TEs or not TEs? That is the evolutionary question (2009)
Vaknin, Keren, Goren, Amir, Ast, Gil
Abstract Transposable elements (TEs) have contributed a wide range of functional sequences to their host genomes. A recent paper in BMC Molecular Biology discusses the creation of new transcripts by...
SROOGLE: webserver for integrative, user-friendly visualization of splicing signals (2009)
Schwartz, Schraga, Hall, Eitan, Ast, Gil
Exons are typically only 140 nt in length and are surrounded by intronic oceans that are thousands of nucleotides long. Four core splicing signals, aided by splicing-regulatory sequences (SRSs),...
Schraga Schwartz, João Silva, David Burstein, Tal Pupko, Eduardo Eyras, Gil Ast, ...
Large-scale comparative analysis of splicing signals and their
The ‘‘Alternative’ ’ Choice of Constitutive Exons throughout Evolution (2008)
Galit Lev-maor, Amir Goren, Noa Sela, Eddo Kim, Hadas Keren, Adi Doron-faigenboim, ...
Alternative cassette exons are known to originate from two processes—exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced...
1Department of Human Molecular Genetics and Biochemistry (2008)
Amir Goren, Oren Ram, Maayan Amit, Hadas Keren, Galit Lev-maor, Ida Vig, ...
Exonic splicing regulatory sequences (ESRs) are cisacting factor binding sites that regulate constitutive and alternative splicing. A computational method based on the conservation level of wobble...
Mersch, Britta, Sela, Noa, Ast, Gil, Suhai, Sandor
Background: Transposed elements (TEs) are known to affect transcriptomes, because either new exons are generated from intronic transposed elements (this is called exonization), or the element inserts...
Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene (2008)
Amit, Maayan, Sela, Noa, Keren, Hadas, Melamed, Zeev, Muler, Inna, Shomron, Noam, ...
Background: Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization of...
Sela, Noa, Stern, Adi, Makalowski, Wojciech, Pupko, Tal, Ast, Gil
Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of...
Sela, Noa, Mersch, Britta, Gal-Mark, Nurit, Lev-Maor, Galit, Ast, Gil
Background: Transposed elements (TEs) have a substantial impact on mammalian evolution and are involved in numerous genetic diseases. We compared the impact of TEs on the human transcriptome and the...
Levy, Asaf, Sela, Noa, Ast, Gil
Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing...
The Alternative Choice of Constitutive Exons throughout Evolution (2008)
Lev-Maor, Galit, Goren, Amir, Sela, Noa, Kim, Eddo, Keren, Hadas, Doron-Faigenboim, Adi, ...
Alternative cassette exons are known to originate from two processes exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced...
Intronic Alus Influence Alternative Splicing (2008)
Lev-Maor, Galit, Ram, Oren, Kim, Eddo, Sela, Noa, Goren, Amir, Levanon, Erez Y, ...
Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the...
Sela, Noa, Stern, Adi, Makalowski, Wojciech, Pupko, Tal, Ast, Gil
Abstract Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is...
Rotem Sorek, Ron Shamir, Gil Ast
How prevalent is functional alternative splicing in the
Levy, Asaf, Sela, Noa, Ast, Gil
Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing...
Alternative approach to a heavy weight problem (2008)
Goren, Amir, Kim, Eddo, Amit, Maayan, Bochner, Ron, Lev-Maor, Galit, Ahituv, Nadav, ...
Obesity is reaching epidemic proportions in developed countries and represents a significant risk factor for hypertension, heart disease, diabetes, and dyslipidemia. Splicing mutations constitute at...
Alternative splicing of Alu exons--two arms are better than one (2008)
Gal-Mark, Nurit, Schwartz, Schraga, Ast, Gil
Alus, primate-specific retroelements, are the most abundant repetitive elements in the human genome. They are composed of two related but distinct monomers, left and right arms. Intronic Alu elements...
Schwartz, Schraga, Silva, João, Burstein, David, Pupko, Tal, Eyras, Eduardo, Ast, Gil
Introns are among the hallmarks of eukaryotic genes. Splicing of introns is directed by three main splicing signals: the 5′ splice site (5′ss), the branch site (BS), and the polypyrimdine...
