Room with lines at back of church (4)
I believe the answer is:
cell
'room' is the definition.
(cell is a kind of room)
'lines at back of church' is the wordplay.
'lines' becomes 'll' (I've seen this in other clues).
'at back of' means one lot of letters go next to another.
'church' becomes 'ce' (abbreviation for Church of England).
'll' put after 'ce' is 'CELL'.
'with' is the link.
(Other definitions for cell that I've seen before include "Where a prisoner is kept" , "Spreadsheet unit" , "Small room for confining a prisoner" , "Chamber" , "Place for a prisoner" .)