Global identification of small RNA targets in plants by sequencing sliced ends of messenger RNAs.
AuthorsLi YF, Sunkar R
JournalMethods Mol Biol
PubMed ID23135849
'Small RNAs (microRNAs and other classes of endogenous small interfering RNAs) play important roles in a wide variety of biological processes. However, integration of small RNAs in diverse biological networks relies on the confirmation of their RNA targets. In plants, miRNAs negatively regulate mRNA targets by guiding a cleavage in ... More
Cloning of stress-responsive microRNAs and other small RNAs from plants.
AuthorsReyes JL, Arenas-Huertero C, Sunkar R
JournalMethods Mol Biol
PubMed ID20387050
'In plants, small RNA (microRNAs and other endogenous small RNAs)-guided target gene expression is vital for a wide variety of biological processes including adaptation to stress conditions. Identification of stress-regulated microRNAs or other classes of endogenous small RNAs advances our understanding of post-transcriptional gene regulation important for plant stress tolerance. ... More
DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.
AuthorsSong L, Crawford GE,
JournalCold Spring Harb Protoc
PubMed ID20150147
Transcriptional profiling of Dictyostelium with RNA sequencing.
AuthorsMiranda ER, Rot G, Toplak M, Santhanam B, Curk T, Shaulsky G, Zupan B
JournalMethods Mol Biol
PubMed ID23494306
Transcriptional profiling methods have been utilized in the analysis of various biological processes in Dictyostelium. Recent advances in high-throughput sequencing have increased the resolution and the dynamic range of transcriptional profiling. Here we describe the utility of RNA sequencing with the Illumina technology for production of transcriptional profiles. We also ... More
Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing.
AuthorsHafner M, Renwick N, Farazi TA, Mihailovic A, Pena JT, Tuschl T
JournalMethods
PubMed ID22885844
The characterization of post-transcriptional gene regulation by small regulatory (20-30 nt) RNAs, particularly miRNAs and piRNAs, has become a major focus of research in recent years. A prerequisite for characterizing small RNAs is their identification and quantification across different developmental stages, and in normal and disease tissues, as well as ... More
Cloning of small RNAs for the discovery of novel microRNAs in plants.
AuthorsJagadeeswaran G, Sunkar R
JournalMethods Mol Biol
PubMed ID23135848
Endogenous small RNAs can be grouped into several distinct classes of 21-nt-long microRNAs (miRNAs), short interfering RNAs (siRNAs), trans-acting siRNAs (tasiRNAs), and 24-nt long heterochromatic siRNAs. miRNAs are increasingly being recognized as significant effectors of gene regulation in a wide range of organisms. These molecules are typically ~21-nt long and ... More
Assessment and quantification of telomerase enzyme activity.
AuthorsMaritz MF, Richards LA, Mackenzie KL
JournalMethods Mol Biol
PubMed ID23296661
The enzyme telomerase is activated in 80-90% of all human malignancies and immortal cell lines, where it functions to maintain the integrity of chromosomal-end structures called telomeres. Telomerase enzyme activity can be detected in whole cell lysates by a polymerase chain reaction (PCR)-based method referred to as the telomeric repeat ... More
Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease.
AuthorsChristodoulou DC, Gorham JM, Herman DS, Seidman JG
JournalCurr Protoc Mol Biol
PubMed ID21472699
RNA-seq is a method for studying the transcriptome of cells or tissues by massively parallel sequencing of tens of millions of short DNA fragments. However, the broad dynamic range of gene expression levels, which span more than five orders of magnitude, necessitates considerable over-sequencing to characterize low-abundance RNAs at sufficient ... More