Biology Direct BioMed Central Discovery notes (2008)
Noa Sela, Adi Stern, Wojciech Makalowski, Tal Pupko, Gil Ast, Tal Pupko, ...
Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans
Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene (2007)
Amit, Maayan, Sela, Noa, Keren, Hadas, Melamed, Ze'ev, Muler, Inna, Shomron, Noam, ...
Abstract Background Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization...
How Prevalent is Functional Alternative Splicing in the (2007)
Human Genome Rotem, Rotem Sorek, Ron Shamir, Gil Ast
this article can be found at doi: 10.1016/j.tig.2003.12.004 Corresponding author: Gil Ast (gilast@post.tau.ac.il)
Mersch, Britta, Sela, Noa, Ast, Gil, Suhai, Sándor, Hotz-Wagenblatt, Agnes
Abstract Background Transposed elements (TEs) are known to affect transcriptomes, because either new exons are generated from intronic transposed elements (this is called exonization ), or the...
The “Alternative” Choice of Constitutive Exons throughout Evolution (2007)
Galit Lev-Maor, Amir Goren, Noa Sela, Eddo Kim, Hadas Keren, Adi Doron-Faigenboim, ...
Alternative cassette exons are known to originate from two processes—exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced...
Alberstein, Moti, Amit, Maayan, Vaknin, Keren, O'Donnell, Amanda, Farhy, Chen, Lerenthal, Yaniv, ...
Alternative splicing plays a major role in transcriptome diversity and plasticity, but it is largely unknown how tissue-specific and embryogenesis-specific alternative splicing is regulated. The...
Cheishvili, David, Maayan, Channa, Smith, Yoav, Ast, Gil, Razin, Aharon
The gene affected in the congenital neuropathy familial dysautonomia (FD) is IKBKAP that codes for the IKAP/hELP1 protein. Several different functions have been suggested for this protein, but none...
Sela, Noa, Mersch, Britta, Gal-Mark, Nurit, Lev-Maor, Galit, Hotz-Wagenblatt, Agnes, Ast, Gil
Abstract Background Transposed elements (TEs) have a substantial impact on mammalian evolution and are involved in numerous genetic diseases. We compared the impact of TEs on the human transcriptome...
The Emergence of Alternative 3′ and 5′ Splice Site Exons from Constitutive Exons (2007)
Eli Koren, Galit Lev-Maor, Gil Ast
Alternative 3′ and 5′ splice site (ss) events constitute a significant part of all alternative splicing events. These events were also found to be related to several aberrant splicing diseases....
RNA-editing-mediated exon evolution (2007)
Lev-Maor, Galit, Sorek, Rotem, Levanon, Erez Y, Paz, Nurit, Eisenberg, Eli, Ast, Gil
Abstract Background Alu retroelements are specific to primates and abundant in the human genome. Through mutations that create functional splice sites within intronic Alu s, these elements can become...
Different levels of alternative splicing among eukaryotes (2007)
Kim, Eddo, Magen, Alon, Ast, Gil
Alternative splicing increases transcriptome and proteome diversification. Previous analyses aiming at comparing the rate of alternative splicing between different organisms provided contradicting...
Different levels of alternative splicing among eukaryotes (2006)
Kim, Eddo, Magen, Alon, Ast, Gil
Alternative splicing increases transcriptome and proteome diversification. Previous analyses aiming at comparing the rate of alternative splicing between different organisms provided contradicting...
Different levels of alternative splicing among eukaryotes (2006)
Kim, Eddo, Magen, Alon, Ast, Gil
Alternative splicing increases transcriptome and proteome diversification. Previous analyses aiming at comparing the rate of alternative splicing between different organisms provided contradicting...
The importance of being divisible by three in alternative splicing (2005)
Alternative splicing events that are conserved in orthologous genes in different species are commonly viewed as reliable evidence of authentic, functionally significant alternative splicing events....
Kol, Guy, Lev-Maor, Galit, Ast, Gil
The formation of base-pairing between the branch-site (BS) sequence and the U2 snRNP is an important step in mRNA splicing. We developed a new algorithm to identify both the BS sequence and the...
