In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements
In silico identification of conserved intercoding sequences (CICS) in three Leishmania genomes reveals potential cis-acting elements on the control of gene expression. [Display omitted] ► In silico identification of conserved intercoding sequences in Leishmania genomes. ► Data will be made available...
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| Veröffentlicht in: | Molecular and biochemical parasitology 2012-06, Vol.183 (2), p.140-150 |
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| creator | Vasconcelos, E.J.R. Terrão, M.C. Ruiz, J.C. Vêncio, R.Z.N. Cruz, A.K. |
| description | In silico identification of conserved intercoding sequences (CICS) in three Leishmania genomes reveals potential cis-acting elements on the control of gene expression. [Display omitted]
► In silico identification of conserved intercoding sequences in Leishmania genomes. ► Data will be made available to the community. ► Some CICS are potential regulatory cis-elements. ► Common CICS are placed within transcripts sharing similar pattern of expression.
In silico analyses of Leishmania spp. genome data are a powerful resource to improve the understanding of these pathogens’ biology. Trypanosomatids such as Leishmania spp. have their protein-coding genes grouped in long polycistronic units of functionally unrelated genes. The control of gene expression happens by a variety of posttranscriptional mechanisms. The high degree of synteny among Leishmania species is accompanied by highly conserved coding sequences (CDS) and poorly conserved intercoding untranslated sequences. To identify the elements involved in the control of gene expression, we conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L. major, L. infantum, and L. braziliensis.
We used a combination of computational tools, such as Linux-Shell, PERL and R languages, BLAST, MSPcrunch, SSAKE, and Pred-A-Term algorithms to construct a pipeline which was able to: (i) search for conservation in target-regions, (ii) eliminate CICS redundancy and mask repeat elements, (iii) predict the mRNA's extremities, (iv) analyze the distribution of orthologous genes within the generated LeishCICS-clusters, (v) assign GO terms to the LeishCICS-clusters, and (vi) provide statistical support for the gene-enrichment annotation. We associated the LeishCICS-cluster data, generated at the end of the pipeline, with the expression profile of L. donovani genes during promastigote–amastigote differentiation, as previously evaluated by others (GEO accession: GSE21936). A Pearson's correlation coefficient greater than 0.5 was observed for 730 LeishCICS-clusters containing from 2 to 17 genes. The designed computational pipeline is a useful tool and its application identified potential regulatory cis elements and putative regulons in Leishmania. |
| doi_str_mv | 10.1016/j.molbiopara.2012.02.009 |
| format | Article |
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► In silico identification of conserved intercoding sequences in Leishmania genomes. ► Data will be made available to the community. ► Some CICS are potential regulatory cis-elements. ► Common CICS are placed within transcripts sharing similar pattern of expression.
In silico analyses of Leishmania spp. genome data are a powerful resource to improve the understanding of these pathogens’ biology. Trypanosomatids such as Leishmania spp. have their protein-coding genes grouped in long polycistronic units of functionally unrelated genes. The control of gene expression happens by a variety of posttranscriptional mechanisms. The high degree of synteny among Leishmania species is accompanied by highly conserved coding sequences (CDS) and poorly conserved intercoding untranslated sequences. To identify the elements involved in the control of gene expression, we conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L. major, L. infantum, and L. braziliensis.
