In silico transcriptional regulation and functional analysis of dengue shock syndrome associated SNPs in PLCE1 and MICB genes
Single nucleotide polymorphisms (SNPs) in PLCE1 and MICB genes increase risk for the development of dengue shock syndrome (DSS). We used Bioinformatics tools to predict alterations at the transcriptional and posttranslational levels driven by PLCE1 and MICB SNPs associated with DSS. Functional and p...
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| Veröffentlicht in: | Functional & integrative genomics 2016-05, Vol.16 (3), p.335-345 |
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| creator | Taqi, Malik Mumtaz Waseem, Durdana Ismatullah, Humaira Haider, Syed Aleem Faisal, Muhammad |
| description | Single nucleotide polymorphisms (SNPs) in
PLCE1
and
MICB
genes increase risk for the development of dengue shock syndrome (DSS). We used Bioinformatics tools to predict alterations at the transcriptional and posttranslational levels driven by
PLCE1
and
MICB
SNPs associated with DSS. Functional and phenotypic analysis conducted to determine deleterious SNPs and impact of amino acid substitution on the structure and function of proteins identified rs2274223 (H1619R) as deleterious to protein coding as it induces structural change in the C2 domain of PLCε, with the mutant residue more positively charged than the wild-type residue (RMSD score, 1.75 Å). Moreover, rs2274223 condenses the chromatin-repressing PLCε expression in DSS. Briefly, this study presents the impact of a single nucleotide transition at SNPs associated with DSS on differential protein binding patterns with
PLCE1
and
MICB
genes and on protein structure modification and their possible role in the pathogenesis of DSS. |
| doi_str_mv | 10.1007/s10142-016-0489-9 |
| format | Article |
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PLCE1
and
MICB
genes increase risk for the development of dengue shock syndrome (DSS). We used Bioinformatics tools to predict alterations at the transcriptional and posttranslational levels driven by
PLCE1
and
MICB
SNPs associated with DSS. Functional and phenotypic analysis conducted to determine deleterious SNPs and impact of amino acid substitution on the structure and function of proteins identified rs2274223 (H1619R) as deleterious to protein coding as it induces structural change in the C2 domain of PLCε, with the mutant residue more positively charged than the wild-type residue (RMSD score, 1.75 Å). Moreover, rs2274223 condenses the chromatin-repressing PLCε expression in DSS. Briefly, this study presents the impact of a single nucleotide transition at SNPs associated with DSS on differential protein binding patterns with
PLCE1
and
MICB
genes and on protein structure modification and their possible role in the pathogenesis of DSS.</description><identifier>ISSN: 1438-793X</identifier><identifier>EISSN: 1438-7948</identifier><identifier>DOI: 10.1007/s10142-016-0489-9</identifier><identifier>PMID: 27038471</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Amino Acid Substitution - genetics ; Animal Genetics and Genomics ; Biochemistry ; Bioinformatics ; Biomedical and Life Sciences ; Cell Biology ; Chromatin - genetics ; Computational Biology ; Dengue fever ; Gene Expression Regulation ; Genotype ; Histocompatibility Antigens Class I - biosynthesis ; Histocompatibility Antigens Class I - chemistry ; Histocompatibility Antigens Class I - genetics ; Life Sciences ; Microbial Genetics and Genomics ; Mutation ; Original ; Original Article ; Phosphoinositide Phospholipase C - biosynthesis ; Phosphoinositide Phospholipase C - chemistry ; Phosphoinositide Phospholipase C - genetics ; Plant Genetics and Genomics ; Polymorphism ; Polymorphism, Single Nucleotide - genetics ; Protein Conformation ; Protein Processing, Post-Translational - genetics ; Proteins ; Severe Dengue - genetics ; Severe Dengue - virology ; Transcription, Genetic</subject><ispartof>Functional & integrative genomics, 2016-05, Vol.16 (3), p.335-345</ispartof><rights>The Author(s) 2016</rights><rights>Springer-Verlag Berlin Heidelberg 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c503t-a994eb820e1a5c2cafbb7ead6420a9ebe0d659c032ddfc523b1da71b1d48fd583</citedby><cites>FETCH-LOGICAL-c503t-a994eb820e1a5c2cafbb7ead6420a9ebe0d659c032ddfc523b1da71b1d48fd583</cites><orcidid>0000-0003-4885-4251</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10142-016-0489-9$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10142-016-0489-9$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,780,784,885,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27038471$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Taqi, Malik Mumtaz</creatorcontrib><creatorcontrib>Waseem, Durdana</creatorcontrib><creatorcontrib>Ismatullah, Humaira</creatorcontrib><creatorcontrib>Haider, Syed Aleem</creatorcontrib><creatorcontrib>Faisal, Muhammad</creatorcontrib><title>In silico transcriptional regulation and functional analysis of dengue shock syndrome associated SNPs in PLCE1 and MICB genes</title><title>Functional & integrative genomics</title><addtitle>Funct Integr Genomics</addtitle><addtitle>Funct Integr Genomics</addtitle><description>Single nucleotide polymorphisms (SNPs) in
