The UCSC Genome Browser database: 2021 update

Gonzalez, Jairo Navarro; Zweig, Ann S.; Speir, Matthew L; Schmelter, Daniel; Rosenbloom, Kate R.; Raney, Brian J.; Powell, Conner C; Nassar, Luis R; Maulding, Nathan D; Lee, Christopher M.; Hinrichs, Angie S.; Fyfe, Alastair Charles; Fernandes, Jason D; Diekhans, Mark; Clawson, Hiram; Casper, Jonathan D.; Benet‐Pagès, Anna; Barber, Galt P.; Haussler, David; Kuhn, Robert M.; Haeussler, Maximilian; Kent, W. James

doi:10.1093/nar/gkaa1070

Cited by 405 publications

(381 citation statements)

References 45 publications

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“…The repeats used in our study were annotated in the annotation file of hg19, which can be obtained at the download site of UCSC Genome Browser ( Fernandes et al, 2020 ; Navarro Gonzalez et al, 2020 ) ( http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz ). “Simple repeats” and “Satellites” were selected as the TRRs from the file.…”

Section: Methodsmentioning

confidence: 99%

Comparative Analysis for the Performance of Long-Read-Based Structural Variation Detection Pipelines in Tandem Repeat Regions

Guo

Zhou

et al. 2021

Front. Pharmacol.

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There has been growing recognition of the vital links between structural variations (SVs) and diverse diseases. Research suggests that, with much longer DNA fragments and abundant contextual information, long-read technologies have advantages in SV detection even in complex repetitive regions. So far, several pipelines for calling SVs from long-read sequencing data have been proposed and used in human genome research. However, the performance of these pipelines is still lack of deep exploration and adequate comparison. In this study, we comprehensively evaluated the performance of three commonly used long-read SV detection pipelines, namely PBSV, Sniffles and PBHoney, especially the performance on detecting the SVs in tandem repeat regions (TRRs). Evaluated by using a robust benchmark for germline SV detection as the gold standard, we thoroughly estimated the precision, recall and F1 score of insertions and deletions detected by the pipelines. Our results revealed that all these pipelines clearly exhibited better performance outside TRRs than that in TRRs. The F1 scores of Sniffles in and outside TRRs were 0.60 and 0.76, respectively. The performance of PBSV was similar to that of Sniffles, and was generally higher than that of PBHoney. In conclusion, our findings can be benefit for choosing the appropriate pipelines in real practice and are good complementary to the application of long-read sequencing technologies in the research of rare diseases.

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Section: Methodsmentioning

confidence: 99%

Comparative Analysis for the Performance of Long-Read-Based Structural Variation Detection Pipelines in Tandem Repeat Regions

Guo

Zhou

et al. 2021

Front. Pharmacol.

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“…The uniquely mapped reads were then used for counting the mapped reads for individual SINE loci by a Python script. The location and orientation of SINE loci were retrieved from the UCSC table browser [ 6 ]. For normalization of SINE expression, reads matching the sense strand of 5S or 5.8S rRNA (position in query start and position in repeat start both being 1 or 2, and query left and repeat left both being 5 or less) in the repeatmasker outputs were counted.…”

Section: Methodsmentioning

confidence: 99%

melRNA-seq for Expression Analysis of SINE RNAs and Other Medium-Length Non-Coding RNAs

Mori

Ichiyanagi

2021

Mobile DNA

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Background Small interspersed elements (SINEs) are transcribed by RNA polymerase III (Pol III) to produce RNAs typically 100–500 nucleotides in length. Although their RNA abundance can be evaluated by Northern blotting and primer extension, the nature (sequence, exact length, and genomic origin) of these RNAs cannot be revealed by these methods. Moreover, mRNA sequencing (mRNA-seq) is not able to distinguish bona fide SINE RNAs or SINE sequences present in longer transcripts. Results To elucidate the abundance, source loci, and sequence nature of SINE RNAs, we established a deep sequencing method, designated as melRNA-seq (medium-length RNA-seq), which can determine whole-length RNA sequences. Total RNA samples were treated with 5′ pyrophosphohydrolase (RppH), which allowed ligation of an RNA adaptor to the 5′ end of intact SINE RNAs. Similarly, another adaptor was ligated to the 3′ end, followed by reverse transcription, PCR amplification, size selection, and single-end deep sequencing. The analysis of two biological replicates of RNAs from mouse spermatogonia showed high reproducibility of SINE expression data both at family and locus levels. Conclusions This new method can be used for quantification and detailed sequence analysis of medium-length non-coding RNAs, such as rRNA, snRNA, tRNAs, and SINE RNAs. Further, its dynamic range is much wider than Northern blotting and primer extension.

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“…Genome Alignments. Visualiziation of genome alignments and genomic annotations were generated using the UCSC Genome Browser database (https:// genome.ucsc.edu) (51).…”

Section: Aldea Et Almentioning

confidence: 99%

Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution

Aldea¹,

Atsuta

Kokalari³

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Humans sweat to cool their bodies and have by far the highest eccrine sweat gland density among primates. Humans’ high eccrine gland density has long been recognized as a hallmark human evolutionary adaptation, but its genetic basis has been unknown. In humans, expression of the Engrailed 1 (EN1) transcription factor correlates with the onset of eccrine gland formation. In mice, regulation of ectodermal En1 expression is a major determinant of natural variation in eccrine gland density between strains, and increased En1 expression promotes the specification of more eccrine glands. Here, we show that regulation of EN1 has evolved specifically on the human lineage to promote eccrine gland formation. Using comparative genomics and validation of ectodermal enhancer activity in mice, we identified a human EN1 skin enhancer, hECE18. We showed that multiple epistatically interacting derived substitutions in the human ECE18 enhancer increased its activity compared with nonhuman ape orthologs in cultured keratinocytes. Repression of hECE18 in human cultured keratinocytes specifically attenuated EN1 expression, indicating this element positively regulates EN1 in this context. In a humanized enhancer knock-in mouse, hECE18 increased developmental En1 expression in the skin to induce the formation of more eccrine glands. Our study uncovers a genetic basis contributing to the evolution of one of the most singular human adaptations and implicates multiple interacting mutations in a single enhancer as a mechanism for human evolutionary change.

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The UCSC Genome Browser database: 2021 update

Cited by 405 publications

References 45 publications

Comparative Analysis for the Performance of Long-Read-Based Structural Variation Detection Pipelines in Tandem Repeat Regions

Comparative Analysis for the Performance of Long-Read-Based Structural Variation Detection Pipelines in Tandem Repeat Regions

melRNA-seq for Expression Analysis of SINE RNAs and Other Medium-Length Non-Coding RNAs

Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution

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