The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly
June 2017
Authors:
An-Yun Chang, Stephane Castel, Evan Ernst, Hyun Soo Kim, Robert Martienssen
Info:
Cold Spring Harbor Laboratory researchers studied the Rct1 protein in S. pombe and found that it is involved in processing pericentromeric transcripts into siRNAs. For the study, small RNA libraries were size-selected on a BluePippin and sequenced on a MiSeq instrument.
Citation:
Cell Reports
Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports the expression of active dense gene clusters
June 2017
Authors:
Kobe Yuen, Brian Slaughter, and Jennifer Gerton
Info:
Scientists in Kansas used the 4C-seq method to study the chromosome complex condensin II in mouse and human genomes. They found that it plays a role in maintaining high expression of histone gene clusters. The team used BluePippin to size-select 4C-seq libraries.
Citation:
Science Advances 21 Jun 2017: Vol. 3, no. 6, e1700191
DOI: 10.1126/sciadv.1700191
Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1
June 2017
Authors:
Dóra Tombácz, Zsolt Csabai, Attila Szűcs, Zsolt Balázs, et al.
Info:
Scientists from Hungary and California conducted isoform sequencing with PacBio to analyze the transcriptome of herpes simplex virus type 1. They discovered dozens of previously unidentified protein-coding genes and non-coding RNAs and found that transcription may facilitate crosstalk between distant genes. They used both BluePippin and SageELF to remove shorter fragments and focus libraries on the longest molecules.
Citation:
Front Microbiol. 2017; 8: 1079.
doi: 10.3389/fmicb.2017.01079
Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
June 2017
Authors:
Jason Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, Kin Fai Au
Info:
In this F1000 publication, scientists describe an evaluation of long-read sequencing technologies, finding that PacBio provides better data quality while Oxford Nanopore generates higher yield. They used SageELF to fractionate cDNAs into four contiguous size ranges.
Citation:
F1000Research 2017, 6:100
quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage
May 2017
Authors:
Franchini P, Monné Parera D, Kautt AF, Meyer A
Info:
Scientists from the University of Konstanz modified the original ddRAD-seq protocol to make it faster, more cost-effective, and higher-capacity. They report results from validating the new method on a population of Neotropical cichlid fish. Pippin Prep was used to size-select fragments prior to Illumina sequencing.
Citation:
Mol Ecol. 2017 May;26(10):2783-2795
doi: 10.1111/mec.14077