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...
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...
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...
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...
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...