PLCE1
and
MICB
genes increase risk for the development of dengue shock syndrome (DSS). We used Bioinformatics tools to predict alterations at the transcriptional and posttranslational levels driven by
PLCE1
and
MICB
SNPs associated with DSS. Functional and phenotypic analysis conducted to determine deleterious SNPs and impact of amino acid substitution on the structure and function of proteins identified rs2274223 (H1619R) as deleterious to protein coding as it induces structural change in the C2 domain of PLCε, with the mutant residue more positively charged than the wild-type residue (RMSD score, 1.75 Å). Moreover, rs2274223 condenses the chromatin-repressing PLCε expression in DSS. Briefly, this study presents the impact of a single nucleotide transition at SNPs associated with DSS on differential protein binding patterns with
PLCE1
and
MICB
genes and on protein structure modification and their possible role in the pathogenesis of DSS.</description><subject>Amino Acid Substitution - genetics</subject><subject>Animal Genetics and Genomics</subject><subject>Biochemistry</subject><subject>Bioinformatics</subject><subject>Biomedical and Life Sciences</subject><subject>Cell Biology</subject><subject>Chromatin - genetics</subject><subject>Computational Biology</subject><subject>Dengue fever</subject><subject>Gene Expression Regulation</subject><subject>Genotype</subject><subject>Histocompatibility Antigens Class I - biosynthesis</subject><subject>Histocompatibility Antigens Class I - chemistry</subject><subject>Histocompatibility Antigens Class I - genetics</subject><subject>Life Sciences</subject><subject>Microbial Genetics and Genomics</subject><subject>Mutation</subject><subject>Original</subject><subject>Original Article</subject><subject>Phosphoinositide Phospholipase C - biosynthesis</subject><subject>Phosphoinositide Phospholipase C - chemistry</subject><subject>Phosphoinositide Phospholipase C - genetics</subject><subject>Plant Genetics and Genomics</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Protein Conformation</subject><subject>Protein Processing, Post-Translational - genetics</subject><subject>Proteins</subject><subject>Severe Dengue - genetics</subject><subject>Severe Dengue - virology</subject><subject>Transcription, Genetic</subject><issn>1438-793X</issn><issn>1438-7948</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNp1kU2P0zAQhi0EYj_gB3BBlrhwCdhJnNgXJKgWqFRgJUDiZjn2JOsltbueBKmH_e-421ItSFzGtubxOx8vIc84e8UZa18jZ7wuC8abgtVSFeoBOeV1JYtW1fLh8V79OCFniNeMMcFU9ZiclC2rZN3yU3K7DBT96G2kUzIBbfKbycdgRppgmEeze1ATHO3nYA8Zk8MWPdLYUwdhmIHiVbQ_KW6DS3EN1CBG680Ejn79fInUB3q5WlzwO6VPy8U7OkAAfEIe9WZEeHo4z8n39xffFh-L1ZcPy8XbVWEFq6bCKFVDJ0sG3AhbWtN3XQvGNXXJjIIOmGuEsqwqneutKKuOO9PyHGvZOyGrc_Jmr7uZuzU4CyEPO-pN8muTtjoar__OBH-lh_hL11IwLlUWeHkQSPFmBpz02qOFcTQB4oyat7JVUqhKZPTFP-h1nFPe2B0leNPkxWeK7ymbImKC_tgMZ3pnrt6bq7O5emeu3jXx_P4Uxx9_3MxAuQcwp8IA6V7p_6r-Bhl5sj4</recordid><startdate>20160501</startdate><enddate>20160501</enddate><creator>Taqi, Malik Mumtaz</creator><creator>Waseem, Durdana</creator><creator>Ismatullah, Humaira</creator><creator>Haider, Syed Aleem</creator><creator>Faisal, Muhammad</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PADUT</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7U9</scope><scope>H94</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-4885-4251</orcidid></search><sort><creationdate>20160501</creationdate><title>In silico transcriptional regulation and functional analysis of dengue shock syndrome associated SNPs in PLCE1 and MICB genes</title><author>Taqi, Malik Mumtaz ; Waseem, Durdana ; Ismatullah, Humaira ; Haider, Syed Aleem ; Faisal, Muhammad</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c503t-a994eb820e1a5c2cafbb7ead6420a9ebe0d659c032ddfc523b1da71b1d48fd583</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Amino Acid Substitution - genetics</topic><topic>Animal Genetics and