The Experts below are selected from a list of 105 Experts worldwide ranked by ideXlab platform
Andrei V. Mironov - One of the best experts on this subject based on the ideXlab platform.
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RECOMB - Evidence for widespread association of mammalian splicing and conserved long-range RNA structures
Lecture Notes in Computer Science, 2012Co-Authors: Dmitri D. Pervouchine, Ekaterina E. Khrameeva, Marina Yu. Pichugina, Oleksii Nikolaienko, Mikhail S. Gelfand, Petr M. Rubtsov, Andrei V. MironovAbstract:Pre-mRNA structure impacts many cellular processes, including splicing in Genes associated with disease. The contemporary paradigm of RNA structure prediction is biased toward secondary structures that occur within short ranges of pre-mRNA, although long-range base-pairings are known to be at least as important. Recently, we developed an efficient method for detecting conserved RNA structures on the genome-wide scale, one that does not require multiple sequence alignments and works equally well for the detection of local and long-range base-pairings. Using an enhanced method that detects base-pairings at all possible combinations of splice sites within each Gene, we report a list of RNA structures that could be involved in the regulation of splicing in mammals. We demonstrate statistically that there is a strong association between the occurrence of conserved RNA structures and alternative splicing, where local RNA structures are Generally more frequent at alternative donor splice sites, while long-range structures are more associated with weak alternative acceptor splice sites. A fraction of the reported structures is associated with unannotated splicing events that are confirmed by RNA-seq data. As an example, we validated the RNA structure in the human SF1 Gene using mini-Genes in the HEK293 cell line. Point mutations that disrupted the base-pairing of two complementary boxes between exons 9 and 10 of this Gene altered the splicing pattern, while the compensatory mutations that reestablished the base-pairing reverted splicing to that of the wild-type. There is statistical evidence for a Dscam-like class of mammalian Genes, in which mutually exclusive RNA structures control mutually exclusive alternative splicing. In sum, we propose that long-range base-pairings carry an important, yet unconsidered part of the splicing code, and that, even by modest estimates, there must be thousands of such potentially regulatory structures conserved throughout the evolutionary history of mammals.
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Evidence for widespread association of mammalian splicing and conserved long-range RNA structures
RNA (New York N.Y.), 2011Co-Authors: Dmitri D. Pervouchine, Ekaterina E. Khrameeva, Marina Yu. Pichugina, Oleksii Nikolaienko, Mikhail S. Gelfand, Petr M. Rubtsov, Andrei V. MironovAbstract:Pre-mRNA structure impacts many cellular processes, including splicing in Genes associated with disease. The contemporary paradigm of RNA structure prediction is biased toward secondary structures that occur within short ranges of pre-mRNA, although long-range base-pairings are known to be at least as important. Recently, we developed an efficient method for detecting conserved RNA structures on the genome-wide scale, one that does not require multiple sequence alignments and works equally well for the detection of local and long-range base-pairings. Using an enhanced method that detects base-pairings at all possible combinations of splice sites within each Gene, we now report RNA structures that could be involved in the regulation of splicing in mammals. Statistically, we demonstrate strong association between the occurrence of conserved RNA structures and alternative splicing, where local RNA structures are Generally more frequent at alternative donor splice sites, while long-range structures are more associated with weak alternative acceptor splice sites. As an example, we validated the RNA structure in the human SF1 Gene using miniGenes in the HEK293 cell line. Point mutations that disrupted the base-pairing of two complementary boxes between exons 9 and 10 of this Gene altered the splicing pattern, while the compensatory mutations that reestablished the base-pairing reverted splicing to that of the wild-type. There is statistical evidence for a Dscam-like class of mammalian Genes, in which mutually exclusive RNA structures control mutually exclusive alternative splicing. In sum, we propose that long-range base-pairings carry an important, yet unconsidered part of the splicing code, and that, even by modest estimates, there must be thousands of such potentially regulatory structures conserved throughout the evolutionary history of mammals.
Moxian Chen - One of the best experts on this subject based on the ideXlab platform.
