What are centromeres *really*?

Question

I've gathered that a centromere is a a region* where the DNA is bundles up even tighter (around protein different to Histone) and chromatids are 'joined'. However I'm still mostly in the dark regarding its physical structure and functioning.

At what point during DNA replication is the centromere created, and how is it created? How does it hold the chromatids together (what are its components)?

Specifically:

When it is being created (presumably during cell division) how is the positioning of the centromere controlled? Which flags are used by the enzymes in the process of making the centromere to tell them that it is the right spot: a section of DNA that 'says' "Right part of centromere, to be attached to left part"?

Secondly, after their condensation into chromosomes (e.g. during prophase), are the sister chromatids physically intertwined around each other** for the purpose of joining, or are they simply adjacent?

• Is there a 'loop' in the centromere slung over the adjacent chromatids to join them?
• If they are intertwined, how is this achieved during DNA replication, whilst the non-centromere parts of the sister chromatids are not intertwined?

How does the centromere break down to allow the chromatids to separate (e.g. during meoisis 2 and anaphase)?

On a somewhat unrelated note, what in the centromeres do the spindle fibres attach to, and how do the tips of the growing fibres notice it to head it its general direction?

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*(i.e. there is not a separate physical object dubbed 'the centromere', rather it is a collection of objects in a region)

**(That is, considering no other molecules than the chromatids, if you were to pinch the top and bottom ends of the left and right chromatids and pull them apart, could you separate them without them locking together (basically, do they intersect knot-theoretically)?)

Answer 1

There are many questions in your question. I'll try to answer each question pointwise.

Which flags are used by the enzymes in the process of making the centromere to tell them that it is the right spot

There are some centromere associated repeats in the DNA which mark the site for centromere assembly. There is no particular consensus sequence of this repeat. However, this study says that in certain cases stable chromosomes are formed in the absence of centromeric repeats.

are the sister chromatids physically intertwined around each other for the purpose of joining, or are they simply adjacent?

They are joined by proteins called cohesins. Cohesins looks like rings which form around the sister chromatids. During anaphase, the anaphase promoting complex (APC) activates an enzyme called separase, which in turn degrades cohesin.

what in the centromeres do the spindle fibres attach to, and how do the tips of the growing fibres notice it to head it its general direction?

Centromeres serve as a site for the assembly of kinetochore. Kinetochore is a multi-protein complex which forms contact with the spindle fibres (specifically, K-fibres. Refer this previous post). An essential component of kinetochore is the motor protein dynein which makes the kitetochore to crawl along the spindle fibres, towards the pole. The wikipedia article on kinetochore is quite descriptive and you can refer that for details.

Answer 2

Supplemental

When it is being created (presumably during cell division) how is the positioning of the centromere controlled?

The marks of "centromere" is added the G1 (CENPA) and S phase (all other members of the CCAN) of the cell cycle. As for how the positioning is controlled... the answer is unknown. But it does appear that when a centromere sequence is replicated, the proteins from the original centromere are divided between the two new copies of the centromere DNA sequence . So a DNA sequence is a centromere because it was a centromere. But how did it get to become a centromere in the first place is currently unknown.