PMC:3396637 / 24933-27560 JSONTXT

{"project":"2_test","denotations":[{"id":"22807622-16485020-29768513","span":{"begin":199,"end":201},"obj":"16485020"},{"id":"22807622-16449982-29768514","span":{"begin":443,"end":445},"obj":"16449982"},{"id":"22807622-17108319-29768515","span":{"begin":690,"end":692},"obj":"17108319"},{"id":"22807622-15642949-29768515","span":{"begin":690,"end":692},"obj":"15642949"},{"id":"22807622-17495008-29768515","span":{"begin":690,"end":692},"obj":"17495008"},{"id":"22807622-22112745-29768516","span":{"begin":849,"end":851},"obj":"22112745"},{"id":"22807622-21362639-29768517","span":{"begin":981,"end":983},"obj":"21362639"},{"id":"22807622-21362639-29768518","span":{"begin":1277,"end":1279},"obj":"21362639"},{"id":"22807622-17070957-29768519","span":{"begin":1280,"end":1282},"obj":"17070957"},{"id":"22807622-21920901-29768520","span":{"begin":1785,"end":1787},"obj":"21920901"},{"id":"22807622-20333231-29768521","span":{"begin":2308,"end":2310},"obj":"20333231"},{"id":"22807622-19924226-29768522","span":{"begin":2440,"end":2442},"obj":"19924226"}],"text":"It is vital for us to track down the precise timing of intron evolution and expansion, such as in a context of lineages, especially the number of introns per gene and the length variation of introns.32 Spliceosomal introns are the great majority in vertebrate genomes, albeit opposing hypotheses on the origin of introns, “intron-early” and “intron-late”, which argue that introns of this particular type is either more ancient or late comers.33 Further analyses on genomes based on taxonomy suggested that intron loss is the dominant phenomenon with position- and phase-specificity in modern mammals and perhaps large amount of intron gains occurred at the early stage of animal evolution,34–36 and recent study has found several cases of intron gains happened in the ancestor of placental mammals in transposon-derived domestication-related genes.37 Moreover, gene length is correlated with gene expression levels and breaths and is affected by RS insertions, such as L1 and MIR.38 Housekeeping genes are often highly-expressed and harbor smaller introns to reduce the processing cost of transcription, including time and energy. In contrast, tissue-specific genes are often lowly-expressed and harbor larger introns, requiring more effective and complex regulatory elements.38,39 Our data, based on a RS-centric stratification approach, showed that intron expansion is strongly influenced by not only RS types but also insertion timing, and the latter is manifested as species-specific propagation of distinct RSs. A comparative study concerning the five teleost genomes indicated that zebrafish experienced an ancient large-scale RS-induced intron expansion, and RS profiles of such expansion is rather distinct from the other four fishes with relatively lower insertion frequency.40 Based on these observations, we suspect that the RS content diversity that we observed among vertebrate introns or genes may not be straightforward to characterize with regard to precise timing as the samples we used are still in a limited scope. Insertions of both TEs and SSs should avoid making damages to key regulatory sequences, such as the splice sites, the branch point, the polypyrimidine tract, and other uncharacterized functional elements, and have potential co-evolving patterns with neighbouring sequences;41 and in particular, TEs (eg, SINEs) facilitate the splicing of larger introns via the formation of secondary structure in mammals.42 TE- and SS-derived RSs are forced to cluster or locate in intronic regions and seldom occur in core regulatory regions that are constantly under strong positive or negative selections."}

{"project":"MyTest","denotations":[{"id":"22807622-16485020-29768513","span":{"begin":199,"end":202},"obj":"16485020"},{"id":"22807622-16449982-29768514","span":{"begin":443,"end":446},"obj":"16449982"},{"id":"22807622-17108319-29768515","span":{"begin":690,"end":692},"obj":"17108319"},{"id":"22807622-15642949-29768515","span":{"begin":690,"end":692},"obj":"15642949"},{"id":"22807622-17495008-29768515","span":{"begin":690,"end":692},"obj":"17495008"},{"id":"22807622-22112745-29768516","span":{"begin":849,"end":852},"obj":"22112745"},{"id":"22807622-21362639-29768517","span":{"begin":981,"end":984},"obj":"21362639"},{"id":"22807622-21362639-29768518","span":{"begin":1277,"end":1279},"obj":"21362639"},{"id":"22807622-17070957-29768519","span":{"begin":1280,"end":1283},"obj":"17070957"},{"id":"22807622-21920901-29768520","span":{"begin":1785,"end":1788},"obj":"21920901"},{"id":"22807622-20333231-29768521","span":{"begin":2308,"end":2311},"obj":"20333231"},{"id":"22807622-19924226-29768522","span":{"begin":2440,"end":2443},"obj":"19924226"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"It is vital for us to track down the precise timing of intron evolution and expansion, such as in a context of lineages, especially the number of introns per gene and the length variation of introns.32 Spliceosomal introns are the great majority in vertebrate genomes, albeit opposing hypotheses on the origin of introns, “intron-early” and “intron-late”, which argue that introns of this particular type is either more ancient or late comers.33 Further analyses on genomes based on taxonomy suggested that intron loss is the dominant phenomenon with position- and phase-specificity in modern mammals and perhaps large amount of intron gains occurred at the early stage of animal evolution,34–36 and recent study has found several cases of intron gains happened in the ancestor of placental mammals in transposon-derived domestication-related genes.37 Moreover, gene length is correlated with gene expression levels and breaths and is affected by RS insertions, such as L1 and MIR.38 Housekeeping genes are often highly-expressed and harbor smaller introns to reduce the processing cost of transcription, including time and energy. In contrast, tissue-specific genes are often lowly-expressed and harbor larger introns, requiring more effective and complex regulatory elements.38,39 Our data, based on a RS-centric stratification approach, showed that intron expansion is strongly influenced by not only RS types but also insertion timing, and the latter is manifested as species-specific propagation of distinct RSs. A comparative study concerning the five teleost genomes indicated that zebrafish experienced an ancient large-scale RS-induced intron expansion, and RS profiles of such expansion is rather distinct from the other four fishes with relatively lower insertion frequency.40 Based on these observations, we suspect that the RS content diversity that we observed among vertebrate introns or genes may not be straightforward to characterize with regard to precise timing as the samples we used are still in a limited scope. Insertions of both TEs and SSs should avoid making damages to key regulatory sequences, such as the splice sites, the branch point, the polypyrimidine tract, and other uncharacterized functional elements, and have potential co-evolving patterns with neighbouring sequences;41 and in particular, TEs (eg, SINEs) facilitate the splicing of larger introns via the formation of secondary structure in mammals.42 TE- and SS-derived RSs are forced to cluster or locate in intronic regions and seldom occur in core regulatory regions that are constantly under strong positive or negative selections."}