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Related Concept Videos

MicroRNAs01:22

MicroRNAs

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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After...
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MicroRNAs01:22

MicroRNAs

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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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Transcription01:10

Transcription

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Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
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Transcription Factors02:16

Transcription Factors

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Eukaryotic Transcription Inhibitors01:52

Eukaryotic Transcription Inhibitors

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Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a...
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Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

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Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
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High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes
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High-Throughput Characterization of Primary microRNA Transcripts.

Tsung-Cheng Chang1, Joshua T Mendell2,3,4,5

  • 1Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Methods in Molecular Biology (Clifton, N.J.)
|July 1, 2018
PubMed
Summary
This summary is machine-generated.

This study presents new methods to enrich and analyze microRNA (miRNA) primary transcripts (pri-miRNAs) using RNA sequencing. These techniques improve the characterization of complex miRNA gene structures for better disease research.

Keywords:
Primary transcriptRNA-seqTranscriptome assemblymicroRNApri-miRNA

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • MicroRNA (miRNA) expression is vital for development and health, with dysregulation linked to diseases.
  • Accurate annotation of miRNA primary transcripts (pri-miRNAs) is challenging due to their complex, poorly characterized nature as noncoding RNAs.
  • Low steady-state abundance of pri-miRNAs, due to efficient DROSHA processing, hinders structural elucidation.

Purpose of the Study:

  • To develop a strategy for enriching intact pri-miRNAs for improved RNA sequencing (RNA-seq) coverage.
  • To establish a computational pipeline for reconstructing pri-miRNA structures from RNA-seq data.
  • To enable detailed exploration and annotation of miRNA gene structures across different cell types and organisms.

Main Methods:

  • A novel enrichment strategy was developed to isolate intact pri-miRNAs.
  • RNA sequencing (RNA-seq) was employed to capture and analyze pri-miRNA transcripts.
  • A computational pipeline was designed for the reconstruction and visualization of pri-miRNA annotations from raw sequencing reads.

Main Results:

  • The described methods significantly enhance the coverage and integrity of pri-miRNAs in RNA-seq experiments.
  • The computational pipeline successfully reconstructs pri-miRNA structures, including promoters, splice sites, and polyadenylation signals.
  • Publication-ready visualizations of pri-miRNA annotations were generated, facilitating interpretation.

Conclusions:

  • This integrated approach overcomes limitations in pri-miRNA annotation, providing a robust framework for studying miRNA gene regulation.
  • Researchers can now define and explore miRNA gene structures with greater accuracy in their specific biological contexts.
  • The findings are crucial for understanding miRNA roles in normal physiology and disease pathogenesis.