Kol, Guy, Lev-Maor, Galit, Ast, Gil
The formation of base-pairing between the branch-site sequence and U2 snRNP is an important step in mRNA splicing. We developed a new algorithm to identify both the branch-site sequence and the...
A Non-EST-Based Method for Exon-Skipping Prediction (2004)
Sorek, Rotem, Shemesh, Ronen, Cohen, Yuval, Basechess, Ortal, Ast, Gil, Shamir, Ron
It is estimated that between 35% and 74% of all human genes can undergo alternative splicing. Currently, the most efficient methods for large-scale detection of alternative splicing use expressed...
Comparative analysis detects dependencies among the 5' splice-site positions (2004)
CARMEL, IDO, TAL, SAAR, VIG, IDA, AST, GIL
Human–mouse comparative genomics is an informative tool to assess sequence functionality as inferred from its conservation level. We used this approach to examine dependency among different...
AluGene: a database of Alu elements incorporated within protein-coding genes (2004)
Dagan, Tal, Sorek, Rotem, Sharon, Eilon, Ast, Gil, Graur, Dan
Alu elements are short interspersed elements (SINEs) ∼300 nucleotides in length. More than 1 million Alus are found in the human genome. Despite their being genetically functionless, recent...
Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse (2003)
Comparison of the sequences of mouse and human genomes revealed a surprising number of nonexonic, nonexpressed conserved sequences, for which no function could be assigned. To study the possible...
Shomron, Noam, Malca, Hadar, Vig, Ida, Ast, Gil
A multicomponent complex of proteins and RNA is assembled on the newly synthesized pre‐mRNA to form the spliceosome. This complex catalyzes a two‐step transesterification reaction required...
Ast, Gil, Pavelitz, Thomas, Weiner, Alan M.
Three different base paired stems form between U2 and U6 snRNA over the course of the mRNA splicing reaction (helices I, II and III). One possible function of U2/U6 helix II is to facilitate...
Ast, Gil, Goldblatt, Drora, Waisman, Ari, Sperling, Ruth, Mozes, Edna, Sperling, Joseph
We have previously shown that nuclear transcripts of several pre-mRNAs can be released from nuclei of mammalian cells in a form of large nuclear ribonucleoprotein (InRNP) particles. These particles,...
Ast, Gil, Pavelitz, Thomas, Weiner, Alan M.
Three different base paired stems form between U2 and U6 snRNA over the course of the mRNA splicing reaction (helices I, II and III). One possible function of U2/U6 helix II is to facilitate...
Shomron, Noam, Malca, Hadar, Vig, Ida, Ast, Gil
A multicomponent complex of proteins and RNA is assembled on the newly synthesized pre-mRNA to form the spliceosome. This complex catalyzes a two-step transesterification reaction required to remove...
The U1 snRNP Base Pairs with the 5′ Splice Site within a Penta-snRNP Complex
Malca, Hadar, Shomron, Noam, Ast, Gil
Recognition of the 5′ splice site is an important step in mRNA splicing. To examine whether U1 approaches the 5′ splice site as a solitary snRNP or as part of a multi-snRNP complex, we used a...
Alu-Containing Exons are Alternatively Spliced
Sorek, Rotem, Ast, Gil, Graur, Dan
Alu repetitive elements are found in ∼1.4 million copies in the human genome, comprising more than one-tenth of it. Numerous studies describe exonizations of Alu elements, that is,...
AluGene: a database of Alu elements incorporated within protein-coding genes
Dagan, Tal, Sorek, Rotem, Sharon, Eilon, Ast, Gil, Graur, Dan
Alu elements are short interspersed elements (SINEs) ∼300 nucleotides in length. More than 1 million Alus are found in the human genome. Despite their being genetically functionless, recent...
Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse
Comparison of the sequences of mouse and human genomes revealed a surprising number of nonexonic, nonexpressed conserved sequences, for which no function could be assigned. To study the possible...
Shomron, Noam, Reznik, Mika, Ast, Gil
Precursor-mRNA splicing removes the introns and ligates the exons to form a mature mRNA. This process is carried out in a spliceosomal complex containing >150 proteins and five small nuclear...
