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Transcription Elongation Factors02:35

Transcription Elongation Factors

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Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
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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.
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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.
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Transcription01:17

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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.
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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.
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Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
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A machine learning-based framework for modeling transcription elongation.

Peiyuan Feng1, An Xiao1, Meng Fang2

  • 1Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China.

Proceedings of the National Academy of Sciences of the United States of America
|February 2, 2021
PubMed
Summary
This summary is machine-generated.

We developed PEPMAN, a deep learning model to predict RNA polymerase II pausing sites using NET-seq data. This tool aids in understanding transcription elongation, splicing, and epigenetic regulation.

Keywords:
Pol II pausingalternative splicingdeep learning

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA polymerase II (Pol II) pausing is crucial for gene expression regulation and cotranscriptional processes like splicing.
  • Experimental measurement of Pol II elongation rates is challenging and resource-intensive.

Purpose of the Study:

  • To develop an accurate and efficient computational model for predicting Pol II pausing sites.
  • To leverage deep learning to identify sequence features influencing Pol II pausing.
  • To investigate the relationship between Pol II pausing, alternative splicing, and epigenetic modifications.

Main Methods:

  • Developed PEPMAN, a deep learning model utilizing an attention mechanism.
  • Trained and validated PEPMAN using native elongating transcript sequencing (NET-seq) data.
  • Analyzed PEPMAN predictions in conjunction with alternative splicing events and epigenetic features.

Main Results:

  • PEPMAN accurately predicts Pol II pausing sites from NET-seq data.
  • The attention mechanism in PEPMAN identifies key sequence determinants of Pol II pausing.
  • PEPMAN analysis provides insights into cotranscriptional splicing and the role of epigenetic factors in transcription elongation.

Conclusions:

  • PEPMAN is an effective tool for modeling transcription elongation dynamics.
  • The model facilitates the understanding of biological processes influenced by Pol II pausing.
  • PEPMAN enables the analysis of high-throughput sequencing data to reveal regulatory mechanisms.