As part of my study I have been given this hypothesis:

HIF 1a and HIF 2a regulate different genes in multiple myeloma

What ways do we have to identify that these proteins are regulating different genes in multiple myeloma? I recall in lectures something being mentioned about using antibodies to isolate the regulatory elements, but can't find any specifics.

Any help is seriously appreciated!


Chromatin immunoprecipitation (ChIP) or ChIP-Seq are the first methods that pop into my mind. Essentially, DNA is cross-linked to bound proteins (transcription factors, histones, etc.) by various methods, then broken into pieces by either sonication or digestion with micrococcal nuclease. An immunoprecipitation is then performed by adding antibodies targeting your protein of interest (HIF-1α and HIF-2α in this case), allowing them to bind to their targets, enriching them using bead-conjugated Protein G (or Protein A), then reversing the cross-linking. The enriched DNA can then either be subjected to PCR for known genes (ChIP), or it can be sequenced and aligned with a reference genome to determine all bound sequences (ChIP-Seq).

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