Transcriptomics technologies

Transcriptomics technologies are the techniques used to study an organism’s transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst noncoding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline. Transcriptomics has been defined by repeated technological innovations that transform the field. There are two key contemporary techniques in the field: microarrays, which quantify a set of predetermined sequences, and RNA sequencing (RNA-Seq), which uses high-throughput sequencing to capture all sequences. Measuring the expression of an organism’s genes in different tissues, conditions, or time points gives information on how genes are regulated and reveals details of an organism’s biology. It can also help to infer the functions of previously unannotated genes. Transcriptomic analysis has enabled the study of how gene expression changes in different organisms and has been instrumental in the understanding of human disease. An analysis of gene expression in its entirety allows detection of broad coordinated trends which cannot be discerned by more targeted assays.Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan, Thomas Shafe

UCHL1 protein synthesis upon rapamycin treatment involves its antisense RNA trough embedded SINEB2 repeat

The initial description of genomes organization has consisted in the separation between regulatory and protein-coding DNA stretches. This simple and elegant model has supported the \u201cone region-one function\u201d theory: a genome is a linear arrangement of functional elements interspersed with nonfunctional regions. Recently the advances in transcriptomics technologies have shown that a genomic region can be used for different purposes and that functional elements can co-locate in the same region of the genome

Single cell transcriptomics comes of age

Single cell transcriptomics technologies have vast potential in advancing our understanding of biology and disease. Here, Sarah Aldridge and Sarah Teichmann review the last decade of technological advancements in single-cell transcriptomics and highlight some of the recent discoveries enabled by this technology

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

The recent remarkable development of transcriptomics technologies, especially next generation sequencing technologies, allows deeper exploration of the hidden landscapes of complex traits and creates great opportunities to improve livestock productivity and welfare. Non-coding RNAs (ncRNAs), RNA molecules that are not translated into proteins, are key transcriptional regulators of health and production traits, thus, transcriptomics analyses of ncRNAs are important for a better understanding of the regulatory architecture of livestock phenotypes. In this chapter, we present an overview of common frameworks for generating and processing RNA sequence data to obtain ncRNA transcripts. Then, we review common approaches for analyzing ncRNA transcriptome data and present current state of the art methods for identification of ncRNAs and functional inference of identified ncRNAs, with emphasis on tools for livestock species. We also discuss future challenges and perspectives for ncRNA transcriptome data analysis in livestock species

Astrocytes in Alzheimer’s Disease: Pathological Significance and Molecular Pathways

Astrocytes perform a wide variety of essential functions defining normal operation of the nervous system and are active contributors to the pathogenesis of neurodegenerative disorders such as Alzheimer’s among others. Recent data provide compelling evidence that distinct astrocyte states are associated with specific stages of Alzheimer´s disease. The advent of transcriptomics technologies enables rapid progress in the characterisation of such pathological astrocyte states. In this review, we provide an overview of the origin, main functions, molecular and morphological features of astrocytes in physiological as well as pathological conditions related to Alzheimer´s disease. We will also explore the main roles of astrocytes in the pathogenesis of Alzheimer´s disease and summarize main transcriptional changes and altered molecular pathways observed in astrocytes during the course of the disease.This work was supported by the FEDER/Ministerio de Ciencia e Innovación—Agencia Estatal de Investigación grant RTI2018-101850-A-I00 to A.M.A. (Spain), and a start-up grant from the IKERBASQUE Basque Foundation of Science to A.M.A

Tecnologías transcriptómicas y su potencial en la gestión del chancro resinoso del pino

