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The human genome has a lot of non-coding regions, which include regulatory elements, repetitive DNA, and introns. Suppose there are two adjacent genes on a chromosome, and their positions on the chromosome are, say,

For the first gene: 11,785,723 to 11,803,245 bp.

For the second gene: 11,806,096 to 11,806,143 bp. These values include their regulatory elements, promoter and introns as well.

So what sequence is present between bases 11,803,245 and 11,806,096? Are they satellite sequences? Is this non-coding, non-regulatory region 11,803,245 to 11,806,096 bp heterochromatin?

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  • $\begingroup$ possible duplicate of biology.stackexchange.com/q/43120/3340 $\endgroup$ – WYSIWYG Sep 6 '16 at 14:35
  • $\begingroup$ It is the same question, but with an additional query - are those regions heterochromatin? Are all regions of repititive DNA, like microsatellites, heterochromatin? Or is heterochromatin only the repetitive sequences of telomeres and centomeres? $\endgroup$ – Charles Sep 6 '16 at 16:33
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No. The intergenic regions are not necessarily heterochromatin. Chromatin conformations are usually very long range and are not usually confined to a single gene. The spread of chromatin state can be prevented by insulators/boundary elements, which again are not a part of the transcribed region. The intergenic regions can also harbour distal regulatory elements such as enhancers and silencers; they can have microsatellites, transposons etc too. To know what all are there in a specific region, you can look at the different tracks in the UCSC genome browser.

In short, there can be functional and/or non-functional DNA in-between the transcribed regions.

Repeat regions need not be heterochromatinized and conversely not all heterochromatic regions consist of repeats.

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  • $\begingroup$ Can it at least be said all repeat sequences are non-functional? $\endgroup$ – Charles Sep 17 '16 at 6:29
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    $\begingroup$ @Charles No you can't really say that. Telomeric repeats are important. So are centromeric repeats. There are non-tandem repeats like LINEs; they have been implicated in somatic heterogeneity in the brain. $\endgroup$ – WYSIWYG Sep 17 '16 at 7:30
  • $\begingroup$ Are all non-functional parts of the genome - such as non-functional satellite sequences - heterochromatinized? $\endgroup$ – Charles Sep 30 '16 at 14:12

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