Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

Park, Seung Gu; Hannenhalli, Sridhar; Choi, Sun Shim

doi:10.1186/1471-2164-15-526

Cited by 71 publications

(85 citation statements)

References 79 publications

(82 reference statements)

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“…One factor contributing to the ASM, particularly near the transcription start sites (Fig. 1D), may be the presence of transcriptional regulatory signals (29). …”

Section: Resultsmentioning

confidence: 99%

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

Onuchic

Lurie

Carrero

et al. 2018

Science

100

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To assess the impact of genetic variation in regulatory loci on human health, we construct a high-resolution map of allelic imbalances in DNA methylation, histone marks, and gene transcription in 71 epigenomes from 36 distinct cell and tissue types from 13 donors. Deep whole-genome bisulfite sequencing of 49 methylomes reveals sequence-dependent CpG methylation imbalances at thousands of heterozygous regulatory loci. Such loci are enriched for stochastic switching, defined as random transitions between fully methylated and unmethylated states of DNA. The methylation imbalances at thousands of loci are explainable by different relative frequencies of the methylated and unmethylated states for the two alleles. Further analyses provide a unifying model that links sequence-dependent allelic imbalances of the epigenome, stochastic switching at gene regulatory loci, and disease-associated

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“…One factor contributing to the ASM, particularly near the transcription start sites (Fig. 1D), may be the presence of transcriptional regulatory signals (29). …”

Section: Resultsmentioning

confidence: 99%

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

Onuchic

Lurie

Carrero

et al. 2018

Science

100

View full text Add to dashboard Cite

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“…This indicates a possibility of further variations in this gene in future. In concurrence with studies on eukaryotic genes 95 , the first exons/introns in most hair keratin genes show relatively higher conservation, although there are length differences. For example, the first exons of many orthologues in chimp are longer.…”

Section: Structural Organizationmentioning

confidence: 51%

Few Simple Sequence Repeats in Human Hair

2017

JCBSC

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Abstract:Keratin genes are subgroup of intermediate filament (IF) genes. Keratins expressed in hair are called "hair keratins". Comparison of keratin gene sequences and structural organization has been done earlier but no study has been undertaken that compares human hair keratin genes with orthologues in chimp, orangutan, macaque and platypus, with specific references to simple sequence repeats (SSRs) or microsatellites. This study seeks presence of SSRs in human hair keratin genes and compares their positions in orthologue genes. Although the structural organization of keratin genes is largely conserved, as reported in other studies; some human keratin genes show differences in the number of exons and the lengths of exons/introns, when compared with the orthologues. The present study shows few SSRs in human hair keratin genes, where only one repeat is found in exon of Type I keratin gene KRT31, while additional repeats are present in introns. Some repeats are longer in the human genes whereas some indicate reduction in length compared with orthologues. Many repeats are present in regions that are known for intronic variations. This study revisits the comparisons of structural organization of human hair keratin genes and compares them with the orthologues. The SSRs found here could be useful for monitoring variations in human hair keratin genes that may happen due to hypermutable nature of SSRs.

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“…As with other stimulating introns, the close proximity of the 5’UTR intron to the TSS may allow better access of the transcriptional initiation machinery to the intron [51–52], enhancing transcription initiation. In addition, the first introns relative to other introns of the same gene usually display significant enrichment of active chromatin marks, further indicating certain regions in first introns have potential regulatory roles [53]. …”

Section: Discussionmentioning

confidence: 99%

A Leader Intron of a Soybean Elongation Factor 1A (eEF1A) Gene Interacts with Proximal Promoter Elements to Regulate Gene Expression in Synthetic Promoters

2016

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Introns, especially the first intron in the 5’ untranslated region (5’UTR), can significantly impact gene expression via intron-mediated enhancement (IME). In this study, we demonstrate the leader intron of a soybean elongation factor 1A (eEF1A) gene (GmScreamM8) was essential for the high activity of the native promoter. Furthermore, the interaction of the GmScreamM8 leader intron with regulatory element sequences from several soybean eEF1A promoters was studied using synthetic promoters, which consisted of element tetramers upstream of a core promoter used to regulate a green fluorescent protein (gfp) reporter gene. Element tetramers, placed upstream of a GmScreamM8 core promoter, showed very high activity using both transient expression in lima bean cotyledons and stable expression in soybean hairy roots, only if the native leader intron was included, suggesting an interaction between intronic sequences and promoter elements. Partial deletions of the leader intron showed that a 222 bp intronic sequence significantly contributed to very high levels of GFP expression. Generation of synthetic intron variants with a monomeric or trimeric repeat of the 222 bp intronic sequence, yielded almost two-fold higher expression compared to the original intron, while partial deletion of the 222 bp intronic repeated sequence significantly decreased gene expression, indicating that this intronic sequence was essential for the intron-element interaction enhancement.

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Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

Cited by 71 publications

References 79 publications

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

Few Simple Sequence Repeats in Human Hair

A Leader Intron of a Soybean Elongation Factor 1A (eEF1A) Gene Interacts with Proximal Promoter Elements to Regulate Gene Expression in Synthetic Promoters

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