Pine pitch canker (PPC) is a serious disease of Pinus spp. and Pseudotsuga menziesii globally. The infection of its causal agent, Fusarium circinatum, causes pitch or resin-soaked cankers on trunks and lateral branches of mature hosts, which may eventually die due to girdling or stem breakage. In nurseries, the main symptoms are damping-off and tip dieback of seedlings. However, the pathogen, with a hemibiotrophic nature, can remain endophytic in pine seedlings that do not show symptoms of infection and even inconspicuous in some herbaceous species. Since the first report in 1945 in North America, the presence of F. circinatum has been notified in 14 countries in America, Asia, Africa and Europe. Several factors have contributed to the spread of the disease to all these continents, the most important being globalization in terms of trade in reproductive plant material. Wind, raindrops and forest insects associated with pines contribute to the local dispersion of the pathogen. Despite its importance, no effective measures are available to eradicate or control PPC disease either in nurseries or in the field. The main objective of this doctoral thesis was to shed light on effective regulatory mechanisms for the control of PPC disease. For this purpose, firstly, a review focused on collecting current information on pathways of pathogen spread and proposing preventive mechanisms to avoid its introduction into disease-free areas was elaborated. The multiple pathways of spread make F. circinatum challenging to prevent, exacerbated by the recent discovery of its endophytic colonization of non-reported host species that illustrates the importance of the biological and ecological knowledge for the design of effective intervention strategies. In addition, eradication of the disease may be feasible only if its entry is detected at a very early stage. In this regard, new methods for detection and diagnosis for the prompt detection of F. circinatum in seeds, plants, and vector insects are urgently needed. For that, it is essential the collaboration between phytosanitary authorities and researchers through interdisciplinary networks that allows increasing knowledge of the disease and raising awareness of the risks and mitigation measures among crucial target groups. The review also identified weak points in current regulations and provided suggestions for implementation.El chancro resinoso del pino (PPC, por sus siglas en inglés) es una grave enfermedad que afecta a Pinus spp. y Pseudotsuga menziesii en todo el mundo. La infección por su agente causal, Fusarium circinatum, provoca chancros de resina en los troncos y ramas laterales de los huéspedes maduros, que pueden acabar muriendo por anillamiento o rotura del tronco. En los viveros, los principales síntomas son el puntisecado, marchitamiento y muerte de las plántulas. Sin embargo, el patógeno, de naturaleza hemibiotrófica, puede permanecer endofítico en plántulas de pino sin mostrar síntomas de infección e incluso ser inadvertido en algunas especies herbáceas. Desde el primer registro en 1945 en Norteamérica, se ha notificado la presencia de F. circinatum en 14 países de América, Asia, África y Europa. Varios factores han contribuido a la propagación de la enfermedad a todos estos continentes, siendo el más importante la globalización en lo que respecta al comercio de material vegetal de reproducción. El viento, las gotas de lluvia y los insectos forestales asociados a los pinos contribuyen a la dispersión local del patógeno. A pesar de su importancia, no se dispone de medidas eficaces para erradicar o controlar la enfermedad del PPC ni en los viveros ni en el monte. El objetivo principal de esta tesis doctoral fue esclarecer los mecanismos de regulación eficaces para el control de la enfermedad PPC. Para ello, en primer lugar, se llevó a cabo una recopilación de información actual sobre las vías de propagación del patógeno, proponiendo mecanismos preventivos para evitar su introducción en zonas libres de la enfermedad. Las múltiples vías de propagación hacen de F. circinatum un reto a prevenir, agravado por el reciente descubrimiento de su colonización endofítica de especies no contampladas previamente como hospedantes que ilustra la importancia del conocimiento biológico y ecológico para el diseño de estrategias de intervención eficaces. Además, la erradicación de la enfermedad puede ser factible sólo si se detecta de forma inmediata a su introducción. En este sentido, se necesitan urgentemente nuevos métodos de detección y diagnóstico para la pronta detección de F. circinatum en semillas, plantas e insectos vectores. Para ello, es fundamental la colaboración entre las autoridades fitosanitarias y los investigadores a través de redes interdisciplinarias que permitan aumentar el conocimiento de la enfermedad y sensibilizar a los agentes implicados sobre los riesgos y las medidas de mitigación. En este trabajo también se identificaron los puntos débiles de la normativa actual y se aportaron sugerencias para su aplicación.Departamento de Producción Vegetal y Recursos ForestalesDoctorado en Conservación y Uso Sostenible de Sistemas Forestale

Power analysis for RNA sequencing and mass spectrometry-based proteomics data

RNA-sequencing and mass spectrometry technologies have facilitated the differential expression discoveries in transcriptome and proteome studies. However, the determination of sample size to achieve adequate statistical power has been a major challenge in experimental design. The objective of this study is to develop a power analysis tool applicable to both RNA-seq and MS-based proteomics data. The methods proposed in this study are capable of both prospective and retrospective power analyses. In terms of the performance, the benchmarking results indicated that the proposed methods can give distinct power estimates for both differentially and equivalently expressed genes or proteins without prior differential expression analysis and other assumptions, such as, expected fraction of differentially expressed features, minimal fold changes and expected mean expressions. Using the proposed methods, not only can researchers evaluate the reliability of their acquired significant results, but also estimate the sufficient sample size for a desired power. The proposed methods in this study were implemented as an R package, which can be freely accessed from Bioconductor project at http://bioconductor.org/packages/PowerExplorer/

Integrative analysis of the colorectal cancer proteome : potential clinical impact

Peer reviewedPostprin