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Related Concept Videos

Transcription Initiation01:47

Transcription Initiation

22.1K
Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
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Bacterial Transcription01:53

Bacterial Transcription

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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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General Transcription Factors01:30

General 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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Transcription01:17

Transcription

36.3K
Transcription is the synthesis of 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 correctly synthesizing messenger RNA (mRNA). Transcriptional regulation is responsible for the differentiation of different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds of RNA Molecules
In eukaryotes,...
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Transcription01:10

Transcription

159.5K
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 in Prokaryotes01:28

Transcription in Prokaryotes

4.0K
Transcription is a highly regulated process that converts genetic information into RNA molecules. The transcription cycle is divided into three key stages: initiation, elongation, and termination, each driven by specific molecular mechanisms.Initiation of TranscriptionIn bacteria, transcription begins when the RNA polymerase core enzyme associates with a sigma factor to form a holoenzyme. For example, the E. coli sigma factor called σ70 forms a holoenzyme, which recognizes the -10 (Pribnow...
4.0K

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The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision
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TIPR: transcription initiation pattern recognition on a genome scale.

Taj Morton1, Weng-Keen Wong1, Molly Megraw2

  • 1Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA.

Bioinformatics (Oxford, England)
|August 9, 2015
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Summary
This summary is machine-generated.

A new machine learning model, Transcription Initiation Pattern Recognizer (TIPR), accurately identifies gene transcription start sites (TSSs) and their spatial patterns. This advances gene annotation and understanding of transcriptional regulation.

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Area of Science:

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • Accurate identification of gene transcription start sites (TSSs) is crucial for understanding gene regulation and function.
  • Predicting TSSs with high resolution, especially those with diverse spatial patterns, remains a significant challenge in genomics.
  • Computational methods offer a cost-effective alternative to experimental approaches for TSS identification, particularly in under-annotated organisms.

Purpose of the Study:

  • To develop a novel, high-resolution computational model for identifying gene transcription start sites (TSSs).
  • To enable the characterization of diverse spatial distribution patterns of TSSs along the genome.
  • To predict not only TSS locations but also their associated spatial initiation patterns.

Main Methods:

  • Development of a sequence-based machine learning model named Transcription Initiation Pattern Recognizer (TIPR).
  • Utilizing sequence data to predict TSS locations and their spatial initiation patterns.
  • Validation of the model's accuracy and resolution in identifying various TSS spatial distributions.

Main Results:

  • TIPR achieves high accuracy and nucleotide-level resolution (within 10 nucleotides on average) in TSS prediction.
  • The model successfully identifies broadly distributed TSS patterns previously difficult to characterize.
  • TIPR offers a novel capability by predicting the spatial initiation pattern associated with each identified TSS.

Conclusions:

  • TIPR represents a significant advancement in TSS prediction, offering high accuracy and novel pattern recognition capabilities.
  • The ability to predict spatial initiation patterns can enhance gene annotations and deepen the understanding of transcription regulation.
  • This tool has the potential to improve functional genomics studies and the interpretation of gene expression data.