ABSTRACT
Members of the genus Polynucleobacter belonging to the subcluster PnecA comprise freshwater bacterioplankton with worldwide distribution. Here, we report the complete genome sequences of two Polynucleobacter sp. strains (PnecA), SHI2 and SHI8, isolated from the surface water of an oligotrophic-dystrophic lake in a humid continental climate in Japan.
ABSTRACT
The globally distributed freshwater bacterioplankton of the genus Aurantimicrobium belong to the tribe Luna2. Here, we report the complete genome sequence of Aurantimicrobium sp. strain INA4, which was isolated from an oligotrophic lake surface water in Japan.
ABSTRACT
The genus Rhodoluna belongs to the ubiquitous freshwater bacterioplankton tribe Luna1-A2. Here, we report the complete sequences of Rhodoluna sp. strains KAS3 and KACHI23, which were isolated from freshwater lake and river surface water in Japan.
ABSTRACT
The globally distributed bacterioplankton of the genus Aquiluna belong to the tribe Luna1-A1. Here, we report the complete genome sequence of Aquiluna sp. strain KACHI24, which was isolated from river surface water in Japan.
ABSTRACT
In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
Subject(s)
Gene Expression Profiling , Genome , Animals , Gene Expression Regulation , Humans , Mice , Promoter Regions, Genetic , Species SpecificityABSTRACT
Next-generation sequencing experiments have shown that microRNAs (miRNAs) are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found that mature miR-21, the most widely researched miRNA because of its importance in human disease, is produced in two prevalent isomiR forms that differ by 1 nt at their 3' end, and moreover that the 3' end of miR-21 is posttranscriptionally adenylated by the noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase in the miR-21 expression level, suggesting that PAPD5-mediated adenylation of miR-21 leads to its degradation. Exoribonuclease knockdown experiments followed by small-RNA sequencing suggested that PARN degrades miR-21 in the 3'-to-5' direction. In accordance with this model, microarray expression profiling demonstrated that PAPD5 knockdown results in a down-regulation of miR-21 target mRNAs. We found that disruption of the miR-21 adenylation and degradation pathway is a general feature in tumors across a wide range of tissues, as evidenced by data from The Cancer Genome Atlas, as well as in the noncancerous proliferative disease psoriasis. We conclude that PAPD5 and PARN mediate degradation of oncogenic miRNA miR-21 through a tailing and trimming process, and that this pathway is disrupted in cancer and other proliferative diseases.
Subject(s)
Adenine/metabolism , MicroRNAs/metabolism , Neoplasms/genetics , RNA Nucleotidyltransferases/metabolism , RNA Stability , Base Sequence , Cytosine/metabolism , Exoribonucleases/metabolism , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Gene Knockdown Techniques , High-Throughput Nucleotide Sequencing , Humans , MCF-7 Cells , MicroRNAs/chemistry , MicroRNAs/genetics , Models, Biological , Molecular Sequence Data , Neoplasms/pathology , Nucleic Acid Conformation , Protein Isoforms/chemistry , Protein Isoforms/genetics , Protein Isoforms/metabolism , Ribonuclease III/metabolismABSTRACT
To explore the estrogen-regulated genes genome-widely in breast cancer, cap analysis of gene expression (CAGE) sequencing was performed in MCF-7 cells under estrogen treatment. Estrogen-regulated expressional changes were found in 1537 CAGE tag clusters (TCs) (⩾1.5 or ⩽0.66-folds). Among them, 15 TCs were situated in the vicinity of (⩽10 kb) reported estrogen receptor-binding sites. Knockdown experiments of the 15 TC-associated genes demonstrated that the genes such as RAMP3, ISOC1 and GPRC5C potentially regulate the growth or migration of MCF-7 cells. These results suggest that CAGE sequencing will reveal novel estrogen target genes in breast cancer.
