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Related Concept Videos

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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Transcription Elongation Factors02:35

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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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Cooperative Binding of Transcription Regulators02:13

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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The Evidence for Evolution02:55

The Evidence for Evolution

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Genetic variations accumulating within populations over generations give rise to biological evolution. Evolutionary changes can result in the formation of novel varieties and entire new species. These changes are responsible for the diverse forms of life inhabiting the planet. The evidence for evolution suggests that all living organisms descended from common ancestors.
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Molecular Evolution of the Tre Recombinase
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Retroelement-Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human

Daniil Nikitin1,2,3, Andrew Garazha4,5, Maxim Sorokin6,7

  • 1I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia. danya.nikitin.orel@gmail.com.

Cells
|February 10, 2019
PubMed
Summary
This summary is machine-generated.

Retroelements (REs) significantly impact human gene regulation by providing transcription factor binding sites (TFBS). This study reveals RE-linked TFBS evolution rates across genes and pathways, highlighting accelerated evolution in immunity and metabolism.

Keywords:
ChIP-seqHuman genome evolutiongene ontologymolecular pathwaysomics approach in geneticsretrotransposonstranscription factor

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Retroelements (REs) comprise ~40% of the human genome.
  • REs can influence gene regulation by introducing transcription factor binding sites (TFBS).
  • RE-linked TFBS profiles offer insights into the evolutionary history of gene regulation.

Purpose of the Study:

  • To characterize the evolutionary trajectory of human gene transcriptional regulation.
  • To quantify regulatory evolution using RE-linked TFBS accumulation as a metric.
  • To identify genes and molecular pathways with distinct evolutionary rates driven by REs.

Main Methods:

  • Analysis of human genes and molecular pathways for enrichment or deficiency in RE-linked TFBS regulation.
  • Utilized the ENCODE database for TFBS data across 563 transcription factors in 13 human cell lines.
  • Calculated RE-linked TFBS regulation scores for 24,389 genes and 3124 pathways to assess evolutionary rates.

Main Results:

  • Groups enriched in RE regulation include microRNA-mediated gene regulation, olfaction, color vision, fertilization, immune response, and metabolism.
  • Groups deficient in RE regulation are associated with translation, RNA transcription/processing, chromatin organization, and molecular signaling.
  • Identified distinct evolutionary patterns in human genes and pathways influenced by REs.

Conclusions:

  • Human genes and molecular processes exhibit varied evolutionary rates influenced by RE-linked TFBS.
  • REs play a significant role in shaping the regulatory landscape of specific biological functions.
  • This metric provides a novel approach to study regulatory evolution in genomes rich in repetitive elements.