research highlights GENOMICS Worthington Chromatin-associated RNA sequencing elucidates the role of RNAs in The Feeling genome regulation. is Mutual tart local, then go global: this is the detect noncoding RNAs known to coat the trajectory followed by Aaron Straight X chromosome in male flies. Sand his collaborators at Stanford Unexpectedly, they also found RNAs that University. “We had been interested in bound every single chromosome. “At first, the idea that RNA might be structuring we thought it was an artifact,” remembers chromatin in some way,” recalls Straight. Straight, but upon closer inspection they In 2017, his team discovered that RNAs identified some of the RNAs as components encoded by repeats remain associated in cis of the spliceosome and realized they were with the mitotic chromosome and recruit looking at cotranscriptional splicing. The methyltransferases that help generate high resolution of ChAR-seq allowed the heterochromatin. This finding prompted a team to map the spliceosomes to the open more general search for RNAs involved in reading frames they were associating with. genome regulation. The first requirement Other ubiquitously binding RNAs remain was a method to profile all genome- to be characterized. “There are interesting associated RNAs. classes of RNA that coat every chromosome; What initially started as a side project was for some of them we have no idea what they We love our customers and boosted by a seed grant from the Stanford are doing,” says Straight. “There is a lot of it seems they love us too! Center for Systems Biology to students and biology here to dig into.” postdoctoral fellows in support of projects Another fertile area for ChAR-seq is the With over 100 citations deemed risky. Jason Bell, a postdoc in the functional characterization of noncoding published in leading scientific Straight lab, teamed up with David Jukam RNAs. Even if the function of a particular from Jan Skotheim’s lab; Viviana Risca, RNA is unknown, its binding site can be journals monthly, Worthington working with Will Greenleaf; and three correlated with other marks in that region, enzymes have been critical to rotation students in the Straight lab—Owen such as histone modifications, that may give Smith, Nikki Teran and Whitney Johnson. a clue as to the RNA’s function. Straight is research for 70 years. Together they developed an approach to particularly excited about this capability, Authoring technical manuals enrich RNAs bound to the genome. which he wants to apply to human genomes. Their chromatin-associated RNA- “Of the roughly 20,000 noncoding RNAs, and guides both print and sequencing (ChAR-seq) approach tackles the we know the function of about 50 of digital, we look to serve the challenging aspects of generating a covalent them,” he says; “ChAR-seq is a great needs of up-and-coming linkage between DNA and RNA. The team hypothesis generator.” first cross-linked RNA and chromatin in Straight’s team is also planning to use research scientists worldwide. situ, then appended an adenylated and ChAR-seq in Xenopus embryos to map the biotinylated linker to the 3’ end of RNA, RNAs that bind the genome in the absence using an RNA ligase that will link only an of transcription and characterize the Feeling it’s time to discover adenylated DNA substrate, to avoid spurious change in RNA occupancy as the genome is RNA–DNA ligation. Then, after reverse activated and transcription begins. Worthington enzymes? Visit: transcription and digestion of the genomic ChAR-seq joins similar approaches such Worthington-Biochem.com DNA, they ligated the other end of the linker as GRID-seq, developed in Xiang-Dong Fu’s to DNA. Biotin allowed easy purification of lab at UCSD, each with its unique strengths, the complex followed by amplification and each contributing to understanding of the Come see us at WPC - sequencing. This procedure not only kept interplay between RNA and chromatin to RNA and DNA together but also retained ensure proper genome function. Booth 201 the polarity of the chimeric reads; the read sequence upstream of the linker came Nicole Rusk from RNA, the downstream sequence from DNA. The researchers could then map each Published online: 31 May 2018 segment to the transcriptome or genome https://doi.org/10.1038/s41592-018-0030-2 and derive contact maps for cis or trans binding RNA. Research papers To ensure that ChAR-seq worked as Bell, J. C. et al. Chromatin-associated RNA expected, the researchers first applied it to sequencing (ChAR-seq) maps genome-wide 800.445.9603 • 732.942.1660 the fly genome and verified that they could RNA-to-DNA contacts. eLife 7, e27024 (2018). Nature Methods | VOL 15 | JUNE 2018 | 403–409 | www.nature.com/naturemethods © 2018 Nature America Inc., part of Springer Nature. All rights reserved.
Nature Methods – Springer Journals
Published: May 31, 2018
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