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1.
Sci Data ; 5(1): 2, 2018 12 11.
Artigo em Inglês | MEDLINE | ID: mdl-30538238

RESUMO

The authors regret that Luba M. Pardo was omitted in error from the author list of the original version of this Data Descriptor. This omission has now been corrected in the HTML and PDF versions. The authors also regret that Anemieke Rozemuller was omitted in error from the Acknowledgements of the original version of this Data Descriptor. This omission has now been corrected in the HTML and PDF versions.

2.
Sci Data ; 4: 170163, 2017 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-29087374

RESUMO

Rhesus macaque was the second non-human primate whose genome has been fully sequenced and is one of the most used model organisms to study human biology and disease, thanks to the close evolutionary relationship between the two species. But compared to human, where several previously unknown RNAs have been uncovered, the macaque transcriptome is less studied. Publicly available RNA expression resources for macaque are limited, even for brain, which is highly relevant to study human cognitive abilities. In an effort to complement those resources, FANTOM5 profiled 15 distinct anatomical regions of the aged macaque central nervous system using Cap Analysis of Gene Expression, a high-resolution, annotation-independent technology that allows monitoring of transcription initiation events with high accuracy. We identified 25,869 CAGE peaks, representing bona fide promoters. For each peak we provide detailed annotation, expanding the landscape of 'known' macaque genes, and we show concrete examples on how to use the resulting data. We believe this data represents a useful resource to understand the central nervous system in macaque.


Assuntos
Sistema Nervoso Central , Macaca mulatta , Sítio de Iniciação de Transcrição , Animais , Sistema Nervoso Central/anatomia & histologia , Transcriptoma
3.
Sci Data ; 4: 170112, 2017 08 29.
Artigo em Inglês | MEDLINE | ID: mdl-28850106

RESUMO

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.


Assuntos
Perfilação da Expressão Gênica , Genoma , Animais , Regulação da Expressão Gênica , Humanos , Camundongos , Regiões Promotoras Genéticas , Especificidade da Espécie
4.
Proc Natl Acad Sci U S A ; 111(31): 11467-72, 2014 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-25049417

RESUMO

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.


Assuntos
Adenina/metabolismo , MicroRNAs/metabolismo , Neoplasias/genética , RNA Nucleotidiltransferases/metabolismo , Estabilidade de RNA , Sequência de Bases , Citosina/metabolismo , Exorribonucleases/metabolismo , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Técnicas de Silenciamento de Genes , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Células MCF-7 , MicroRNAs/química , MicroRNAs/genética , Modelos Biológicos , Dados de Sequência Molecular , Neoplasias/patologia , Conformação de Ácido Nucleico , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Ribonuclease III/metabolismo
5.
Cold Spring Harb Protoc ; 2011(1): pdb.prot5559, 2011 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-21205859

RESUMO

Cap analysis gene expression (CAGE) is a method to identify the 5' ends of transcripts, allowing the discovery of new promoters and the quantification of gene activity. Combining promoter location and their expression levels, CAGE data are essential for annotation-agnostic studies of regulatory gene networks. However, CAGE requires large amounts of input RNA, which usually are not obtainable from highly refined samples such as tissue microdissections or subcellular fractions. The nanoCAGE method can capture the 5' ends of transcripts from as little as 10 ng of total RNA and takes advantage of the capacity of current sequencers to produce longer (50-100 bp) reads. The method prepares cap-selected cDNAs ready for direct sequencing of their 5' ends (optionally mate-paired with the 3' end) that can provide information about downstream sequences. This protocol describes how to prepare nanoCAGE libraries from as little as 50 ng of total RNA within two working days. The libraries can be sequenced using an Illumina sequencer Genome Analyzer IIX [corrected] with a level of sensitivity 1000 times higher than CAGE.


Assuntos
Perfilação da Expressão Gênica/métodos , Nanotecnologia/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos
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