Nucleotide diversity analysis highlights functionally important genomic regions

We analyzed functionality and relative distribution of genetic variants across the complete Oryza sativa genome, using the 40 million single nucleotide polymorphisms (SNPs) dataset from the 3,000 Rice Genomes Project (http://snp-seek.irri.org), the largest and highest density SNP collection for any higher plant. We have shown that the DNA-binding transcription factors (TFs) are the most conserved group of genes, whereas kinases and membrane-localized transporters are the most variable ones. TFs may be conserved because they belong to some of the most connected regulatory hubs that modulate transcription of vast downstream gene networks, whereas signaling kinases and transporters need to adapt rapidly to changing environmental conditions. In general, the observed profound patterns of nucleotide variability reveal functionally important genomic regions. As expected, nucleotide diversity is much higher in intergenic regions than within gene bodies (regions spanning gene models), and protein-coding sequences are more conserved than untranslated gene regions. We have observed a sharp decline in nucleotide diversity that begins at about 250 nucleotides upstream of the transcription start and reaches minimal diversity exactly at the transcription start. We found the transcription termination sites to have remarkably symmetrical patterns of SNP density, implying presence of functional sites near transcription termination. Also, nucleotide diversity was significantly lower near 3′ UTRs, the area rich with regulatory regions.

• Publication year

  2016

• Venue

  Scientific Reports

• Publication date

  2016-10-24

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/srep35730PMID 27774999PMCID 5075931
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• Transcription termination sites show remarkably symmetrical SNP density patterns, implying functional sites near termination.

  Confidence 0.90

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review
• Nucleotide diversity declines sharply beginning about 250 nucleotides upstream of the transcription start site, reaches minimal diversity at the transcription start site, and is significantly lower near 3' UTRs.

  Confidence 0.95

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review
• Nucleotide diversity is much higher in intergenic regions than within gene bodies.

  Confidence 0.96

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review
• DNA-binding transcription factors are the most conserved gene group, whereas kinases and membrane-localized transporters are the most variable ones.

  Confidence 0.98

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review

• 3' utrs

  transcript region

  The untranslated region at the 3' end of a transcript after the coding sequence.

  Aliases: 3-prime UTR, 3 prime UTR

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review
• dna-binding transcription factors

  gene family

  Transcription factor genes that encode proteins binding DNA to regulate downstream gene expression.

  Aliases: DNA-binding TFs

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review
• gene bodies

  genomic region

  Annotated genomic segments spanning rice gene models, including coding and untranslated regions.

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review
• intergenic regions

  genomic region

  Genomic sequence between annotated genes in the rice genome.

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review
• kinases

  gene family

  Genes encoding protein kinases that mediate signaling through phosphorylation.

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review
• membrane-localized transporters

  gene family

  Genes encoding transport proteins associated with cellular membranes.

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review
• transcription start site

  genomic site

  The genomic position where transcription begins for a gene.

  Aliases: TSS

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review
• transcription termination site

  genomic site

  The genomic position where transcription ends for a gene.

  Aliases: TTS

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewimjlk (vdp8mqzes2) reviewAnonymous (n259mg7uxy) reviewjihoonc (k5vuy3tzcm) review

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