About neighborhood genes
1. Are neighborhood genes more likely to be co-expressed?
Yes. There are some papers provided evidences for this hypothesis. The following are some of them:
PMID: 11017073, PMID: 9702192, PMID: 14667251, PMID: 15659243, PMID: 15229555 (based on Escherichia coli), PMID: 12214599, PMID: 11181992, PMID: 12144710, PMID: 12384402
2. Why?
1) Chromatin-based mechanisms that regulate gene expression[PMID: 16160692]
2) Transcription factors may have effect at both direction [PMID: 9702192]:
Because many eukaryotic transcription factor–binding sites are either nearly palindromic or are active on both strands, it is possible that these gene pairs are regulated by the same upstream sequence. Consistent with this hypothesis, 51% of these gene pairs are transcribed divergently on opposite strands, many with fewer than 1500 bp bases separating their 5′ ends. 38% of adjacent genes were transcribed in the same orientation, while only 11% were transcribed convergently. Fewer than 25% of the adjacent gene pairs that were divergently transcribed displayed different patterns of mRNA fluctuation.
3) Transcription factors may have effect at long distance[PMID: 11017073].
4) Locus control regions [PMID: 15075390, PMID: 12384402, or Locus control regions[title] at PubMed]
5) Be imprinted [PMID: 15075390]
3. Who is altered first, Transcription factor or chromatin structure?
Although the nuclear localization of CFTR changed after altering its transcription levels, the transcriptional status of CFTR was not changed by driving this gene into a different nuclear environment. This implied that the transcriptional activity affected the nuclear positioning, and not vice versa. Together, the results show that small chromosomal subregions can display highly flexible nuclear organizations that are regulated at the level of individual genes in a transcription-dependent manner. [PMID: 15364959]
Yes. There are some papers provided evidences for this hypothesis. The following are some of them:
PMID: 11017073, PMID: 9702192, PMID: 14667251, PMID: 15659243, PMID: 15229555 (based on Escherichia coli), PMID: 12214599, PMID: 11181992, PMID: 12144710, PMID: 12384402
2. Why?
1) Chromatin-based mechanisms that regulate gene expression[PMID: 16160692]
2) Transcription factors may have effect at both direction [PMID: 9702192]:
Because many eukaryotic transcription factor–binding sites are either nearly palindromic or are active on both strands, it is possible that these gene pairs are regulated by the same upstream sequence. Consistent with this hypothesis, 51% of these gene pairs are transcribed divergently on opposite strands, many with fewer than 1500 bp bases separating their 5′ ends. 38% of adjacent genes were transcribed in the same orientation, while only 11% were transcribed convergently. Fewer than 25% of the adjacent gene pairs that were divergently transcribed displayed different patterns of mRNA fluctuation.
3) Transcription factors may have effect at long distance[PMID: 11017073].
4) Locus control regions [PMID: 15075390, PMID: 12384402, or Locus control regions[title] at PubMed]
5) Be imprinted [PMID: 15075390]
3. Who is altered first, Transcription factor or chromatin structure?
Although the nuclear localization of CFTR changed after altering its transcription levels, the transcriptional status of CFTR was not changed by driving this gene into a different nuclear environment. This implied that the transcriptional activity affected the nuclear positioning, and not vice versa. Together, the results show that small chromosomal subregions can display highly flexible nuclear organizations that are regulated at the level of individual genes in a transcription-dependent manner. [PMID: 15364959]
posted by Yiming Zhou at 7:58 AM
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