Functional significance of graded properties of insect cuticle supported by an evolutionary analysis.
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ABSTRACT:
SUBMITTER: Jafarpour M
PROVIDER: S-EPMC7423415 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Our recent study on the functional analysis of the Knickkopf protein from T. castaneum (TcKnk), indicated a novel role for this protein in protection of chitin from degradation by chitinases. Knk is also required for the laminar organization of chitin in the procuticle. During a bioinformatics search using this protein sequence as the query, we discovered the existence of a small family of three Knk-like genes (including the prototypical TcKnk) in the T. castaneum genome as well as in all insects with completed genome assemblies. The two additional Knk-like genes have been named TcKnk2 and TcKnk3. Further complexity arises as a result of alternative splicing and alternative polyadenylation of transcripts of TcKnk3, leading to the production of three transcripts (and by inference, three proteins) from this gene. These transcripts are named TcKnk3-Full Length (TcKnk3-FL), TcKnk3-5' and TcKnk3-3'. All three Knk-family genes appear to have essential and non-redundant functions. RNAi for TcKnk led to developmental arrest at every molt, while down-regulation of either TcKnk2 or one of the three TcKnk3 transcripts (TcKnk3-3') resulted in specific molting arrest only at the pharate adult stage. All three Knk genes appear to influence the total chitin content at the pharate adult stage, but to variable extents. While TcKnk contributes mostly to the stability and laminar organization of chitin in the elytral and body wall procuticles, proteins encoded by TcKnk2 and TcKnk3-3' transcripts appear to be required for the integrity of the body wall denticles and tracheal taenidia, but not the elytral and body wall procuticles. Thus, the three members of the Knk-family of proteins perform different essential functions in cuticle formation at different developmental stages and in different parts of the insect anatomy.
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Project description:This SuperSeries is composed of the SubSeries listed below. Data for miR-429, miR-205, miR-200b, and miR-141 were each compared independently to the same negative control data contained in the raw .CEL files nc-miR-1-1.CEL, nc-miR-1-2.CEL and nc-miR-1-3.CEL. For each miRNA, the negative control data were re-normalized together with data only from that specific miRNA. The experiment for M12 was performed at a later date and an independent set of negative control data was collected at that time. Therefore, only M12 data was compared to the negative control data contained in the raw .CEL files nc-miR-2-1.CEL, nc-miR-2-2.CEL, and nc-miR-2-3.CEL.
2015-01-30 | E-GEOD-56973 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2015-01-30 | GSE56973 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt M-bM-^@M-^\seed regionM-bM-^@M-^] mapping to positions 2-8 at the moleculeM-bM-^@M-^Ys 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control. mRNAs were collected from 3 M12 miRNA treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the M12 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.
2015-01-30 | E-GEOD-56972 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt M-bM-^@M-^\seed regionM-bM-^@M-^] mapping to positions 2-8 at the moleculeM-bM-^@M-^Ys 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control. mRNAs were collected from 3 M5 miRNA treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the M5 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.
2015-01-30 | E-GEOD-61229 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt M-bM-^@M-^\seed regionM-bM-^@M-^] mapping to positions 2-8 at the moleculeM-bM-^@M-^Ys 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control. mRNAs were collected from 3 M14 miRNA treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the M14 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.
2015-01-30 | E-GEOD-61230 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt “seed region” mapping to positions 2-8 at the molecule’s 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control.
2015-01-30 | GSE61229 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt “seed region” mapping to positions 2-8 at the molecule’s 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control.
2015-01-30 | GSE56972 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt “seed region” mapping to positions 2-8 at the molecule’s 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control.
2015-01-30 | GSE61230 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt M-bM-^@M-^\seed regionM-bM-^@M-^] mapping to positions 2-8 at the moleculeM-bM-^@M-^Ys 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control. mRNAs were collected from 3 miR-429 treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the miR-429 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.
2015-01-30 | E-GEOD-56967 | biostudies-arrayexpress