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Related Concept Videos

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...
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
Ribosome Profiling02:24

Ribosome Profiling

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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Bacterial Transcription01:53

Bacterial Transcription

RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:

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Updated: May 24, 2026

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis
12:44

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

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Comment on "Widespread RNA and DNA sequence differences in the human transcriptome".

Joseph K Pickrell1, Yoav Gilad, Jonathan K Pritchard

  • 1Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA. pickrell@uchicago.edu

Science (New York, N.Y.)
|March 17, 2012
PubMed
Summary
This summary is machine-generated.

Technical errors, not gene regulation, likely explain over 10,000 RNA-DNA sequence mismatches. Our analysis indicates artifacts like mapping errors and genetic variation account for most discrepancies found in gene expression studies.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Recent studies reported numerous messenger RNA (mRNA) and DNA sequence mismatches.
  • These discrepancies were initially attributed to novel gene regulatory mechanisms.

Purpose of the Study:

  • To re-evaluate the cause of the reported mRNA-DNA sequence mismatches.
  • To determine the extent to which technical artifacts contribute to these observed differences.

Main Methods:

  • Analysis of sequencing read mapping to a reference genome.
  • Assessment of sequencing error rates.
  • Evaluation of genetic variation within individuals.

Main Results:

  • At least 88% of the >10,000 reported mRNA-DNA mismatches can be attributed to technical artifacts.
  • Identified key artifacts including read mapping errors, sequencing errors, and genetic variation.

Conclusions:

  • The majority of previously reported mRNA-DNA sequence mismatches are likely due to technical limitations, not novel gene regulation.
  • Revisiting data analysis pipelines is crucial for accurate interpretation of gene expression and regulation studies.