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Related Concept Videos

RNA-seq03:21

RNA-seq

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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. 
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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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Regulation of Expression at Multiple Steps01:23

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Regulation of Expression Occurs at Multiple Steps02:24

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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
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Alternative RNA Splicing02:18

Alternative RNA Splicing

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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

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Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from

Eun Yong Kang1, Lisa J Martin2, Serghei Mangul1

  • 1Department of Computer Science, University of California, Los Angeles, California 90095-1596.

Genetics
|October 22, 2016
PubMed
Summary
This summary is machine-generated.

This study introduces a novel method for analyzing allele-specific expression (ASE) to identify genetic variants regulating gene expression. This approach enhances understanding of complex diseases by pinpointing regulatory single nucleotide polymorphisms (SNPs).

Keywords:
Allele specific expressioncausal variantsexpression quantitative trait loci

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Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Understanding the genetic basis of complex diseases requires studying gene expression.
  • Expression quantitative trait loci (eQTL) analysis is a common method for linking genetic variation to gene expression.
  • Limitations exist in current eQTL approaches for fully characterizing regulatory variants.

Purpose of the Study:

  • To develop and validate a novel analytical method to identify cis-acting regulatory variants.
  • To enhance the power of expression quantitative trait loci (eQTL) analysis using allele-specific expression (ASE) data.
  • To map regulatory variants impacting gene expression in human cell lines.

Main Methods:

  • Designed a new analytical method combining genome sequencing and RNA-sequencing (RNA-seq) data to measure allele-specific expression (ASE).
  • Evaluated the method's power and resolution using simulated data.
  • Applied the method to lymphoblastoid cell lines (LCLs) from 77 individuals (CEU) from the HapMap project.

Main Results:

  • Identified 2309 single nucleotide polymorphisms (SNPs) associated with allele-specific expression (ASE) patterns.
  • ASE-associated SNPs were enriched in promoter regions, indicating a strong regulatory role.
  • Discovered 108 candidate regulatory SNPs previously linked to human immune diseases.

Conclusions:

  • The novel ASE-based method effectively identifies cis-acting regulatory variants.
  • This approach provides a powerful complement to traditional eQTL analysis for understanding gene regulation.
  • Future applications of this method are expected to advance the study of complex diseases.