Locus control regions -- Li et al. 100 (9): 3077 -- Blood

Locus control regions -- Li et al. 100 (9): 3077 -- Blood

gene length, intron length and gene epression

1. Selection for short introns in highly expressed genes (In eukaryotes, approximately 20 nucleotides can be transcribed per second at the expense of at least two ATP molecules per nucleotide).[PMID: 12134150]

mRNA and protein abundance in a cell

mRNA abundance range from 0.001 to 200 copies per cell:
1. Analysis of 60,633 transcripts in yeast revealed 4,665 genes, with expression levels ranging from 0.3 to over 200 transcripts per cell.[PMID: 9008165].
2. Steady-state transcript levels encoded by all 65 genes on the left arm of chromosome III and 185 transcription factor genes in yeast are quantitated using kinetically monitored, reverse transcriptase-initiated PCR (kRT-PCR). [PMID: 11882647].

Protein abundance range from 50 to 1,000,000 copies per cell.
1. The abundance of proteins ranges from fewer than 50 to more than 10(6) molecules per cell in yeast. Many of these molecules, including essential proteins and most transcription factors, are present at levels that are not readily detectable by other proteomic techniques nor predictable by mRNA levels or codon bias measurements.[PMID: 14562106]

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]

How long may distance be between transcription and translation start site?

Ensembl has annotated transcription and translation start site for 85% of all human genes. For large fraction of these genes (33%), this distance is more than 1,000bp. [PMID: |Prakash1 A.,Tompa M., Nature Biotechnology, 23, 1249 - 1256 (2005)]

This paper is definitely a very good introduction for 'Discovery of regulatory elements in vertebrates through comparative genomics'.