Citations

Chromosomal rearrangements but no change of genes and transposable elements repertoires in an invasive forest-pathogenic fungus

Authors:
Arthur Demené , Benoît Laurent , Sandrine Cros-Arteil , Christophe Boury , Cyril Dutech

Info:
The authors present a high-quality de novo genome assembly of Cryphonectria parasitica, and invasive fungus that causes chestnut blight, using Oxford Nanopore and Illumina sequencing. The assembly was compared to a recently published reference genome. The comparison showed little difference in gene and transposable element repertoires but showed significant chromosomal rearrangements. The authors suggest that the differences likely have implications with regard to gene regulation and mating of invasive fungi.
BluePippin was used to High-Pass size select (>20KB) using the High Pass Plus cassettes prior to library preparation for the Oxford Nanopore GridION.

Author Affiliations:
BIOGECO, INRAE, Univ. Bordeaux, Cestas France
BGPI, INRAE, CIRAD, Montpellier FRANCE.

Citation:
bioRxiv preprint
DOI: 10.1101/2021.03.09.434572

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Resetting of 24-nt siRNA landscape is initiated before the first zygotic division in rice

January 2021

Authors:
Chenxin Li, Jonathan I. Gent, Hengping Xu, Hong Fu, Scott D. Russell, and Venkatesan Sundaresan

Info:
In this preprint, the authors report on a study of siRNA profiling in zygotes from the rice plant. They report that the zygote has widespread siRNA loci that correlate to the endosperm rather than the egg, and that these loci have abundant CHH methylation. A small fraction of siRNA “siren” loci correlate to the egg and account for 75% of the zygote siRNAs and are not associated with methylation. The results suggest that the resetting of the gametic epigenome toward the canonical vegetative profile initiates before the first embryonic division.

PippinHT is used to isolate the microRNA libraries from NEXTFlex small RNA kits (Perkin Elmer/Bioo Scientific) prior to Illumina sequencing.

Author Affiliations:
Department of Plant Biology, University of California, Davis, CA
Department of Plant Biology, University of Georgia, Athens, GA
Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK
Department of Plant Sciences, University of California, Davis, CA

Citation:
bioRxiv preprint
DOI: 10.1101/2020.08.31.275958

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A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol

January 2021

Authors:
Dimitrios G Anastasakis, Alexis Jacob, Parthena Konstantinidou, Kazuyuki Meguro, Duncan Claypool, Pavol Cekan, Astrid D Haase, Markus Hafner

Info:
The authors offer an improvement to the PAR-CLIP method that is more streamlined and does not require the use of radioactive labels. CLIP-seq (CrossLinking and ImmunoPrecipitation) is used to evaluate protein-RNA interactions during gene expression. PAR-CLIP uses in vivo labelling of RNA with photoreactive nucleosides . The method outlined in this protocol (fPAR-CLIP) uses direct ligation of fluorescent adapters to RNA/protein complexes, followed by the isolation of the RNA. The original PAR-CLIP method requires size fractionation on denaturing polyacrylamide gels. The fPAR-CLIP method presented here eliminates this requirement, is more sensitive, and is completed in 2 rather than 4 days.

Pippin Prep is used to size select PCR fragments and eliminate primers and adapters.

Author Affiliations:
Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, NIH, Bethesda MD

Laboratory of Cellular and Molecular Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda MD

Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda MD

MultiplexDX, Bratislava, Slovakia

Citation:
Nucleic Acids Research
DOI: 10.1093/nar/gkab011

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isoCirc catalogs full-length circular RNA isoforms in human transcriptomes

January 2021

Authors:
Ruijiao Xin, Yan Gao, Yuan Gao, Robert Wang, Kathryn E. Kadash-Edmondson, Bo Liu, Yadong Wang, Lan Lin & Yi Xing

Info:
The authors present a protocol, isoCirc, for the full-length sequence determination of circular RNAs. The method features rolling circle amplification followed by nanopore sequencing, and includes a description of an integrated computation pipeline. A catalogue of over 100,000 circular RNAs across 12 human tissues and the HEK293 cell line was produced, including ~40,000 isoforms.
BluePippin was used to size select the RCA products after debranching prior to ONT MinION library prep.

Author Affiliations:
Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA
Genomics and Computational Biology Graduate Program, University of Pennsylvania
Department of Computer Science and Technology, Center for Bioinformatics, Harbin Institute of Technology, Harbin, China
Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA

Citation:
Nature Communications
DOI: 10.1038/s41467-020-20459-8

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ATAC-seq with unique molecular identifiers improves quantification and footprinting

November 2020

Authors:
Tao Zhu, Keyan Liao, Rongfang Zhou, Chunjiao Xia & Weibo Xie

Info:
The authors suggest an improvement on the ATAC-seq method (Assay for Transposase-Accessible Chromatin with high-throughput sequencing). By using unique molecular identifiers to distinguish between transposase insertions and PCR duplicates. They go on to demonstrate the UMI-ATAC-seq method more accurately quantifies chromatin accessibility and improve the sensitivity of identifying transcription footprints.

The PippinHT was used to size select libraries prior to sequencing.

Author Affiliations:
Huazhong Agricultural University, Wuhan China

Citation:
Nature Communications Biology
DOI: 10.1038/s42003-020-01403-4

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