A Non-EST-Based Method for Exon-Skipping Prediction
Sorek, Rotem, Shemesh, Ronen, Cohen, Yuval, Basechess, Ortal, Ast, Gil, Shamir, Ron
It is estimated that between 35% and 74% of all human genes can undergo alternative splicing. Currently, the most efficient methods for large-scale detection of alternative splicing use expressed...
The importance of being divisible by three in alternative splicing
Alternative splicing events that are conserved in orthologous genes in different species are commonly viewed as reliable evidence of authentic, functionally significant alternative splicing events....
Comparative analysis detects dependencies among the 5′ splice-site positions
CARMEL, IDO, TAL, SAAR, VIG, IDA, AST, GIL
Human–mouse comparative genomics is an informative tool to assess sequence functionality as inferred from its conservation level. We used this approach to examine dependency among different...
Ast, Gil, Pavelitz, Thomas, Weiner, Alan M.
Three different base paired stems form between U2 and U6 snRNA over the course of the mRNA splicing reaction (helices I, II and III). One possible function of U2/U6 helix II is to facilitate...
Shomron, Noam, Malca, Hadar, Vig, Ida, Ast, Gil
A multicomponent complex of proteins and RNA is assembled on the newly synthesized pre-mRNA to form the spliceosome. This complex catalyzes a two-step transesterification reaction required to remove...
The U1 snRNP Base Pairs with the 5′ Splice Site within a Penta-snRNP Complex
Malca, Hadar, Shomron, Noam, Ast, Gil
Recognition of the 5′ splice site is an important step in mRNA splicing. To examine whether U1 approaches the 5′ splice site as a solitary snRNP or as part of a multi-snRNP complex, we used a...
Alu-Containing Exons are Alternatively Spliced
Sorek, Rotem, Ast, Gil, Graur, Dan
Alu repetitive elements are found in ∼1.4 million copies in the human genome, comprising more than one-tenth of it. Numerous studies describe exonizations of Alu elements, that is,...
AluGene: a database of Alu elements incorporated within protein-coding genes
Dagan, Tal, Sorek, Rotem, Sharon, Eilon, Ast, Gil, Graur, Dan
Alu elements are short interspersed elements (SINEs) ∼300 nucleotides in length. More than 1 million Alus are found in the human genome. Despite their being genetically functionless, recent...
Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved Between Human and Mouse
Comparison of the sequences of mouse and human genomes revealed a surprising number of nonexonic, nonexpressed conserved sequences, for which no function could be assigned. To study the possible...
Shomron, Noam, Reznik, Mika, Ast, Gil
Precursor-mRNA splicing removes the introns and ligates the exons to form a mature mRNA. This process is carried out in a spliceosomal complex containing >150 proteins and five small nuclear...
A Non-EST-Based Method for Exon-Skipping Prediction
Sorek, Rotem, Shemesh, Ronen, Cohen, Yuval, Basechess, Ortal, Ast, Gil, Shamir, Ron
It is estimated that between 35% and 74% of all human genes can undergo alternative splicing. Currently, the most efficient methods for large-scale detection of alternative splicing use expressed...
The importance of being divisible by three in alternative splicing
Alternative splicing events that are conserved in orthologous genes in different species are commonly viewed as reliable evidence of authentic, functionally significant alternative splicing events....
Comparative analysis detects dependencies among the 5′ splice-site positions
CARMEL, IDO, TAL, SAAR, VIG, IDA, AST, GIL
Human–mouse comparative genomics is an informative tool to assess sequence functionality as inferred from its conservation level. We used this approach to examine dependency among different...
Different levels of alternative splicing among eukaryotes
Kim, Eddo, Magen, Alon, Ast, Gil
Alternative splicing increases transcriptome and proteome diversification. Previous analyses aiming at comparing the rate of alternative splicing between different organisms provided contradicting...
RNA-editing-mediated exon evolution
Lev-Maor, Galit, Sorek, Rotem, Levanon, Erez Y, Paz, Nurit, Eisenberg, Eli, Ast, Gil
A primate-specific exon is found to be dependent on RNA editing for its exonization.