Genomics</topic><topic>Biochemistry</topic><topic>Bioinformatics</topic><topic>Biomedical and Life Sciences</topic><topic>Cell Biology</topic><topic>Chromatin - genetics</topic><topic>Computational Biology</topic><topic>Dengue fever</topic><topic>Gene Expression Regulation</topic><topic>Genotype</topic><topic>Histocompatibility Antigens Class I - biosynthesis</topic><topic>Histocompatibility Antigens Class I - chemistry</topic><topic>Histocompatibility Antigens Class I - genetics</topic><topic>Life Sciences</topic><topic>Microbial Genetics and Genomics</topic><topic>Mutation</topic><topic>Original</topic><topic>Original Article</topic><topic>Phosphoinositide Phospholipase C - biosynthesis</topic><topic>Phosphoinositide Phospholipase C - chemistry</topic><topic>Phosphoinositide Phospholipase C - genetics</topic><topic>Plant Genetics and Genomics</topic><topic>Polymorphism</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Protein Conformation</topic><topic>Protein Processing, Post-Translational - genetics</topic><topic>Proteins</topic><topic>Severe Dengue - genetics</topic><topic>Severe Dengue - virology</topic><topic>Transcription, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Taqi, Malik Mumtaz</creatorcontrib><creatorcontrib>Waseem, Durdana</creatorcontrib><creatorcontrib>Ismatullah, Humaira</creatorcontrib><creatorcontrib>Haider, Syed Aleem</creatorcontrib><creatorcontrib>Faisal, Muhammad</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Research Library China</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Functional & integrative genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Taqi, Malik Mumtaz</au><au>Waseem, Durdana</au><au>Ismatullah, Humaira</au><au>Haider, Syed Aleem</au><au>Faisal, Muhammad</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>In silico transcriptional regulation and functional analysis of dengue shock syndrome associated SNPs in PLCE1 and MICB genes</atitle><jtitle>Functional & integrative genomics</jtitle><stitle>Funct Integr Genomics</stitle><addtitle>Funct Integr Genomics</addtitle><date>2016-05-01</date><risdate>2016</risdate><volume>16</volume><issue>3</issue><spage>335</spage><epage>345</epage><pages>335-345</pages><issn>1438-793X</issn><eissn>1438-7948</eissn><abstract>Single nucleotide polymorphisms (SNPs) in
PLCE1
and
MICB
genes increase risk for the development of dengue shock syndrome (DSS). We used Bioinformatics tools to predict alterations at the transcriptional and posttranslational levels driven by
PLCE1
and
MICB
SNPs associated with DSS. Functional and phenotypic analysis conducted to determine deleterious SNPs and impact of amino acid substitution on the structure and function of proteins identified rs2274223 (H1619R) as deleterious to protein coding as it induces structural change in the C2 domain of PLCε, with the mutant residue more positively charged than the wild-type residue (RMSD score, 1.75 Å). Moreover, rs2274223 condenses the chromatin-repressing PLCε expression in DSS. Briefly, this study presents the impact of a single nucleotide transition at SNPs associated with DSS on differential protein binding patterns with
PLCE1
and
MICB
genes and on protein structure modification and their possible role in the pathogenesis of DSS.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>27038471</pmid><doi>10.1007/s10142-016-0489-9</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0003-4885-4251</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Functional & integrative genomics, 2016-05, Vol.16 (3), p.335-345 |
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| subjects | Amino Acid Substitution - genetics Animal Genetics and Genomics Biochemistry Bioinformatics Biomedical and Life Sciences Cell Biology Chromatin - genetics Computational Biology Dengue fever Gene Expression Regulation Genotype Histocompatibility Antigens Class I - biosynthesis Histocompatibility Antigens Class I - chemistry Histocompatibility Antigens Class I - genetics Life Sciences Microbial Genetics and Genomics Mutation Original Original Article Phosphoinositide Phospholipase C - biosynthesis Phosphoinositide Phospholipase C - chemistry Phosphoinositide Phospholipase C - genetics Plant Genetics and Genomics Polymorphism Polymorphism, Single Nucleotide - genetics Protein Conformation Protein Processing, Post-Translational - genetics Proteins Severe Dengue - genetics Severe Dengue - virology Transcription, Genetic |
| title | In silico transcriptional regulation and functional analysis of dengue shock syndrome associated SNPs in PLCE1 and MICB genes |
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