NDLI: Screening of nucleotide variations in genomic sequences encoding charged protein regions in the human genome

Content Provider	Springer Nature : BioMed Central
Author	Belmabrouk, Sabrine Kharrat, Najla Abdelhedi, Rania Ben Ayed, Amine Benmarzoug, Riadh Rebai, Ahmed
Abstract	Background Studying genetic variation distribution in proteins containing charged regions, called charge clusters (CCs), is of great interest to unravel their functional role. Charge clusters are 20 to 75 residue segments with high net positive charge, high net negative charge, or high total charge relative to the overall charge composition of the protein. We previously developed a bioinformatics tool (FCCP) to detect charge clusters in proteomes and scanned the human proteome for the occurrence of CCs. In this paper we investigate the genetic variations in the human proteins harbouring CCs. Results We studied the coding regions of 317 positively charged clusters and 1020 negatively charged ones previously detected in human proteins. Results revealed that coding parts of CCs are richer in sequence variants than their corresponding genes, full mRNAs, and exonic + intronic sequences and that these variants are predominately rare (Minor allele frequency < 0.005). Furthermore, variants occurring in the coding parts of positively charged regions of proteins are more often pathogenic than those occurring in negatively charged ones. Classification of variants according to their types showed that substitution is the major type followed by Indels (Insertions-deletions). Concerning substitutions, it was found that within clusters of both charges, the charged amino acids were the greatest loser groups whereas polar residues were the greatest gainers. Conclusions Our findings highlight the prominent features of the human charged regions from the DNA up to the protein sequence which might provide potential clues to improve the current understanding of those charged regions and their implication in the emergence of diseases.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-017-4000-3.pdf
Ending Page	10
Page Count	10
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-017-4000-3
Journal	BMC Genomics
Issue Number	1
Volume Number	18
Language	English
Publisher	BioMed Central
Publisher Date	2017-08-08
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Charge cluster Genetic variant Mutation Substitution Deletion Insertion
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

The genomic pattern of insertion/deletion variations during rice improvement

Microarray-based ultra-high resolution discovery of genomic deletion mutations

Insertion/deletion-activated frame-shift fluorescence protein is a sensitive reporter for genomic DNA editing

Identification of genomic indels and structural variations using split reads

A genomic overview of short genetic variations in a basal chordate, Ciona intestinalis

Screening for clusters of charge in human virus proteomes

Ploidy level and nucleotide variations in inflorescence dichotomous cultivars of plantain (Musa spp. AAB genome)

Asymmetric somatic hybridization induces point mutations and indels in wheat

The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen’s lifestyle

Screening of nucleotide variations in genomic sequences encoding charged protein regions in the human genome

Similar Documents

The genomic pattern of insertion/deletion variations during rice improvement

Microarray-based ultra-high resolution discovery of genomic deletion mutations

Insertion/deletion-activated frame-shift fluorescence protein is a sensitive reporter for genomic DNA editing

Identification of genomic indels and structural variations using split reads

A genomic overview of short genetic variations in a basal chordate, Ciona intestinalis

Screening for clusters of charge in human virus proteomes

Ploidy level and nucleotide variations in inflorescence dichotomous cultivars of plantain (Musa spp. AAB genome)

Asymmetric somatic hybridization induces point mutations and indels in wheat

The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen’s lifestyle

Screening of nucleotide variations in genomic sequences encoding charged protein regions in the human genome