PMC:3396637 / 22179-24932 JSONTXT

{"project":"2_test","denotations":[{"id":"22807622-21342519-29768505","span":{"begin":589,"end":591},"obj":"21342519"},{"id":"22807622-17181857-29768506","span":{"begin":1067,"end":1069},"obj":"17181857"},{"id":"22807622-19154005-29768507","span":{"begin":1249,"end":1251},"obj":"19154005"},{"id":"22807622-14963101-29768508","span":{"begin":1532,"end":1534},"obj":"14963101"},{"id":"22807622-21233348-29768509","span":{"begin":2131,"end":2133},"obj":"21233348"},{"id":"22807622-17825083-29768510","span":{"begin":2134,"end":2136},"obj":"17825083"},{"id":"22807622-15961452-29768511","span":{"begin":2633,"end":2635},"obj":"15961452"},{"id":"22807622-15961478-29768512","span":{"begin":2636,"end":2638},"obj":"15961478"}],"text":"To understand the possible roles of RS families on gene and intron size expansions, we paid special attention on intron length and positioning within a transcript and on functional enrichment in the context of TE- vs. SS dichotomy among species and lineages. For instance, we found that TS-containing introns have a 5′-end bias in all vertebrates but zebrafish and that the RS-free (or the N class) introns have a 3′-end bias in all mammals but platypus. We have recently identified distinct functional profiles of genes at different evolving rates in primates, large mammals, and rodents,25 and in this study we used a similar classification scheme to investigate protein-coding genes with RS-driven intron expansion. For instance, DNA transposon-containing introns tend to be smaller in fraction, larger in size, and biased toward 5′-end enrichment in mouse and rat. We also pointed out that genes with TE-free introns are enriched in both development and transcription and genes with SS-containing introns are mostly immunity-related in primates and large mammals.13 We also extracted function categories in nervous systems for mammalian genes possessing SS-containing introns since microsatellite alternations may lead to neurological disorders.26 Previous studies proposed that microsatellites are unevenly positioned within different regions of protein-coding genes such as UTRs, exons, and introns, and they may play functional roles in regulating gene expression, splicing, mRNA export, and response to external environment.27 Most SSs that we studied are microsatellites, and we demonstrated that there are functional biases in SS-insertions, such as promoter-related regulatory genes as one of the major categories. In addition, SSs preferentially reside in heterochromatins at or near centromeres and telomeres, where transcriptional activities are rarely discovered. However, if detected, the genes are usually development-related and involved in epigenetic regulation and DNA methylation; the latter two lead to the alteration of chromatin state and may in turn regulate the expression of SS-containing noncoding RNAs.28,29 We concluded that combined or independent effects of species/lineage-specific TEs and SSs may play an important role in functional differentiations of intron-containing protein-coding genes. At present, the sequence-similarity-based RS library is mostly composed of known TEs, especially the collection of mammal-specific sequences. As increasing number of completed high-quality non-mammalian vertebrate genomes are being sequenced, together with the help of de novo identification technologies,30,31 there should be more novel species-specific TEs discovered, adding stronger validation power to the current study."}

{"project":"MyTest","denotations":[{"id":"22807622-21342519-29768505","span":{"begin":589,"end":592},"obj":"21342519"},{"id":"22807622-17181857-29768506","span":{"begin":1067,"end":1070},"obj":"17181857"},{"id":"22807622-19154005-29768507","span":{"begin":1249,"end":1252},"obj":"19154005"},{"id":"22807622-14963101-29768508","span":{"begin":1532,"end":1535},"obj":"14963101"},{"id":"22807622-21233348-29768509","span":{"begin":2131,"end":2133},"obj":"21233348"},{"id":"22807622-17825083-29768510","span":{"begin":2134,"end":2137},"obj":"17825083"},{"id":"22807622-15961452-29768511","span":{"begin":2633,"end":2635},"obj":"15961452"},{"id":"22807622-15961478-29768512","span":{"begin":2636,"end":2639},"obj":"15961478"}],"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":"To understand the possible roles of RS families on gene and intron size expansions, we paid special attention on intron length and positioning within a transcript and on functional enrichment in the context of TE- vs. SS dichotomy among species and lineages. For instance, we found that TS-containing introns have a 5′-end bias in all vertebrates but zebrafish and that the RS-free (or the N class) introns have a 3′-end bias in all mammals but platypus. We have recently identified distinct functional profiles of genes at different evolving rates in primates, large mammals, and rodents,25 and in this study we used a similar classification scheme to investigate protein-coding genes with RS-driven intron expansion. For instance, DNA transposon-containing introns tend to be smaller in fraction, larger in size, and biased toward 5′-end enrichment in mouse and rat. We also pointed out that genes with TE-free introns are enriched in both development and transcription and genes with SS-containing introns are mostly immunity-related in primates and large mammals.13 We also extracted function categories in nervous systems for mammalian genes possessing SS-containing introns since microsatellite alternations may lead to neurological disorders.26 Previous studies proposed that microsatellites are unevenly positioned within different regions of protein-coding genes such as UTRs, exons, and introns, and they may play functional roles in regulating gene expression, splicing, mRNA export, and response to external environment.27 Most SSs that we studied are microsatellites, and we demonstrated that there are functional biases in SS-insertions, such as promoter-related regulatory genes as one of the major categories. In addition, SSs preferentially reside in heterochromatins at or near centromeres and telomeres, where transcriptional activities are rarely discovered. However, if detected, the genes are usually development-related and involved in epigenetic regulation and DNA methylation; the latter two lead to the alteration of chromatin state and may in turn regulate the expression of SS-containing noncoding RNAs.28,29 We concluded that combined or independent effects of species/lineage-specific TEs and SSs may play an important role in functional differentiations of intron-containing protein-coding genes. At present, the sequence-similarity-based RS library is mostly composed of known TEs, especially the collection of mammal-specific sequences. As increasing number of completed high-quality non-mammalian vertebrate genomes are being sequenced, together with the help of de novo identification technologies,30,31 there should be more novel species-specific TEs discovered, adding stronger validation power to the current study."}