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systematic characterization of the branch point binding protein splicing factor 1 Gene family in plant development and stress responses
BMC Plant Biology, 2020Co-Authors: Kailu Zhang, Jianhua Zhang, Yanming Fang, Zhen Feng, Jingfang Yang, Feng Yang, Tian Yuan, Di Zhang, Gefei Hao, Moxian ChenAbstract:Among eukaryotic organisms, alternative splicing is an important process that can Generate multiple transcripts from one same precursor messenger RNA, which greatly increase transcriptome and proteome diversity. This process is carried out by a super-protein complex defined as the spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting the 5′ and 3′ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoa and mammals. However, its counterpart in plants has been seldomly reported. To this end, we conducted a systematic characterization of the SF1 Gene family across plant lineages. In this work, a total of 92 sequences from 59 plant species were identified. PhyloGenetic relationships of these sequences were constructed, and subsequent bioinformatic analysis suggested that this family likely originated from an ancient Gene transposition duplication event. Most plant species were shown to maintain a single copy of this Gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this Gene family in comparison to their animal and yeast counterparts, indicating that their potential role was preserved in the plant lineage. Our analysis presents General features of the Gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.
Kailu Zhang - One of the best experts on this subject based on the ideXlab platform.
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systematic characterization of the branch point binding protein splicing factor 1 Gene family in plant development and stress responses
BMC Plant Biology, 2020Co-Authors: Kailu Zhang, Jianhua Zhang, Yanming Fang, Zhen Feng, Jingfang Yang, Feng Yang, Tian Yuan, Di Zhang, Gefei Hao, Moxian ChenAbstract:Among eukaryotic organisms, alternative splicing is an important process that can Generate multiple transcripts from one same precursor messenger RNA, which greatly increase transcriptome and proteome diversity. This process is carried out by a super-protein complex defined as the spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting the 5′ and 3′ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoa and mammals. However, its counterpart in plants has been seldomly reported. To this end, we conducted a systematic characterization of the SF1 Gene family across plant lineages. In this work, a total of 92 sequences from 59 plant species were identified. PhyloGenetic relationships of these sequences were constructed, and subsequent bioinformatic analysis suggested that this family likely originated from an ancient Gene transposition duplication event. Most plant species were shown to maintain a single copy of this Gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this Gene family in comparison to their animal and yeast counterparts, indicating that their potential role was preserved in the plant lineage. Our analysis presents General features of the Gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.
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Systematic characterization of branch point binding protein, splicing factor 1, Gene family in plant development and stress responses
2019Co-Authors: Kailu Zhang, Zhen Feng, Jingfang Yang, Tian Yuan, Di Zhang, Gefei Hao, Guang-fu Yang, Yu-chen Song, Cong-cong Shen, Yanming FangAbstract:Abstract Background: Among eukaryotic organisms, the splicing of nuclear precursor messenger RNA (pre-mRNA) is a process of introns excision and sequentially joining of exons, leading multi-exonic Genes to Generate multiple splicing isoforms at transcription level. This process is carried out by a super-protein complex defined as spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting 5’ and 3’ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoan and mammals. However, their counterparts in plants are seldomly reported. Results: Here, we conducted a systematic characterization of SF1 Gene family across plant lineage. In this work, a total of 92 sequences from 59 plant species were identified. PhyloGenetic relationships of these sequences were constructed and subsequent bioinformatic analysis suggested that this family is likely originated from an ancient Gene transposition duplication event. Most plant species were shown to maintain a single copy of this Gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this Gene family in comparison to their animal and yeast counterparts, indicating their potential role conserved in plant lineage. Conclusion: Our comprehensive analysis presents General feature of Gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.