The Emergence of Alternative 3′ and 5′ Splice Site Exons from Constitutive Exons
Koren, Eli, Lev-Maor, Galit, Ast, Gil
Alternative 3′ and 5′ splice site (ss) events constitute a significant part of all alternative splicing events. These events were also found to be related to several aberrant splicing diseases....
The “Alternative” Choice of Constitutive Exons throughout Evolution
Lev-Maor, Galit, Goren, Amir, Sela, Noa, Kim, Eddo, Keren, Hadas, Doron-Faigenboim, Adi, ...
Alternative cassette exons are known to originate from two processes—exonization of intronic sequences and exon shuffling. Herein, we suggest an additional mechanism by which constitutively spliced...
Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene
Amit, Maayan, Sela, Noa, Keren, Hadas, Melamed, Ze'ev, Muler, Inna, Shomron, Noam, ...
Levy, Asaf, Sela, Noa, Ast, Gil
Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing...
Alberstein, Moti, Amit, Maayan, Vaknin, Keren, O'Donnell, Amanda, Farhy, Chen, Lerenthal, Yaniv, ...
Alternative splicing plays a major role in transcriptome diversity and plasticity, but it is largely unknown how tissue-specific and embryogenesis-specific alternative splicing is regulated. The...
Alternative splicing of Alu exons—two arms are better than one
Gal-Mark, Nurit, Schwartz, Schraga, Ast, Gil
Alus, primate-specific retroelements, are the most abundant repetitive elements in the human genome. They are composed of two related but distinct monomers, left and right arms. Intronic Alu elements...
Sela, Noa, Mersch, Britta, Gal-Mark, Nurit, Lev-Maor, Galit, Hotz-Wagenblatt, Agnes, Ast, Gil
Analysis of transposed elements in the human and mouse genomes reveals many effects on the transcriptomes, including a higher level of exonization of Alu elements than other elements.
Schwartz, Schraga, Silva, João, Burstein, David, Pupko, Tal, Eyras, Eduardo, Ast, Gil
Introns are among the hallmarks of eukaryotic genes. Splicing of introns is directed by three main splicing signals: the 5′ splice site (5′ss), the branch site (BS), and the polypyrimdine...
Alternative approach to a heavy weight problem
Goren, Amir, Kim, Eddo, Amit, Maayan, Bochner, Ron, Lev-Maor, Galit, Ahituv, Nadav, ...
Obesity is reaching epidemic proportions in developed countries and represents a significant risk factor for hypertension, heart disease, diabetes, and dyslipidemia. Splicing mutations constitute at...
Multifactorial Interplay Controls the Splicing Profile of Alu-Derived Exons▿ †
Ram, Oren, Schwartz, Schraga, Ast, Gil
Exonization of Alu elements creates primate-specific genomic diversity. Here we combine bioinformatic and experimental methodologies to reconstruct the molecular changes leading to exon selection....
Intronic Alus Influence Alternative Splicing
Lev-Maor, Galit, Ram, Oren, Kim, Eddo, Sela, Noa, Goren, Amir, Levanon, Erez Y., ...
Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the...
Sela, Noa, Stern, Adi, Makalowski, Wojciech, Pupko, Tal, Ast, Gil
Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of...
Schwartz, Schraga, Gal-Mark, Nurit, Kfir, Nir, Oren, Ram, Kim, Eddo, Ast, Gil
Despite decades of research, the question of how the mRNA splicing machinery precisely identifies short exonic islands within the vast intronic oceans remains to a large extent obscure. In this...
SROOGLE: webserver for integrative, user-friendly visualization of splicing signals
Schwartz, Schraga, Hall, Eitan, Ast, Gil
Exons are typically only 140 nt in length and are surrounded by intronic oceans that are thousands of nucleotides long. Four core splicing signals, aided by splicing-regulatory sequences (SRSs),...
The Pivotal Roles of TIA Proteins in 5′ Splice-Site Selection of Alu Exons and Across Evolution
Gal-Mark, Nurit, Schwartz, Schraga, Ram, Oren, Eyras, Eduardo, Ast, Gil
More than 5% of alternatively spliced internal exons in the human genome are derived from Alu elements in a process termed exonization. Alus are comprised of two homologous arms separated by an...