Greatly affect writer in university department (5)
I believe the answer is:
upend
'greatly affect' is the definition.
(I've seen this before)
'writer in university department' is the wordplay.
'writer' becomes 'pen' (something which writes).
'in' indicates putting letters inside.
'university' becomes 'U' (abbreviation as in UMass).
'department' becomes 'd' (abbreviation eg in MOD Ministry of Defence).
'u'+'d'='ud'
'pen' put within 'ud' is 'UPEND'.
(Other definitions for upend that I've seen before include "Overturn" , "Knock over" , "Put into disarray" , "Tip on side" , "Turn upside down" .)