We used a combination of computational tools, such as Linux-Shell, PERL and R languages, BLAST, MSPcrunch, SSAKE, and Pred-A-Term algorithms to construct a pipeline which was able to: (i) search for conservation in target-regions, (ii) eliminate CICS redundancy and mask repeat elements, (iii) predict the mRNA's extremities, (iv) analyze the distribution of orthologous genes within the generated LeishCICS-clusters, (v) assign GO terms to the LeishCICS-clusters, and (vi) provide statistical support for the gene-enrichment annotation. We associated the LeishCICS-cluster data, generated at the end of the pipeline, with the expression profile of L. donovani genes during promastigote–amastigote differentiation, as previously evaluated by others (GEO accession: GSE21936). A Pearson's correlation coefficient greater than 0.5 was observed for 730 LeishCICS-clusters containing from 2 to 17 genes. The designed computational pipeline is a useful tool and its application identified potential regulatory cis elements and putative regulons in Leishmania.</description><identifier>ISSN: 0166-6851</identifier><identifier>EISSN: 1872-9428</identifier><identifier>DOI: 10.1016/j.molbiopara.2012.02.009</identifier><identifier>PMID: 22387760</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Algorithms ; Base Sequence ; Bioinformatics ; Computational Biology ; Computer applications ; Conservation ; Conserved Sequence ; conserved sequences ; correlation ; Data processing ; Differentiation ; DNA, Protozoan - genetics ; Gene expression ; Genome, Protozoan ; Genomes ; Language ; languages ; Leishmania ; Leishmania braziliensis - genetics ; Leishmania infantum - genetics ; Leishmania major - genetics ; messenger RNA ; parasitology ; Pathogens ; Post-transcription ; Post-transcriptional gene regulation ; Putative regulatory motifs ; Regulatory Sequences, Nucleic Acid ; regulon ; Sequence Analysis, DNA ; Statistics ; Synteny ; UTRs</subject><ispartof>Molecular and biochemical parasitology, 2012-06, Vol.183 (2), p.140-150</ispartof><rights>2012 Elsevier B.V.</rights><rights>Copyright © 2012 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c481t-1fb39d55415d8628b0a158ca5ef57af94abf000ec840ee7741b56925e040a83</citedby><cites>FETCH-LOGICAL-c481t-1fb39d55415d8628b0a158ca5ef57af94abf000ec840ee7741b56925e040a83</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.molbiopara.2012.02.009$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22387760$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Vasconcelos, E.J.R.</creatorcontrib><creatorcontrib>Terrão, M.C.</creatorcontrib><creatorcontrib>Ruiz, J.C.</creatorcontrib><creatorcontrib>Vêncio, R.Z.N.</creatorcontrib><creatorcontrib>Cruz, A.K.</creatorcontrib><title>In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements</title><title>Molecular and biochemical parasitology</title><addtitle>Mol Biochem Parasitol</addtitle><description>In silico identification of conserved intercoding sequences (CICS) in three Leishmania genomes reveals potential cis-acting elements on the control of gene expression. [Display omitted]
► In silico identification of conserved intercoding sequences in Leishmania genomes. ► Data will be made available to the community. ► Some CICS are potential regulatory cis-elements. ► Common CICS are placed within transcripts sharing similar pattern of expression.
In silico analyses of Leishmania spp. genome data are a powerful resource to improve the understanding of these pathogens’ biology. Trypanosomatids such as Leishmania spp. have their protein-coding genes grouped in long polycistronic units of functionally unrelated genes. The control of gene expression happens by a variety of posttranscriptional mechanisms. The high degree of synteny among Leishmania species is accompanied by highly conserved coding sequences (CDS) and poorly conserved intercoding untranslated sequences. To identify the elements involved in the control of gene expression, we conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L. major, L. infantum, and L. braziliensis.