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Systematic characterization of branch point binding protein, splicing factor 1, Gene family in plant development and stress responses
2019Co-Authors: Kailu Zhang, Yanming Fang, Zhen Feng, Jingfang Yang, Tian Yuan, Di Zhang, Gefei Hao, Guang-fu Yang, Jianhua ZhangAbstract:Abstract Among eukaryotic organisms, the splicing of nuclear precursor messenger RNA (pre-mRNA) is a process of introns excision and sequentially joining of exons, leading multi-exonic Genes to Generate multiple splicing isoforms at transcription level. This process is carried out by a super-protein complex defined as spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting 5’ and 3’ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoan and mammals. However, their counterparts in plants are seldomly reported. To this end, we conducted a systematic characterization of SF1 Gene family across plant lineage. In this work, a total of 92 sequences from 59 plant species were identified. PhyloGenetic relationships of these sequences were constructed and subsequent bioinformatic analysis suggested that this family is likely originated from an ancient Gene transposition duplication event. Most plant species were shown to maintain a single copy of this Gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this Gene family in comparison to their animal and yeast counterparts, indicating their potential role conserved in plant lineage. Our analysis presents General feature of Gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.
Yanming Fang - One of the best experts on this subject based on the ideXlab platform.
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systematic characterization of the branch point binding protein splicing factor 1 Gene family in plant development and stress responses
BMC Plant Biology, 2020Co-Authors: Kailu Zhang, Jianhua Zhang, Yanming Fang, Zhen Feng, Jingfang Yang, Feng Yang, Tian Yuan, Di Zhang, Gefei Hao, Moxian ChenAbstract:Among eukaryotic organisms, alternative splicing is an important process that can Generate multiple transcripts from one same precursor messenger RNA, which greatly increase transcriptome and proteome diversity. This process is carried out by a super-protein complex defined as the spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting the 5′ and 3′ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoa and mammals. However, its counterpart in plants has been seldomly reported. To this end, we conducted a systematic characterization of the SF1 Gene family across plant lineages. In this work, a total of 92 sequences from 59 plant species were identified. PhyloGenetic relationships of these sequences were constructed, and subsequent bioinformatic analysis suggested that this family likely originated from an ancient Gene transposition duplication event. Most plant species were shown to maintain a single copy of this Gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this Gene family in comparison to their animal and yeast counterparts, indicating that their potential role was preserved in the plant lineage. Our analysis presents General features of the Gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.
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Systematic characterization of branch point binding protein, splicing factor 1, Gene family in plant development and stress responses
2019Co-Authors: Kailu Zhang, Zhen Feng, Jingfang Yang, Tian Yuan, Di Zhang, Gefei Hao, Guang-fu Yang, Yu-chen Song, Cong-cong Shen, Yanming FangAbstract:Abstract Background: Among eukaryotic organisms, the splicing of nuclear precursor messenger RNA (pre-mRNA) is a process of introns excision and sequentially joining of exons, leading multi-exonic Genes to Generate multiple splicing isoforms at transcription level. This process is carried out by a super-protein complex defined as spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting 5’ and 3’ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoan and mammals. However, their counterparts in plants are seldomly reported. Results: Here, we conducted a systematic characterization of SF1 Gene family across plant lineage. In this work, a total of 92 sequences from 59 plant species were identified. PhyloGenetic relationships of these sequences were constructed and subsequent bioinformatic analysis suggested that this family is likely originated from an ancient Gene transposition duplication event. Most plant species were shown to maintain a single copy of this Gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this Gene family in comparison to their animal and yeast counterparts, indicating their potential role conserved in plant lineage. Conclusion: Our comprehensive analysis presents General feature of Gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.
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Systematic characterization of branch point binding protein, splicing factor 1, Gene family in plant development and stress responses
2019Co-Authors: Kailu Zhang, Yanming Fang, Zhen Feng, Jingfang Yang, Tian Yuan, Di Zhang, Gefei Hao, Guang-fu Yang, Jianhua ZhangAbstract:Abstract Among eukaryotic organisms, the splicing of nuclear precursor messenger RNA (pre-mRNA) is a process of introns excision and sequentially joining of exons, leading multi-exonic Genes to Generate multiple splicing isoforms at transcription level. This process is carried out by a super-protein complex defined as spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting 5’ and 3’ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoan and mammals. However, their counterparts in plants are seldomly reported. To this end, we conducted a systematic characterization of SF1 Gene family across plant lineage. In this work, a total of 92 sequences from 59 plant species were identified. PhyloGenetic relationships of these sequences were constructed and subsequent bioinformatic analysis suggested that this family is likely originated from an ancient Gene transposition duplication event. Most plant species were shown to maintain a single copy of this Gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this Gene family in comparison to their animal and yeast counterparts, indicating their potential role conserved in plant lineage. Our analysis presents General feature of Gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.
