There is a code section that disallows, in general, deductions by an employee for any office rental of their dwelling unit.
Sec. 280(A)(c)(6) provides that:
Treatment of rental to employer. Paragraphs [c](1) and [c](3) shall not apply to any item which is attributable to the rental of the dwelling unit (or any portion thereof) by the taxpayer to his employer during any period in which the taxpayer uses the dwelling unit (or portion) in performing services as an employee of the employer
Congress added Sec. 280A(c)(6) expressly to overturn the Tax Court's decision in Feldman, 84 TC 1 (1985), aff'd, 791 F2d 781 (9th Cir. 1986). In enacting Sec. 280(A)(c)(6), Congress observed that the Tax Court's interpretation of Sec. 280A in Feldman could lead to the circumvention of statutory restrictions on the deduction of home-office expenses. In particular, Congress was concerned that (1) employers and employees could arrange sham transactions (by which a portion of salary was paid in the form of rent) and (2) the employer-employee transactions would not be negotiated at arm's length, but would provide added tax deductions for the employee at no additional cost to the employer. Accordingly, Congress provided that no home-office deductions were allowable (other than expenses such as home mortgage interest and real estate taxes that are deductible absent business use) if an employee rents a portion of his home to his employer
This section bars you from deducting what would otherwise be deductible trade or business expenses.
The bad news is that you may not deduct any expenses for rental payments (unless it is for a separate structure). The work around would be for the company to reimburse you; and you would not have to include the reimbursement in your income if done under an accountable plan.
See Rentals to an employer. for more discussion and IRS Provides Guidance on Employee Rental of Home to Employer for the IRS Letter Ruling (TAM)NNN-NN-NNNN/em>
I hope this helps even though it is very likely not the answer you wanted to hear.