We used a combination of computational tools, such as Linux-Shell, PERL and R languages, BLAST, MSPcrunch, SSAKE, and Pred-A-Term algorithms to construct a pipeline which was able to: (i) search for conservation in target-regions, (ii) eliminate CICS redundancy and mask repeat elements, (iii) predict the mRNA's extremities, (iv) analyze the distribution of orthologous genes within the generated LeishCICS-clusters, (v) assign GO terms to the LeishCICS-clusters, and (vi) provide statistical support for the gene-enrichment annotation. We associated the LeishCICS-cluster data, generated at the end of the pipeline, with the expression profile of L. donovani genes during promastigote–amastigote differentiation, as previously evaluated by others (GEO accession: GSE21936). A Pearson's correlation coefficient greater than 0.5 was observed for 730 LeishCICS-clusters containing from 2 to 17 genes. The designed computational pipeline is a useful tool and its application identified potential regulatory cis elements and putative regulons in Leishmania.</description><subject>Algorithms</subject><subject>Base Sequence</subject><subject>Bioinformatics</subject><subject>Computational Biology</subject><subject>Computer applications</subject><subject>Conservation</subject><subject>Conserved Sequence</subject><subject>conserved sequences</subject><subject>correlation</subject><subject>Data processing</subject><subject>Differentiation</subject><subject>DNA, Protozoan - genetics</subject><subject>Gene expression</subject><subject>Genome, Protozoan</subject><subject>Genomes</subject><subject>Language</subject><subject>languages</subject><subject>Leishmania</subject><subject>Leishmania braziliensis - genetics</subject><subject>Leishmania infantum - genetics</subject><subject>Leishmania major - genetics</subject><subject>messenger RNA</subject><subject>parasitology</subject><subject>Pathogens</subject><subject>Post-transcription</subject><subject>Post-transcriptional gene regulation</subject><subject>Putative regulatory motifs</subject><subject>Regulatory Sequences, Nucleic Acid</subject><subject>regulon</subject><subject>Sequence Analysis, DNA</subject><subject>Statistics</subject><subject>Synteny</subject><subject>UTRs</subject><issn>0166-6851</issn><issn>1872-9428</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkU9v1DAQxS1ERZe2XwF85JLFzvpfuEEFtNJKHNqeLceZLLNK7MVOVuqFz15HW-BYpJEsWb95b2YeIZSzNWdcfdyvxzi0GA8uuXXNeL1mpVjziqy40XXViNq8JquCqkoZyc_J25z3jDGplXpDzut6Y7RWbEV-3waacUAfKXYQJuzRuwljoLGnPoYM6QgdxTBB8rHDsKMZfs0QPOTyS7eA-efoAjq6gxBHyJ_oQ0juCMPCHuapqB2BesxVgt08uCmmRwoDjMUtX5Kz3g0Zrp7fC3L37ev99U21_fH99vrztvLC8KnifbtpOikFl51RtWmZ49J4J6GX2vWNcG1ftgNvBAPQWvBWqqaWwARzZnNBPpxUDymW2fNkR8wehsEFiHO25aa60UwJ8R8o4400rGkKak6oTzHnBL09JBxdeizQIqns3v6LyS4xWVaKLa3vnl3mdoTub-OfXArw_gT0Llq3S5jtw11RkMVe8NosO305EVDOdkRINntcYukwgZ9sF_HlOZ4AgrW0oQ</recordid><startdate>20120601</startdate><enddate>20120601</enddate><creator>Vasconcelos, E.J.R.</creator><creator>Terrão, M.C.</creator><creator>Ruiz, J.C.</creator><creator>Vêncio, R.Z.N.</creator><creator>Cruz, A.K.</creator><general>Elsevier B.V</general><scope>6I.</scope><scope>AAFTH</scope><scope>FBQ</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>7X8</scope><scope>M7N</scope></search><sort><creationdate>20120601</creationdate><title>In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements</title><author>Vasconcelos, E.J.R. ; Terrão, M.C. ; Ruiz, J.C. ; Vêncio, R.Z.N. ; Cruz, A.K.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c481t-1fb39d55415d8628b0a158ca5ef57af94abf000ec840ee7741b56925e040a83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Algorithms</topic><topic>Base Sequence</topic><topic>Bioinformatics</topic><topic>Computational Biology</topic><topic>Computer applications</topic><topic>Conservation</topic><topic>Conserved Sequence</topic><topic>conserved sequences</topic><topic>correlation</topic><topic>Data processing</topic><topic>Differentiation</topic><topic>DNA, Protozoan - genetics</topic><topic>Gene expression</topic><topic>Genome, Protozoan</topic><topic>Genomes</topic><topic>Language</topic><topic>languages</topic><topic>Leishmania</topic><topic>Leishmania braziliensis - genetics</topic><topic>Leishmania infantum - genetics</topic><topic>Leishmania major - genetics</topic><topic>messenger RNA</topic><topic>parasitology</topic><topic>Pathogens</topic><topic>Post-transcription</topic><topic>Post-transcriptional gene regulation</topic><topic>Putative regulatory motifs</topic><topic>Regulatory Sequences, Nucleic Acid</topic><topic>regulon</topic><topic>Sequence Analysis, DNA</topic><topic>Statistics</topic><topic>Synteny</topic><topic>UTRs</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Vasconcelos, E.J.R.