The UCSC Genome Browser database: 2018 update

Casper, Jonathan D.; Zweig, Ann S.; Villarreal, Chris; Tyner, Cath; Speir, Matthew L; Rosenbloom, Kate R.; Raney, Brian J.; Lee, Brian T.; Karolchik, Donna; Hinrichs, Angie S.; Haeussler, Maximilian; Guruvadoo, Luvina; Gonzalez, Jairo Navarro; Gibson, David J.; Fiddes, Ian T.; Eisenhart, Christopher; Diekhans, Mark; Clawson, Hiram; Barber, Galt P.; Armstrong, Joel; Haussler, David; Kuhn, Robert M.; Kent, W. James

doi:10.1093/nar/gkx1020

Cited by 484 publications

(465 citation statements)

References 49 publications

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“…Bacterial, archaeal and 72 fungal eukaryotic genomes were obtained from NCBI GenBank, and 101 large eukaryotic genomes were obtained from the UCSC Genome Browser (21) and JGI Phytozome (22). The prediction results of specific genomes highlighted in this manuscript are human (GRCh37/hg19 and GRCh38/hg38), mouse (GRCm38/mm10), cat (Felis_catus_9.0), Saccharomyces cerevisiae S288c (GCA_000146045.2/R64), Escherichia coli str.…”

Section: Trnascan-se Prediction Resultsmentioning

confidence: 99%

tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes

Chan

Lin

Mak

et al. 2019

Preprint

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tRNAscan-SE has been widely used for whole-genome transfer RNA gene prediction for nearly two decades. With the increased availability of new genomes, a vastly larger training set has enabled creation of nearly one hundred specialized isotype-specific models, greatly improving tRNAscan-SE's ability to identify and classify both typical and atypical tRNAs. We employ a new multi-model annotation strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models. A post-filtering feature also better identifies tRNA-derived SINEs that are abundant in many eukaryotic genomes, and provides a "high confidence" tRNA gene set which improves upon prior pseudogene prediction. These new enhancements of tRNAscan-SE will provide researchers more accurate detection and more comprehensive annotation for tRNA genes.

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Section: Trnascan-se Prediction Resultsmentioning

confidence: 99%

tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes

Chan

Lin

Mak

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…The normalized WIG files were then encoded in bigWig format using the Kent utilities (Rhead et al, 2010). Visual inspection of the data was performed using an Assem-blyHub on the UCSC Genome Browser (Casper et al, 2018). The Versatile Aggregate Profiler (VAP) tool (Coulombe et al, 2014; Brunelle et al, 2015) version 1.1.0 was used to generate the average profile using the following parameters: annotation mode, absolute analysis method, 10 bp windows size, mean aggregate value and smoothing of 6, and missing data were considered as "0".…”

Section: Chip-seq Data Analysismentioning

confidence: 99%

Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription

et al. 2019

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R‐loop disassembly by the human helicase Senataxin contributes to genome integrity and to proper transcription termination at a subset of RNA polymerase II genes. Whether Senataxin also contributes to transcription termination at other classes of genes has remained unclear. Here, we show that Sen1, one of two fission yeast homologues of Senataxin, promotes efficient termination of RNA polymerase III (RNAP3) transcription in vivo. In the absence of Sen1, RNAP3 accumulates downstream of RNAP3‐transcribed genes and produces long exosome‐sensitive 3′‐extended transcripts. Importantly, neither of these defects was affected by the removal of R‐loops. The finding that Sen1 acts as an ancillary factor for RNAP3 transcription termination in vivo challenges the pre‐existing view that RNAP3 terminates transcription autonomously. We propose that Sen1 is a cofactor for transcription termination that has been co‐opted by different RNA polymerases in the course of evolution.

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“…Considering that not all of the repeat domains in Xist exhibit conservation across eutherian mammals, we sought to determine whether or not the repeat domains in koala Rsx were conserved in another marsupial. Rsx was originally identified in opossum (Grant et al, 2012), but the most current assembly of the opossum genome (mondom5; (Casper et al, 2018)) harbors significant gaps within the sequence of Rsx.…”

Section: Conservation Of Repeat Domains Between Koala and Opossum Rsxmentioning

confidence: 99%

Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains

Sprague

Waters

Kirk

et al. 2019

Preprint

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The marsupial inactive X chromosome expresses a long noncoding RNA (lncRNA) called Rsx that has been proposed to be the functional analogue of eutherian Xist. Despite the possibility that Xist and Rsx encode related functions, the two lncRNAs harbor no linear sequence similarity.However, both lncRNAs harbor domains of tandemly repeated sequence. In Xist, these repeat domains are known to be critical for function. Using k-mer based comparison, we show that the repeat domains of Xist and Rsx unexpectedly partition into two major clusters that each harbor substantial levels of non-linear sequence similarity. Xist Repeats B, C and D were most similar to each other and to Rsx Repeat 1, whereas Xist Repeats A and E were most similar to each other and to Rsx Repeats 2, 3, and 4. Similarities at the level of k-mers corresponded to domain-specific enrichment of protein-binding motifs. Within individual domains, protein-binding motifs were often enriched to extreme levels. Our data support the hypothesis that Xist and Rsx encode similar functions through different spatial arrangements of functionally analogous protein-binding domains. We propose that the two clusters of repeat domains in Xist and Rsx function in part to cooperatively recruit PRC1 and PRC2 to chromatin. The physical manner in which these domains engage with protein cofactors may be just as critical to the function of the domains as the protein cofactors themselves. The general approaches we outline in this report should prove useful in the study of any set of RNAs.

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The UCSC Genome Browser database: 2018 update

Cited by 484 publications

References 49 publications

tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes

tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes

Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription

Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains

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