Dmitri D. Pervouchine - One of the best experts on this subject based on the ideXlab platform.
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RECOMB - Evidence for widespread association of mammalian splicing and conserved long-range RNA structures
Lecture Notes in Computer Science, 2012Co-Authors: Dmitri D. Pervouchine, Ekaterina E. Khrameeva, Marina Yu. Pichugina, Oleksii Nikolaienko, Mikhail S. Gelfand, Petr M. Rubtsov, Andrei V. MironovAbstract:Pre-mRNA structure impacts many cellular processes, including splicing in Genes associated with disease. The contemporary paradigm of RNA structure prediction is biased toward secondary structures that occur within short ranges of pre-mRNA, although long-range base-pairings are known to be at least as important. Recently, we developed an efficient method for detecting conserved RNA structures on the genome-wide scale, one that does not require multiple sequence alignments and works equally well for the detection of local and long-range base-pairings. Using an enhanced method that detects base-pairings at all possible combinations of splice sites within each Gene, we report a list of RNA structures that could be involved in the regulation of splicing in mammals. We demonstrate statistically that there is a strong association between the occurrence of conserved RNA structures and alternative splicing, where local RNA structures are Generally more frequent at alternative donor splice sites, while long-range structures are more associated with weak alternative acceptor splice sites. A fraction of the reported structures is associated with unannotated splicing events that are confirmed by RNA-seq data. As an example, we validated the RNA structure in the human SF1 Gene using mini-Genes in the HEK293 cell line. Point mutations that disrupted the base-pairing of two complementary boxes between exons 9 and 10 of this Gene altered the splicing pattern, while the compensatory mutations that reestablished the base-pairing reverted splicing to that of the wild-type. There is statistical evidence for a Dscam-like class of mammalian Genes, in which mutually exclusive RNA structures control mutually exclusive alternative splicing. In sum, we propose that long-range base-pairings carry an important, yet unconsidered part of the splicing code, and that, even by modest estimates, there must be thousands of such potentially regulatory structures conserved throughout the evolutionary history of mammals.
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Evidence for widespread association of mammalian splicing and conserved long-range RNA structures
RNA (New York N.Y.), 2011Co-Authors: Dmitri D. Pervouchine, Ekaterina E. Khrameeva, Marina Yu. Pichugina, Oleksii Nikolaienko, Mikhail S. Gelfand, Petr M. Rubtsov, Andrei V. MironovAbstract:Pre-mRNA structure impacts many cellular processes, including splicing in Genes associated with disease. The contemporary paradigm of RNA structure prediction is biased toward secondary structures that occur within short ranges of pre-mRNA, although long-range base-pairings are known to be at least as important. Recently, we developed an efficient method for detecting conserved RNA structures on the genome-wide scale, one that does not require multiple sequence alignments and works equally well for the detection of local and long-range base-pairings. Using an enhanced method that detects base-pairings at all possible combinations of splice sites within each Gene, we now report RNA structures that could be involved in the regulation of splicing in mammals. Statistically, we demonstrate strong association between the occurrence of conserved RNA structures and alternative splicing, where local RNA structures are Generally more frequent at alternative donor splice sites, while long-range structures are more associated with weak alternative acceptor splice sites. As an example, we validated the RNA structure in the human SF1 Gene using miniGenes in the HEK293 cell line. Point mutations that disrupted the base-pairing of two complementary boxes between exons 9 and 10 of this Gene altered the splicing pattern, while the compensatory mutations that reestablished the base-pairing reverted splicing to that of the wild-type. There is statistical evidence for a Dscam-like class of mammalian Genes, in which mutually exclusive RNA structures control mutually exclusive alternative splicing. In sum, we propose that long-range base-pairings carry an important, yet unconsidered part of the splicing code, and that, even by modest estimates, there must be thousands of such potentially regulatory structures conserved throughout the evolutionary history of mammals.