'The core human mitochondrial transcription apparatus is currently regarded as an obligate three-component system comprising the bacteriophage T7-related mitochondrial RNA polymerase, the rRNA methyltransferase-related transcription factor, h-mtTFB2, and the high mobility group box transcription/DNA-packaging factor, h-mtTFA/TFAM. Using a faithful recombinant human mitochondrial transcription system from Escherichia coli, we demonstrate that ... More
Protein-primed terminal transferase activity of hepatitis B virus polymerase.
AuthorsJones SA, Hu J
JournalJ Virol
PubMed ID23255788
'Hepatitis B virus (HBV) replication requires reverse transcription of an RNA pregenome (pgRNA) by a multifunctional polymerase (HP). HP initiates viral DNA synthesis by using itself as a protein primer and an RNA signal on pgRNA, termed epsilon (He), as the obligatory template. We discovered a Mn(2+)-dependent transferase activity of ... More
Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp.
AuthorsEujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K, Zwonitzer JC, Mian MA
JournalTheor Appl Genet
PubMed ID13679975
'Expressed sequence tags (ESTs) are important resources for gene discovery and molecular marker development. From over 147,000 ESTs of Medicago truncatula, we have identified 4,384 ESTs containing perfect simple sequence repeats (EST-SSR) of di-, tri-, tetra- or pentanucleotides. Six hundred sixteen primer pairs (PPs) were designed and screened over a ... More
Development of microsatellite markers for Qualea grandiflora (Vochysiaceae), a typical species of the Brazilian cerrado.
AuthorsRitter LM, Bajay MM, Monteiro M, Souza RG, Moreno MA, Kageyama PY
JournalAm J Bot
PubMed ID22343539
Microsatellite primers were developed to investigate genetic diversity and population structure of Qualea grandiflora, a typical species of the Brazilian cerrado.
Microsatellite markers developed for Utricularia reniformis (Lentibulariaceae).
AuthorsClivati D, Gitzendanner MA, Hilsdorf AW, Araújo WL, Oliveira de Miranda VF
JournalAm J Bot
PubMed ID22947485
Microsatellite markers were developed to study the genetic diversity and population structure of the carnivorous bladderwort Utricularia reniformis, which is endemic to the Atlantic Forest of southern and southeastern Brazil. Cross-species amplification was tested in U. gibba, U. neottioides, U. subulata, and Pinguicula benedicta. ... More
A simple and efficient method for isolating small RNAs from different plant species.
AuthorsRosas-Cárdenas Fde F, Durán-Figueroa N, Vielle-Calzada JP, Cruz-Hernández A, Marsch-Martínez N, de Folter S
JournalPlant Methods
PubMed ID21349188
Small RNAs emerged over the last decade as key regulators in diverse biological processes in eukaryotic organisms. To identify and study small RNAs, good and efficient protocols are necessary to isolate them, which sometimes may be challenging due to the composition of specific tissues of certain plant species. Here we ... More
Preparation and analysis of microRNA libraries using the Illumina massively parallel sequencing technology.
AuthorsMorin RD, Zhao Y, Prabhu AL, Dhalla N, McDonald H, Pandoh P, Tam A, Zeng T, Hirst M, Marra M
JournalMethods Mol Biol
PubMed ID20686952
MicroRNAs are key regulators of gene expression in diverse biological processes and their importance in embryonic stem cells is indisputable. New 'next-generation' technologies such as Illumina massively parallel sequencing offer vast improvements, in both scale and sensitivity, to microRNA profiling studies. We describe a detailed procedure for the preparation of ... More
Construction of small RNA cDNA libraries for high-throughput sequencing.
AuthorsLu C, Shedge V
JournalMethods Mol Biol
PubMed ID21365488
Small RNAs (smRNAs) play an essential role in virtually every aspect of growth and development, by regulating gene expression at the post-transcriptional and/or transcriptional level. New high-throughput sequencing technology allows for a comprehensive coverage of smRNAs in any given biological sample, and has been widely used for profiling smRNA populations ... More
Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome.
AuthorsGerman MA, Luo S, Schroth G, Meyers BC, Green PJ
JournalNat Protoc
PubMed ID19247285
We have developed a novel approach called parallel analysis of RNA ends (PARE) for high-throughput identification of microRNA (miRNA) targets and diverse applications for the study of the RNA degradome. The method described here comprises a modified 5'-rapid amplification of cDNA ends, deep sequencing of 3' cleavage products of mRNA ... More
Small DNA pieces in C. elegans are intermediates of DNA fragmentation during apoptosis.
AuthorsAruscavage PJ, Hellwig S, Bass BL
JournalPLoS One
PubMed ID20585459
While studying small noncoding RNA in C. elegans, we discovered that protocols used for isolation of RNA are contaminated with small DNA pieces. After electrophoresis on a denaturing gel, the DNA fragments appear as a ladder of bands, approximately 10 nucleotides apart, mimicking the pattern of nuclease digestion of DNA ... More