriptional RNA interference (RNAi) pathways. Moreover, in the past decade, small activating (saRNA) sequences targeting promoter regions were also reported, thereby a RNA-based gene activation (RNAa) mechanism has been proposed. In this regard, Turner and colleagues recently discovered an endogenous microRNA (miRNA) which binds its promoter in order to upregulate its own expression. Interestingly, several miRNA-induced RNA activation (miRNAa) phenomena have since then been identified. My objective here is to introduce the reader into the emergent miRNAa research field, as well as bring together important discoveries about this unexplored transcriptional activation pathway.
In a recent past, transposable elements (TEs) were referred to as selfish genetic components only... more In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it. Fortunately, the emergence of genome editing technologies based on programmable nucleases, and especially the arrival of a multipurpose RNA-guided Cas9 endonuclease system, has made it possible to reconsider this challenge. For such purpose, a particular type of transposons referred to as miniature inverted-repeat transposable elements (MITEs) has shown a series of interesting characteristics for designing functional drivers. Here, recent insights into MITE elements and versatile RNA-guided CRISPR/Cas9 genome engineering system are given to understand how to deploy the potential of TEs for control of the host transcriptional activity.
The mechanism of RNA interference (RNAi) mediated by small non-coding RNAs (ncRNAs) was discovere... more The mechanism of RNA interference (RNAi) mediated by small non-coding RNAs (ncRNAs) was discovered only two decades ago, and research into this field has already achieved therapeutical results by the development of a small interfering RNA (siRNA)-based drug for the treatment of the Hereditary Transthyretin Amyloidosis, an autosomal dominant disease [1]. Moreover, microRNAs (miRNAs) known to trigger the RNAi pathway in human cells have also shown to be useful biomarkers for disease diagnosis and therapy response [2-4]. Nowadays, ncRNAs are recognized to be important transcriptional modulators not only capable of suppressing but also of promoting gene expression. This mechanism, referred to as RNA-mediated gene activation (RNAa), is triggered by small activating RNA (saRNA) molecules that bind to complementary gene sequences and activate transcription [5-9]. Recent research into RNAa has started to unravel the underlying basis linked to saRNA-based activation phenomena and enabled the design of saRNAs with ability to regulate the expression of target genes in different cells types [10-13], even being in the process of developing a RNAa therapy against hepatocellular carcinoma [14,15]. Similarly to siR-NAs, short activating RNAs might be used as therapeutic agents for treatment of different diseases, associated in this last case with the occurrence of loss of function mutations and/or haploinsufficiencies [8,16]. In the near future, it is expected that versatile delivery systems consisting of siRNA/saRNA-based drugs enable the setup of personalized therapeutic treatments and targeted molecular therapies, thereby opening exciting new possibilities in clinical medicine and pharmaceutical biotechnology. In this thematic issue, Drs. Yoon and Rossi [17] provided a comprehensive overview about the RNAa mechanism, method-ologies/insights for the design and delivery of saRNAs, intracellular functioning and chemical modifications to increase the oligonucleotide's resistance to nuclease degradation. This work is an analytical overview that focuses on the potential that RNAa have for the development of therapeutic strategies. Moreover, canonical and non-canonical mechanisms involving saRNA-mediated gene activation phenomena are also illustrated here. In the next article, Setten et al. [18] described the progress of MTL-CEBPA (MiNA Therapeutics, UK), the first saRNA-targeting drug currently tested in clinical trials (Phase I). Remarkably, this oligonucleotide can be used to induce targeted expression of the CCAAT/enhancer-binding protein alpha (CEBPα) gene, a known tumor suppressor capable of modulating tran-scriptional activity in hepatic cells [14]. In this work, the authors considered the reasons for which MTL-CEBPA represents a promising saRNA drug against hepatocellular carcinoma, thereby opening the door to the development of new therapeutic agents in the treatment of patients with cancer and other diseases. Finally, Drs. Li and Hu [19] reviewed the state of the research in the RNAa field and underlie the potential of saRNAs to act as gene modulators, with special emphasis on their use in the treatment of kidney diseases. In this article, the authors associated short ncRNA-mediated gene regulation pathways (i.e., RNAi and RNAa), and discussed how research into RNAi might be useful for understanding the molecular mechanisms underlying the endogenous RNAa phenomena. REFERENCES [1] Adams, D.; Gonzalez-Duarte, A.; O'Riordan, W.D.; Yang C.C.; Ueda, M.; Kristen, A.V.; Tournev, I.; Schmidt; H.H.; Coelho, T.; Berk, J.L.; Lin, K.P.; Vita, G.; Attarian, S.; Planté-Bordeneuve, V.; Mezei, M.M.; Campistol, J.M.; Buades, J.; Brannagan T.H.; Kim, B.J.; Oh, J.; Parman, Y.; Sekijima, Y.; Hawkins, P.N.; Solomon, S.D.; Polydefkis, M.; Dyck, P.J.; Gandhi, P.J.; Goyal, S.; Chen, J.; Strahs, A.L.; Nochur, S.V.; Sweetser, M.T.; Garg, P.P.; Vaishnaw, A.K.; Gollob, J.A.; Suhr, O.B. Patisiran, an RNAi therapeutic, for hereditary transthyretin amyloidosis. New Engl. J. Med., 2018, 379(1), 11-21. [2] Grabarek, B.; Wcislo-Dziadecka, D.; Gola, J.; Kruszniewska-Rajs, C.; Brzezinska-Wcislo, L.; Zmarzly, N.; Mazurek, U. Changes in the expression profile of JAK/STAT signaling pathway genes and mirnas regulating their expression under the adalimumab therapy. Xia, Y. Circulating miR-10a as predictor of therapy response in rheumatoid arthritis patients treated with methotrexate. Curr. Pharm. Biotechnol., 2018, 19(1), 79-86. [4] Kranjc, T.; Ostanek, B.; Marc, J. Bone microRNAs and ageing. Curr. Pharm. Biotechnol., 2017, 18(3), 210-220. [5] Li, L.C.; Okino, S.T.; Zhao, H.; Pookot, D.; Place, R.F.; Urakami, S.; Enokida, H.; Dahiya, R. Small dsRNAs induce transcriptional activation in human cells. Younger, S.T.; Hardy, D.B.; Ram, R.; Huffman, K.E.; Corey, D.R. Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nat. Chem. Biol., 2007, 3(3), 166-173. [7] Guo, D.; Barry, L.; Lin, S.S.H.; Huang, V.; Li, L.C. RNAa in action: From the exception to the norm. RNA Biol., 2014, 11(10), 1221-1225. [8] Vaschetto, L.M. RNA activation: A diamond in the rough for genome engineers. J. Cellul. Biochem., 2018a, 119(1), 247-249. [9] Vaschetto, L.M. miRNA activation is an endogenous gene expression pathway. RNA Biol., 2018b, 1-3. [10] Hu, J.; Chen, Z.; Xia, D.; Wu, J.; Xu, H.; Ye, Z.Q. Promoter-associated small double-stranded RNA interacts with heterogeneous nuclear ribonucleo-protein A2/B1 to induce transcriptional activation. Biochem. J., 2012, 447(3), 407-416. [11] Place, R.F.; Noonan, E.J.; Foldes-Papp, Z.; Li, L.C. Defining features and exploring chemical modifications to manipulate RNAa activity. Curr. Pharm. Biotechnol., 2010, 11(5), 518-526. [12] Huang, V.; Place, R.F.; Portnoy, V.; Wang, J.; Qi, Z.; Jia, Z.; Yu, A.; Shuman, M.; Yu, J.; Li, L.C. Upregulation of cyclin B1 by miRNA and its implications in cancer.
Books by Luis María Vaschetto
The objective of this volume is to shed light on current technologies associated with cereal geno... more The objective of this volume is to shed light on current technologies associated with cereal genomics, providing a valuable resource for researchers working in breeding and molecular crop improvement programs. Chapters guide readers through high-throughput DNA extraction protocols, crop genetic resources, meta-Quantitative Trait Loci (QTL) analysis, association mapping, next-sequencing genome sequencing, transposable element variation, transcriptomics analysis, epigenetic variation, identification of imprinted genes, noncoding RNAs (circular RNAs), genome editing technologies, and post-translational protein phosphorylation.Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Uploads
Papers by Luis María Vaschetto
Books by Luis María Vaschetto