</creatorcontrib><creatorcontrib>Terrão, M.C.</creatorcontrib><creatorcontrib>Ruiz, J.C.</creatorcontrib><creatorcontrib>Vêncio, R.Z.N.</creatorcontrib><creatorcontrib>Cruz, A.K.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><jtitle>Molecular and biochemical parasitology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Vasconcelos, E.J.R.</au><au>Terrão, M.C.</au><au>Ruiz, J.C.</au><au>Vêncio, R.Z.N.</au><au>Cruz, A.K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements</atitle><jtitle>Molecular and biochemical parasitology</jtitle><addtitle>Mol Biochem Parasitol</addtitle><date>2012-06-01</date><risdate>2012</risdate><volume>183</volume><issue>2</issue><spage>140</spage><epage>150</epage><pages>140-150</pages><issn>0166-6851</issn><eissn>1872-9428</eissn><abstract>In silico identification of conserved intercoding sequences (CICS) in three Leishmania genomes reveals potential cis-acting elements on the control of gene expression. [Display omitted]
► In silico identification of conserved intercoding sequences in Leishmania genomes. ► Data will be made available to the community. ► Some CICS are potential regulatory cis-elements. ► Common CICS are placed within transcripts sharing similar pattern of expression.
In silico analyses of Leishmania spp. genome data are a powerful resource to improve the understanding of these pathogens’ biology. Trypanosomatids such as Leishmania spp. have their protein-coding genes grouped in long polycistronic units of functionally unrelated genes. The control of gene expression happens by a variety of posttranscriptional mechanisms. The high degree of synteny among Leishmania species is accompanied by highly conserved coding sequences (CDS) and poorly conserved intercoding untranslated sequences. To identify the elements involved in the control of gene expression, we conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L. major, L. infantum, and L. braziliensis.
We used a combination of computational tools, such as Linux-Shell, PERL and R languages, BLAST, MSPcrunch, SSAKE, and Pred-A-Term algorithms to construct a pipeline which was able to: (i) search for conservation in target-regions, (ii) eliminate CICS redundancy and mask repeat elements, (iii) predict the mRNA's extremities, (iv) analyze the distribution of orthologous genes within the generated LeishCICS-clusters, (v) assign GO terms to the LeishCICS-clusters, and (vi) provide statistical support for the gene-enrichment annotation. We associated the LeishCICS-cluster data, generated at the end of the pipeline, with the expression profile of L. donovani genes during promastigote–amastigote differentiation, as previously evaluated by others (GEO accession: GSE21936). A Pearson's correlation coefficient greater than 0.5 was observed for 730 LeishCICS-clusters containing from 2 to 17 genes. The designed computational pipeline is a useful tool and its application identified potential regulatory cis elements and putative regulons in Leishmania.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>22387760</pmid><doi>10.1016/j.molbiopara.2012.02.009</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Algorithms Base Sequence Bioinformatics Computational Biology Computer applications Conservation Conserved Sequence conserved sequences correlation Data processing Differentiation DNA, Protozoan - genetics Gene expression Genome, Protozoan Genomes Language languages Leishmania Leishmania braziliensis - genetics Leishmania infantum - genetics Leishmania major - genetics messenger RNA parasitology Pathogens Post-transcription Post-transcriptional gene regulation Putative regulatory motifs Regulatory Sequences, Nucleic Acid regulon Sequence Analysis, DNA Statistics Synteny UTRs |
| title | In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements |
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