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RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
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Experimental RNAi02:15

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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
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RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs
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Small RNAs in angiosperms: sequence characteristics, distribution and generation.

Dijun Chen1, Yijun Meng, Xiaoxia Ma

  • 1Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences and James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, P. R. China.

Bioinformatics (Oxford, England)
|April 10, 2010
PubMed
Summary

High-throughput sequencing reveals distinct small RNA (sRNA) characteristics in monocots and uniform 5-terminal compositions across angiosperms. Natural antisense transcripts (NATs) influence sRNA generation, with specific types showing organ-specific roles in plants.

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Area of Science:

  • Plant molecular biology
  • Genomics
  • Bioinformatics

Background:

  • High-throughput sequencing (HTS) revolutionized small RNA (sRNA) research.
  • Understanding sRNA composition and distribution is crucial for plant biology.

Purpose of the Study:

  • To globally survey sRNAs in 26 angiosperms using HTS data.
  • To investigate chromosome-wide sRNA distribution patterns.
  • To explore the role of natural antisense transcripts (NATs) in sRNA generation.

Main Methods:

  • Analysis of HTS data from 26 angiosperm species.
  • Scrolling-window analysis for sRNA distribution.
  • De novo prediction of natural antisense transcripts (NATs).

Main Results:

  • Monocots showed elevated GC content in sRNAs; 5'-terminal compositions were uniform across angiosperms.
  • Overlapping regions of trans-NATs, not cis-NATs, were identified as hotspots for sRNA generation.
  • Organ-specific phased natural antisense short interfering RNAs (nat-siRNAs) were identified in Arabidopsis (flowers) and rice (grains).

Conclusions:

  • Distinct sRNA compositional features exist between monocots and other angiosperms.
  • NATs play a significant role in regulating sRNA biogenesis.
  • Specific cis-NATs generate organ-specific nat-siRNAs, indicating specialized regulatory functions in different plant tissues.