tag:blogger.com,1999:blog-37148773.post6619566462372729578..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Debating alternative splicing (Part III)Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger10125tag:blogger.com,1999:blog-37148773.post-5891700493902334312017-06-29T13:12:49.995-04:002017-06-29T13:12:49.995-04:00I did a gross estimation based on the proportion o...I did a gross estimation based on the proportion of (mutually exclusively spliced) homologous exons of ancient origin that were detected with proteomics and the proportion of alternative splicing events detected with proteomics that correspond to ancient homologous exons. The estimate yielded between 1000 and 2000 alternative protein isoforms (i.e. not more than a few thousands). But this is a very gross estimation, not reliable!Federico Abascalhttps://www.blogger.com/profile/10122081847965890500noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36249638629453586562017-06-29T12:32:34.990-04:002017-06-29T12:32:34.990-04:00"It does appear to. Of course everyone here a..."It does appear to. Of course everyone here agrees that there are are some alternatively spliced proteins. The question is how many of them there are."<br /><br />I don't know how many there are but I am suggesting the embryo development is a place to look because cells are very active at this stage especially during cell division. A measurement of low expression levels "noise" is not relevant until you have measured all stages of the cell from initial growth stages to maturity.Bill Colehttps://www.blogger.com/profile/06642212549806694659noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35280843976000658412017-06-29T09:51:25.783-04:002017-06-29T09:51:25.783-04:00It's a simple aspect of logic that seems to es...It's a simple aspect of logic that seems to escape creationists when they try to discuss molecular biology. Demonstrating a single black swan does not mean that all swans are black, or even that black swans are common. Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72199362149250555202017-06-28T22:10:20.284-04:002017-06-28T22:10:20.284-04:00It does appear to. Of course everyone here agrees ...It does appear to. Of course everyone here agrees that there are are some alternatively spliced proteins. The question is how many of them there are.<br /><br />By the way, when citing a paper, you need the journal, volume, and page numbers.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10774243335107287882017-06-28T18:44:10.010-04:002017-06-28T18:44:10.010-04:00I think this paper shows AS proteins who's var...I think this paper shows AS proteins who's variant is used in development.<br /><br />Alternative Splicing Produces Nanog Protein Variants with Different Capacities for Self-renewal and Pluripotency in Embryonic Stem Cells*<br />Satyabrata Das‡, Snehalata Jena‡ and Dana N. Levasseur‡§,1 October 3, 2011<br />doi: 10.1074/jbc.M111.290189<br /><br />"In the present study, we analyzed the genomic neighborhood surrounding the Nanog gene locus for evidence of an expanded Nanog gene structure. We identified novel sequences from ES cells that extend the 5′ region of the known Nanog gene. Two additional new exons and 6 different subexons are differentially processed from alternative splicing. We find that this post-transcriptional regulation results in two new Nanog protein variants and we explore the function of these variants in ES cell self-renewal and pluripotency. Our studies reveal evidence that the first 25 amino acids of the NTD of Nanog are essential for both ES cell pluripotency and self-renewal. Finally, we show that a single serine residue in the NTD of Nanog (Ser-2) is essential for the maintenance of the undifferentiated ES cell state."Bill Colehttps://www.blogger.com/profile/06642212549806694659noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20423800850940904632017-06-28T15:09:41.587-04:002017-06-28T15:09:41.587-04:00So all you're saying is that different protein...So all you're saying is that different proteins are expressed at different times? But you're citing a paper that doesn't look at proteins.John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61868027480870924902017-06-28T12:45:13.619-04:002017-06-28T12:45:13.619-04:00John, "Now of course one could argue that the...John, "Now of course one could argue that the differently spliced RNAs are functional as RNAs, not as proteins. That would be a fallback position that would be even harder to falsify. Would you like to go there?"<br /><br />My point in posting this is that embryo development needs to be explored while trying to solve the junk or splicing puzzle. Other papers show unique AS protein variants expressed uniquely during development.Bill Colehttps://www.blogger.com/profile/06642212549806694659noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55373343844087028022017-06-27T11:06:29.861-04:002017-06-27T11:06:29.861-04:00A tiny problem with the conclusion is that we shou...A tiny problem with the conclusion is that we should expect accidental variants corresponding to genes whose products are involved in development, because those genes are expressed during development.<br /><br />The most convincing piece is that they compare the proportion of variants to that of whole RNA expression. But not convincing enough. Reading the paper would be better, but no time now.Gabohttps://www.blogger.com/profile/17552375541700079254noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-85874235455071057062017-06-26T20:09:00.011-04:002017-06-26T20:09:00.011-04:00Bill, I don't think you've been reading. D...Bill, I don't think you've been reading. Differential concentration of splice variants in different cells is not good evidence of function, because it can be a simple effect of differential levels of transcription of the genes and, conceivably, of regulatory sequences involved in true alternative splicing.<br /><br />I'm not sure I like the use of "expression" to mean "transcription", though perhaps that's standard. Don't know. But note that this study doesn't, at least from what you quote, assay actual proteins, just RNAs.<br /><br />Now of course one could argue that the differently spliced RNAs are functional as RNAs, not as proteins. That would be a fallback position that would be even harder to falsify. Would you like to go there?John Harshmanhttps://www.blogger.com/profile/04478895397136729867noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58229720108793076172017-06-26T13:40:48.586-04:002017-06-26T13:40:48.586-04:00Alternative splicing is frequent during early embr...Alternative splicing is frequent during early embryonic development in mouse<br />Timothée RevilEmail author, Daniel GaffneyEmail author, Christel Dias, Jacek Majewski and Loydie A Jerome-Majewska†<br />†Contributed equally<br />BMC Genomics201011:399<br />DOI: 10.1186/1471-2164-11-399<br /><br /><br />"Alternative splicing is known to increase the complexity of mammalian transcriptomes since nearly all mammalian genes express multiple pre-mRNA isoforms. However, our knowledge of the extent and function of alternative splicing in early embryonic development is based mainly on a few isolated examples. High throughput technologies now allow us to study genome-wide alternative splicing during mouse development.<br /><br />Results<br />A genome-wide analysis of alternative isoform expression in embryonic day 8.5, 9.5 and 11.5 mouse embryos and placenta was carried out using a splicing-sensitive exon microarray. We show that alternative splicing and isoform expression is frequent across developmental stages and tissues, and is comparable in frequency to the variation in whole-transcript expression. The genes that are alternatively spliced across our samples are disproportionately involved in important developmental processes. Finally, we find that a number of RNA binding proteins, including putative splicing factors, are differentially expressed and spliced across our samples suggesting that such proteins may be involved in regulating tissue and temporal variation in isoform expression. Using an example of a well characterized splicing factor, Fox2, we demonstrate that changes in Fox2 expression levels can be used to predict changes in inclusion levels of alternative exons that are flanked by Fox2 binding sites.<br /><br />Conclusions<br />We propose that alternative splicing is an important developmental regulatory mechanism. We further propose that gene expression should routinely be monitored at both the whole transcript and the isoform level in developmental studies"Bill Colehttps://www.blogger.com/profile/06642212549806694659noreply@blogger.com