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  4. Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
 
research article

Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain

Playfoot, Christopher J.
•
Duc, Julien  
•
Sheppard, Shaoline  
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September 1, 2021
Genome Research

Transposable elements (TEs) account for more than 50% of the human genome and many have been co-opted throughout evolution to provide regulatory functions for gene expression networks. Several lines of evidence suggest that these networks are fine-tuned by the largest family of TE controllers, the KRAB-containing zinc finger proteins (KZFPs). One tissue permissive for TE transcriptional activation (termed "transposcription") is the adult human brain, however comprehensive studies on the extent of this process and its potential contribution to human brain development are lacking. To elucidate the spatiotemporal transposcriptome of the developing human brain, we have analyzed two independent RNA-seq data sets encompassing 16 brain regions from eight weeks postconception into adulthood. We reveal a distinct KZFP:TE transcriptional profile defining the late prenatal to early postnatal transition, and the spatiotemporal and cell type-specific activation of TE-derived alternative promoters driving the expression of neurogenesis-associated genes. Long-read sequencing confirmed these TE-driven isoforms as significant contributors to neurogenic transcripts. We also show experimentally that a co-opted antisense L2 element drives temporal protein relocalization away from the endoplasmic reticulum, suggestive of novel TE dependent protein function in primate evolution. This work highlights the widespread dynamic nature of the spatiotemporal KZFP:TE transcriptome and its importance throughout TE mediated genome innovation and neurotypical human brain development. To facilitate interactive exploration of these spatiotemporal gene and TE expression dynamics, we provide the "Brain TExplorer" web application freely accessible for the community.

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Type
research article
DOI
10.1101/gr.275133.120
Web of Science ID

WOS:000692091600003

Author(s)
Playfoot, Christopher J.
Duc, Julien  
Sheppard, Shaoline  
Dind, Sagane  
Coudray, Alexandre  
Planet, Evarist  
Trono, Didier  
Date Issued

2021-09-01

Publisher

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT

Published in
Genome Research
Volume

31

Issue

9

Start page

1531

End page

1545

Subjects

Biochemistry & Molecular Biology

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Biotechnology & Applied Microbiology

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Genetics & Heredity

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genome-wide association

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zinc-finger genes

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endogenous retroviruses

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l1 retrotransposition

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rna-seq

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expression

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evolution

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cells

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identification

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metaanalysis

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LVG  
Available on Infoscience
September 25, 2021
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/181593
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