Amyloid precursor protein (APP) cleavage by the β-secretase produces the C99 transmembrane (TM) protein, which contains three dimerization-inducing Gly-x-x-x-Gly motifs. We demonstrate that dimeric C99 TM orientations regulate the precise cleavage lines by γ-secretase. Of all possible dimeric orientations imposed by a coiled-coil to the C99 TM domain, the dimer containing the 33 Gly-x-x-x-Gly 37 motif in the interface promoted the Aβ 42 processing line and APP intracellular domain-dependent gene transcription, including the induction of BACE1 mRNA, enhancing amyloidogenic processing and signaling. Another orientation exhibiting the 25 Gly-x-x-x-Gly 29 motif in the interface favored processing to Aβ 43/40 . It induced significantly less gene transcription, while promoting formation of SDS-resistant "Aβ-like" oligomers, reminiscent of Aβ peptide oligomers. These required both Val24 of a pro-β motif and the 25 Gly-x-x-x-Gly 29 interface. Thus, crossing angles imposed by precise dimeric orientations control γ-secretase initial cleavage at Aβ 48 or Aβ 49, linking the former to enhanced signaling and Aβ 42 production., Competing Interests: S.N.C. is co-founder of Alsatech – Boston, MA and close family is owning stock in A.C. Immune Lausanne. The work of this manuscript is not linked to any current project at Alsatech or A.C. Immune, which are companies that work in the field of Alzheimer's disease., (© 2020 The Author(s).)