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1.  Annotating non-coding transcription using functional genomics strategies 
Non-coding RNA (ncRNA) transcripts are RNA molecules that do not code for proteins, but elicit function by other mechanisms. The vast majority of RNA produced in a cell is non-coding ribosomal RNA, produced from relatively few loci, however more recently complementary DNA (cDNA) cloning, tag sequencing, and genome tiling array studies suggest that ncRNAs also account for the majority of RNA species produced by a cell. ncRNA based regulation has been referred to as a ‘hidden layer’ of signals or ‘dark matter’ that control gene expression in cellular processes by poorly described mechanisms. These terms have appeared as ncRNAs until recently have been ignored by expression profiling and cDNA annotation projects and their mode of action is diverse (e.g. influencing chromatin structure and epigenetics, translational silencing, transcriptional silencing). Here, we highlight recent functional genomics strategies toward identifying and assigning function to ncRNA transcription.
doi:10.1093/bfgp/elp041
PMCID: PMC2762128  PMID: 19833699
non-coding RNA; Sequencing; transcription; annotation
2.  Multiplicity of 5′ Cap Structures Present on Short RNAs 
PLoS ONE  2014;9(7):e102895.
Most RNA molecules are co- or post-transcriptionally modified to alter their chemical and functional properties to assist in their ultimate biological function. Among these modifications, the addition of 5′ cap structure has been found to regulate turnover and localization. Here we report a study of the cap structure of human short (<200 nt) RNAs (sRNAs), using sequencing of cDNA libraries prepared by enzymatic pretreatment of the sRNAs with cap sensitive-specificity, thin layer chromatographic (TLC) analyses of isolated cap structures and mass spectrometric analyses for validation of TLC analyses. Processed versions of snoRNAs and tRNAs sequences of less than 50 nt were observed in capped sRNA libraries, indicating additional processing and recapping of these annotated sRNAs biotypes. We report for the first time 2,7 dimethylguanosine in human sRNAs cap structures and surprisingly we find multiple type 0 cap structures (mGpppC, 7mGpppG, GpppG, GpppA, and 7mGpppA) in RNA length fractions shorter than 50 nt. Finally, we find the presence of additional uncharacterized cap structures that wait determination by the creation of needed reference compounds to be used in TLC analyses. These studies suggest the existence of novel biochemical pathways leading to the processing of primary and sRNAs and the modifications of their RNA 5′ ends with a spectrum of chemical modifications.
doi:10.1371/journal.pone.0102895
PMCID: PMC4117478  PMID: 25079783
3.  Landscape of transcription in human cells 
Djebali, Sarah | Davis, Carrie A. | Merkel, Angelika | Dobin, Alex | Lassmann, Timo | Mortazavi, Ali M. | Tanzer, Andrea | Lagarde, Julien | Lin, Wei | Schlesinger, Felix | Xue, Chenghai | Marinov, Georgi K. | Khatun, Jainab | Williams, Brian A. | Zaleski, Chris | Rozowsky, Joel | Röder, Maik | Kokocinski, Felix | Abdelhamid, Rehab F. | Alioto, Tyler | Antoshechkin, Igor | Baer, Michael T. | Bar, Nadav S. | Batut, Philippe | Bell, Kimberly | Bell, Ian | Chakrabortty, Sudipto | Chen, Xian | Chrast, Jacqueline | Curado, Joao | Derrien, Thomas | Drenkow, Jorg | Dumais, Erica | Dumais, Jacqueline | Duttagupta, Radha | Falconnet, Emilie | Fastuca, Meagan | Fejes-Toth, Kata | Ferreira, Pedro | Foissac, Sylvain | Fullwood, Melissa J. | Gao, Hui | Gonzalez, David | Gordon, Assaf | Gunawardena, Harsha | Howald, Cedric | Jha, Sonali | Johnson, Rory | Kapranov, Philipp | King, Brandon | Kingswood, Colin | Luo, Oscar J. | Park, Eddie | Persaud, Kimberly | Preall, Jonathan B. | Ribeca, Paolo | Risk, Brian | Robyr, Daniel | Sammeth, Michael | Schaffer, Lorian | See, Lei-Hoon | Shahab, Atif | Skancke, Jorgen | Suzuki, Ana Maria | Takahashi, Hazuki | Tilgner, Hagen | Trout, Diane | Walters, Nathalie | Wang, Huaien | Wrobel, John | Yu, Yanbao | Ruan, Xiaoan | Hayashizaki, Yoshihide | Harrow, Jennifer | Gerstein, Mark | Hubbard, Tim | Reymond, Alexandre | Antonarakis, Stylianos E. | Hannon, Gregory | Giddings, Morgan C. | Ruan, Yijun | Wold, Barbara | Carninci, Piero | Guigó, Roderic | Gingeras, Thomas R.
Nature  2012;489(7414):101-108.
Summary
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific sub-cellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic sub-cellular localizations are also poorly understood. Since RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modifications and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations taken together prompt to a redefinition of the concept of a gene.
doi:10.1038/nature11233
PMCID: PMC3684276  PMID: 22955620

Results 1-3 (3)