English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history

Baar, T., Dümcke, S., Gressel, S., Schwalb, B., Dilthey, A., Cramer, P., et al. (2022). RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history. G3 Genes, Genomes, Genetics, In Press. doi:10.1093/g3journal/jkac054.

Item is

Basic

show hide
Genre: Journal Article

Files

show Files
hide Files
:
3379898.pdf (Preprint), 2MB
Name:
3379898.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-

Locators

show

Creators

show
hide
 Creators:
Baar, T., Author
Dümcke, S., Author
Gressel, S.1, Author              
Schwalb, B.1, Author              
Dilthey, A., Author
Cramer, P.1, Author              
Tresch, A., Author
Steinmetz, L. M., Editor
Affiliations:
1Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Max Planck Society, ou_3350224              

Content

show
hide
Free keywords: Alu elements; Alu transcription; RNA labeling; retrotransposons
 Abstract: Alu elements are one of the most successful groups of RNA retrotransposons and make up 11% of the human genome with over 1 million individual loci. They are linked to genetic defects, increases in sequence diversity, and influence transcriptional activity. Still, their RNA me- tabolism is poorly understood yet. It is even unclear whether Alu elements are mostly transcribed by RNA Polymerase II or III. We have con- ducted a transcription shutoff experiment by a-amanitin and metabolic RNA labeling by 4-thiouridine combined with RNA fragmentation (TT-seq) and RNA-seq to shed further light on the origin and life cycle of Alu transcripts. We find that Alu RNAs are more stable than previ- ously thought and seem to originate in part from RNA Polymerase II activity, as previous reports suggest. Their expression however seems to be independent of the transcriptional activity of adjacent genes. Furthermore, we have developed a novel statistical test for detecting the expression of quantitative trait loci in Alu elements that relies on the de Bruijn graph representation of all Alu sequences. It controls for both statistical significance and biological relevance using a tuned k-mer representation, discovering influential sequence features missed by regular motif search. In addition, we discover several point mutations using a generalized linear model, and motifs of interest, which also match transcription factor-binding motifs.

Details

show
hide
Language(s): eng - English
 Dates: 2022-01-252022-02-252022-03-07
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1093/g3journal/jkac054
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: G3 Genes, Genomes, Genetics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: 14 Volume / Issue: - Sequence Number: In Press Start / End Page: - Identifier: ISSN: 2160-1836