English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

Abyzov, A., Iskow, R., Gokcumen, O., Radke, D. W., Balasubramanian, S., Pei, B., et al. (2013). Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Research, 23(12), 2042-2052. doi:10.1101/gr.154625.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-B2F2-2 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-B2F3-F
Genre: Journal Article

Files

show Files
hide Files
:
Abyzov.pdf (Publisher version), 702KB
Name:
Abyzov.pdf
Description:
-
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
© 2013 by Cold Spring Harbor Laboratory Press
License:
-

Locators

show

Creators

show
hide
 Creators:
Abyzov, Alexej, Author
Iskow, Rebecca, Author
Gokcumen, Omer, Author
Radke, David W. , Author
Balasubramanian, Suganthi , Author
Pei, Baikang, Author
Habegger, Lukas, Author
1000 Genomes Project, Consortium, Author
Timmermann, Bernd1, 2, Author              
Lee, Charles, Author
Gerstein, Mark, Author
Affiliations:
11000 Genomes Project Consortium, ou_persistent22              
2Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479670              

Content

show
hide
Free keywords: -
 Abstract: In primates and other animals, reverse transcription of mRNA followed by genomic integration creates retroduplications. Expressed retroduplications are either “retrogenes” coding for functioning proteins, or expressed “processed pseudogenes,” which can function as noncoding RNAs. To date, little is known about the variation in retroduplications in terms of their presence or absence across individuals in the human population. We have developed new methodologies that allow us to identify “novel” retroduplications (i.e., those not present in the reference genome), to find their insertion points, and to genotype them. Using these methods, we catalogued and analyzed 174 retroduplication variants in almost one thousand humans, which were sequenced as part of Phase 1 of The 1000 Genomes Project Consortium. The accuracy of our data set was corroborated by (1) multiple lines of sequencing evidence for retroduplication (e.g., depth of coverage in exons vs. introns), (2) experimental validation, and (3) the fact that we can reconstruct a correct phylogenetic tree of human subpopulations based solely on retroduplications. We also show that parent genes of retroduplication variants tend to be expressed at the M-to-G1 transition in the cell cycle and that M-to-G1 expressed genes have more copies of fixed retroduplications than genes expressed at other times. These findings suggest that cell division is coupled to retrotransposition and, perhaps, is even a requirement for it.

Details

show
hide
Language(s): eng - English
 Dates: 2013-09-112013-12
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1101/gr.154625
 Degree: -

Event

show

Legal Case

show

Project information

show hide
Project name : 1000 Genomes Project
Grant ID : 01GS08201
Funding program : -
Funding organization : BMBF

Source 1

show
hide
Title: Genome Research
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press
Pages: - Volume / Issue: 23 (12) Sequence Number: - Start / End Page: 2042 - 2052 Identifier: ISSN: 1088-9051
CoNE: /journals/resource/954926997202