Small deletions and duplications frequently occur in the pericentromeric region of chromosomes and many of these are associated with developmental abnormalities. These developmental syndromes are conventionally attributed to abnormal expression of protein-coding genes in the affected region. A hypothesis has recently been published concerning a Master Development Program based on noncoding transcripts from these regions (Parris GE. A hypothetical Master Development Program for multi-cellular organisms: Ontogeny and phylogeny. Biosci Hypotheses 2009;2:3-12.). This paper summarizes and expands the recently published hypothesis to include it application to developmental diseases. The author proposes that development of multi-cellular organisms is guided by a Master Development Program (MDP) located primarily in the pericentromeric heterochromatin. The MDP is believed to consist of a series of Generation-Specific Control Keys (GSCK) transcribed in sequence by Ikaros family transcription factors unless the GSCKs are suppressed by Sall1-family or Dnmt3b-family proteins. The MDP is proposed to increment with each cell cycle to the next GSCK resulting in development of the clone. A clone may be programmed to split into two clones as necessary through a two-cycle mitosis processes. The transcripts of the GSCKs presumably yield noncoding nuclear messenger RNAs (nmRNAs, 8-30 nt units) that act directly (e.g., as primers for RNA polymerase II) and indirectly to regulate HOX and other high-level transcription factor and developmental genes. As envisioned, the MDP would evolve by terminal addition of new GSCKs. The new GSCKs are produced by evolutionary consolidation of retro-transcripts into pyknons that collect and evolve at the end of the pericentromeric heterochromatin and are eventually incorporated into the MDP. The retro-transcripts are though to be produced during episodic retrovirus epidemics and account for punctuated equilibrium in species evolution.
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