The Reverse Transcription Signature of N-\u3csub\u3e1\u3c/sub\u3e-Methyladenosine in RNA-Seq is Sequence Dependent

The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here we simultaneously analyze both parameters in detail with respect to the occurrence of N-1-methyladenosine (m1A) in the template RNA. This naturally occurring modification is associated with structural effects, but it is also known as a mediator of antibiotic resistance in ribosomal RNA. In structural probing experiments with dimethylsulfate, m1A is routinely detected by RT-arrest. A specifically developed RNA-Seq protocol was tailored to the simultaneous analysis of RT-arrest and misincorporation patterns. By application to a variety of native and synthetic RNA preparations, we found a characteristic signature of m1A, which, in addition to an arrest rate, features misincorporation as a significant component. Detailed analysis suggests that the signature depends on RNA structure and on the nature of the nucleotide 3’ of m1A in the template RNA, meaning it is sequence dependent. The RT-signature ofm1Awas used for inspection and confirmation of suspected modification sites and resulted in the identification of hitherto unknown m1A residues in trypanosomal tRNA

Urban Services to Ecosystems - Green Infrastructure Benefits from the Landscape to the Urban Scale

The aim of this book is to bring together multidisciplinary research in the field of green infrastructure design, construction and ecology. The main core of the volume is constituted by contributions dealing with green infrastructure, vegetation science, nature-based solutions and sustainable urban development. The green infrastructure and its ecosystem services, indeed, are gaining space in both political agendas and academic research. However, the attention is focused on the services that nature is giving for free to and for human health and survival. What if we start to see things from another perspective? Our actions shall converge for instance to turn man-made environment like cities from heterotrophic to autotrophic ecosystems. From landscape ecology to urban and building design, like bricks of a wall, from the small scale to the bigger landscape scale via ecological networks and corridors, we should start answering these questions: what are the services that are we offering to Nature? What are we improving? How to implement our actions? This book contains three Open Access chapters, which are licensed under the terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0)