NDLI: Relatively semi-conservative replication and a folded slippage model for short tandem repeats

Content Provider	Springer Nature : BioMed Central
Author	Zhang, Hongxi Li, Douyue Zhao, Xiangyan Pan, Saichao Wu, Xiaolong Peng, Shan Huang, Hanrou Shi, Ruixue Tan, Zhongyang
Abstract	Background The ubiquitous presence of short tandem repeats (STRs) in virtually all genomes implicates their functional relevance, while a widely-accepted definition of STR is yet to be established. Previous studies majorly focus on relatively longer STRs, while shorter repeats were generally excluded. Herein, we have adopted a more generous criteria to define shorter repeats, which has led to the definition of a much larger number of STRs that lack prior analysis. Using this definition, we analyzed the short repeats in 55 randomly selected segments in 55 randomly selected genomic sequences from a fairly wide range of species covering animals, plants, fungi, protozoa, bacteria, archaea and viruses. Results Our analysis reveals a high percentage of short repeats in all 55 randomly selected segments, indicating that the universal presence of high-content short repeats could be a common characteristic of genomes across all biological kingdoms. Therefore, it is reasonable to assume a mechanism for continuous production of repeats that can make the replicating process relatively semi-conservative. We have proposed a folded replication slippage model that considers the geometric space of nucleotides and hydrogen bond stability to explain the mechanism more explicitly, with improving the existing straight-line slippage model. The folded slippage model can explain the expansion and contraction of mono- to hexa- nucleotide repeats with proper folding angles. Analysis of external forces in the folding template strands also suggests that expansion exists more commonly than contraction in the short tandem repeats. Conclusion The folded replication slippage model provides a reasonable explanation for the continuous occurrences of simple sequence repeats in genomes. This model also contributes to the explanation of STR-to-genome evolution and is an alternative model that complements semi-conservative replication.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-020-06949-5.pdf
Ending Page	14
Page Count	14
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-020-06949-5
Journal	BMC Genomics
Issue Number	1
Volume Number	21
Language	English
Publisher	BioMed Central
Publisher Date	2020-08-17
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Short Tandem Repeats in Human Exons: A Target for Disease Mutations

Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes

Relatively semi-conservative replication and a folded slippage model for simple sequence repeats

STaRRRT: a table of short tandem repeats in regulatory regions of the human genome

LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants

STR-realigner: a realignment method for short tandem repeat regions

Tools for the identification of variable and potentially variable tandem repeats

Tandem repeats derived from centromeric retrotransposons

Replication slippage versus point mutation rates in short tandem repeats of the human genome

Relatively semi-conservative replication and a folded slippage model for short tandem repeats

Similar Documents

Short Tandem Repeats in Human Exons: A Target for Disease Mutations

Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes

Relatively semi-conservative replication and a folded slippage model for simple sequence repeats

STaRRRT: a table of short tandem repeats in regulatory regions of the human genome

LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants

STR-realigner: a realignment method for short tandem repeat regions

Tools for the identification of variable and potentially variable tandem repeats

Tandem repeats derived from centromeric retrotransposons

Replication slippage versus point mutation rates in short tandem repeats of the human genome

Relatively semi-conservative replication and a folded slippage model for short tandem repeats