Search results for "Transcriptome"

2015

Primary roots (radicles) represent the first visible developmental stages of the plant and are crucial for nutrient supply and the integration of environmental signals. Few studies have analyzed primary roots at a molecular level, and were mostly limited to Arabidopsis. Here we study the primary root transcriptomes of standard type, heterozygous columnar and homozygous columnar apple (Malus x domestica) by RNA-Seq and quantitative real-time PCR. The columnar growth habit is characterized by a stunted main axis and the development of short fruit spurs instead of long lateral branches. This compact growth possesses economic potential because it allows high density planting and mechanical harv…

TheMedicago truncatulahypermycorrhizal B9 mutant displays an altered response to phosphate and is more susceptible toAphanomyces euteiches

2014

Inorganic phosphate (Pi) plays a key role in the development of arbuscular mycorrhizal (AM) symbiosis, which is favoured when Pi is limiting in the environment. We have characterized the Medicago truncatula hypermycorrhizal B9 mutant for its response to limiting (P/10) and replete (P2) Pi. On P2, mycorrhization was significantly higher in B9 plants than in wild-type (WT). The B9 mutant displayed hallmarks of Pi-limited plants, including higher levels of anthocyanins and lower concentrations of Pi in shoots than WT plants. Transcriptome analyses of roots of WT and B9 plants cultivated on P2 or on P/10 confirmed the Pi-limited profile of the mutant on P2 and highlighted its altered response t…

A computational method for studying the relation between alternative splicing and DNA methylation.

2015

Alternative splicing is an important mechanism in eukaryotes that expands the transcriptome and proteome significantly. It plays an important role in a number of biological processes. Understanding its regulation is hence an important challenge. Recently, increasing evidence has been collected that supports an involvement of intragenic DNA methylation in the regulation of alternative splicing. The exact mechanisms of regulation, however, are largely unknown, and speculated to be complex: different methylation profiles might exist, each of which could be associated with a different regulation mechanism. We present a computational technique that is able to determine such stable methylation pa…

Polyamines in Developing Stress-Resistant Crops

2012

F.Marco,R.Alcazar,T.Altabella,P.Carrasco,SarvajeetSinghGill,NarendraTuteja,andA.F. TiburcioPolyamines (PAs) are small protonated compounds with key roles in plant devel-opmentandphysiologicalprocesses.PAsmayalsofunctionasstressmessengersinplant responses to different stress signals. Recent studies using exogenous appli-cation of polyamines and more contemporary genetic manipulation of polyaminelevelsincropsandmodelspeciespointtotheirinvolvementinstressprotection.Thedifferentmechanismsbywhichpolyaminesexerttheirfunctionsarepresentlybeingunraveledandinvolvedifferentmodesofactionthataresummarizedinthischapter.Polyamines are integrated with other stress-related hormone pathways, such asabscisic…

Integration of polyamins in the cold acclimation response

2011

8 páginas, 1 figura, 3 tablas -- PAGS nros. 31-38

Machine learning of reverse transcription signatures of variegated polymerases allows mapping and discrimination of methylated purines in limited tra…

2020

AbstractReverse transcription (RT) of RNA templates containing RNA modifications leads to synthesis of cDNA containing information on the modification in the form of misincorporation, arrest, or nucleotide skipping events. A compilation of such events from multiple cDNAs represents an RT-signature that is typical for a given modification, but, as we show here, depends also on the reverse transcriptase enzyme. A comparison of 13 different enzymes revealed a range of RT-signatures, with individual enzymes exhibiting average arrest rates between 20 and 75%, as well as average misincorporation rates between 30 and 75% in the read-through cDNA. Using RT-signatures from individual enzymes to trai…

NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination

2020

Abstract Methods for the detection of m6A by RNA-Seq technologies are increasingly sought after. We here present NOseq, a method to detect m6A residues in defined amplicons by virtue of their resistance to chemical deamination, effected by nitrous acid. Partial deamination in NOseq affects all exocyclic amino groups present in nucleobases and thus also changes sequence information. The method uses a mapping algorithm specifically adapted to the sequence degeneration caused by deamination events. Thus, m6A sites with partial modification levels of ∼50% were detected in defined amplicons, and this threshold can be lowered to ∼10% by combination with m6A immunoprecipitation. NOseq faithfully d…

Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic…

2019

AbstractBackgroundProduction conditions of layer chicken can vary in terms of temperature or diet energy content compared to the controlled environment where pure-bred selection is undertaken. The aim of this study was to better understand the long-term effects of a 15%-energy depleted diet on egg-production, energy homeostasis and metabolism via a multi-tissue transcriptomic analysis. Study was designed to compare effects of the nutritional intervention in two layer chicken lines divergently selected for residual feed intake.ResultsChicken adapted to the diet in terms of production by significantly increasing their feed intake and decreasing their body weight and body fat composition, whil…

Single-cell RNA sequencing of oocytes from ovarian endometriosis patients reveals a differential transcriptomic profile associated with lower quality

2018

Abstract STUDY QUESTION Do oocytes from women with ovarian endometriosis (OE) have a different transcriptomic profile than those from healthy women? SUMMARY ANSWER Oocytes from endometriosis patients, independently of whether they came from the affected ovary, exhibited a differential transcriptomic profile compared to oocytes from healthy egg donors. WHAT IS KNOWN ALREADY Studies of endometriosis have sought to determine whether OE affects oocyte quality. While many reports indicate that oocytes recovered from endometriotic ovaries may be affected by the disease, other studies have found no significant differences among oocyte/embryo quality and fertilization, implantation and pregnancy ra…

CAF-like state in primary skin fibroblasts with constitutional BRCA1 epimutation sheds new light on tumor suppressor deficiency-related changes in he…

2016

Constitutive epimutations of tumor suppressor genes are increasingly considered as cancer predisposing factors equally to sequence mutations. In light of the emerging role of the microenvironment for cancer predisposition, initiation, and progression, we aimed to characterize the consequences of a BRCA1 epimutation in cells of mesenchymal origin. We performed a comprehensive molecular and cellular comparison of primary dermal fibroblasts taken from a monozygous twin pair discordant for recurrent cancers and BRCA1 epimutation, whose exceptional clinical case we previously reported in this journal. Comparative transcriptome analysis identified differential expression of extracellular matrix-r…