Exhibit 4.1

 



ZQ|CERT#|COY|CLS|RGSTRY|ACCT#|TRANSTYPE|RUN#|TRANS#   . COMMON STOCK PAR VALUE $0.001 COMMON STOCK THIS CERTIFICATE IS TRANSFERABLE   IN CANTON, MA, JERSEY CITY, NJ AND COLLEGE STATION, TX Shares * * 000000 * *   * * * * * * * * * * * * * * * * * * * 000000 * * * * * * * * * * * * * * * *   * * * * * 000000 * * * * * * * * * * * * * * * * * * * * * 000000 * * * * * *   * * * * * * * * * * * * * * * 000000 * * * * * * * * * * * * * * Certificate   Number ZQ00000000 SYROS PHARMACEUTICALS, INC. INCORPORATED UNDER THE LAWS OF   THE STATE OF DELAWARE ** Mr. Alexander David Sample **** Mr. Alexander David   Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample ****   Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David THIS CERTIFIES THAT Sample **** Mr. Alexander David   Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample ****   Mr. Alexander David Sample **** Mr. Alexander Alexander David SamMple ***R*   Mr. A.lexaSnderADavidMSampPle ***L* MrE. Alexan&der DavMid SamRple **S**   Mr.. AleSxandeAr DaMvid SamPple *L*** MEr. Alex&ander David Sample ****   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr. Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   Sample **** Mr. AlexandeMr DaviRd Sam.ple S**** MAr. AleMxandePr DavLid   SEample *&*** Mr. AMlexanRder DaSvid S.ampSle ***A* Mr.MAlexanPder   DLavidESample **** Mr. Alexander **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander David   Sample **** Mr. Alexander David SEE REVERSE FOR CERTAIN DEFINITIONS David   Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample ****   Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Alexander David Sample   **** Mr. Alexander David Sample **** Mr. Alexander David Sample **** Mr.   Alexander David Sample **** Mr. Alexander David Sample **** Mr. Alexander   David Sample **** Mr. Alexander David Sample **** Mr. Sample **** Mr. Sample   is the owner of   **000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares***   *000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****   000000**Shar*es****0*000Z00**SEhareRs****00O0000**ShHares**U**0000N00**SDhares*R***000E000**DShares**T**000H000**SOhares*U***000S000**AShareNs****00D0000**Shares****0   00000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****00   0000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000   000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****0000   00**Shares****0Z0000E0**ShRares***O*000000*H*ShareUs****0N00000D**SharRes****0E0000D0**ShareAs****0N00000D**SharesZ****00E0000R**SharOes****0*000*00**Shares****00000   0**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000   **Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000*   *Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**   Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**Shares****000000**S   FULLY-PAID AND NON-ASSESSABLE SHARES OF COMMON STOCK OF Syros   Pharmaceuticals, Inc. (hereinafter called the “Company”), transferable on the   books of the Company in person or by duly authorized attorney, upon surrender   of this Certificate properly endorsed. This Certificate and the shares   represented hereby are issued and shall be held subject to all of the provisions   of the Certificate of Incorporation and the By-Laws of the Company, as such   documents may be amended and/or restated from time to time (copies of which   are on file with the Company and with the Transfer Agent), to all of which   each holder, by acceptance hereof, assents. This Certificate is not valid   unless countersigned and registered by the Transfer Agent and Registrar.   Witness the facsimile seal of the Company and the facsimile signatures of its   duly authorized officers. DATED DD-MMM-YYYY COUNTERSIGNED AND REGISTERED:   COMPUTERSHARE TRUST COMPANY, N.A. TRANSFER AGENT AND REGISTRAR Chief   Financial Officer November 9, 2011 DELAWARE By Chief Operating Officer   AUTHORIZED SIGNATURE N CUSIP Holder ID Insurance Value Number of Shares DTC   Certificate Numbers 1234567890/1234567890 1234567890/1234567890   1234567890/1234567890 1234567890/1234567890 1234567890/1234567890   1234567890/1234567890 Total Transaction XXXXXX XX X XXXXXXXXXX 1,000,000.00   123456 12345678 123456789012345 PO BOX 43004, Providence, RI 02940-3004   Num/No. Denom. Total 1 2 3 4 5 6 7 1 2 3 4 5 6 1 2 3 4 5 6 MR A SAMPLE   DESIGNATION (IF ANY) ADD 1 ADD 2 ADD 3 ADD 4 CUSIP87184Q 10 7 


    




 






 



. SYROS   PHARMACEUTICALS, INC. THE COMPANY WILL FURNISH WITHOUT CHARGE TO EACH   SHAREHOLDER WHO SO REQUESTS A COPY OF THE CERTIFICATE OF INCORPORATION OF THE   COMPANY, AS AMENDED. SUCH REQUEST MAY BE MADE TO THE OFFICE OF THE SECRETARY   OF THE COMPANY OR TO THE TRANSFER AGENT. THE BOARD OF DIRECTORS MAY REQUIRE   THE OWNER OF A LOST OR DESTROYED STOCK CERTIFICATE, OR HIS LEGAL   REPRESENTATIVES, TO GIVE THE COMPANY A BOND TO INDEMNIFY IT AND ITS TRANSFER   AGENTS AND REGISTRARS AGAINST ANY CLAIM THAT MAY BE MADE AGAINST THEM ON   ACCOUNT OF THE ALLEGED LOSS OR DESTRUCTION OF ANY SUCH CERTIFICATE. (Cust)   (Minor) (State) (Cust) and not as tenants in common (Minor) (State) PLEASE   INSERT SOCIAL SECURITY OR OTHER IDENTIFYING NUMBER OF ASSIGNEE For value   received, hereby sell, assign and transfer unto (PLEASE PRINT OR TYPEWRITE   NAME AND ADDRESS, INCLUDING POSTAL ZIP CODE, OF ASSIGNEE) Shares of the   common stock represented by the within Certificate, and do hereby irrevocably   constitute and appoint Attorney to transfer the said stock on the books of   the within-named Company with full power of substitution in the premises.   Dated: 20 Signature: Signature: Notice: The signature to this assignment must   correspond with the name as written upon the face of the certificate, in   every particular, without alteration or enlargement, or any change whatever.   The IRS requires that the named transfer agent (“we”) report the cost basis   of certain shares or units acquired after January 1, 2011. If your shares or   units are covered by the legislation, and you requested to sell or transfer   the shares or units using a specific cost basis calculation method, then we   have processed as you requested. If you did not specify a cost basis   calculation method, then we have defaulted to the first in, first out (FIFO)   method. Please consult your tax advisor if you need additional information   about cost basis. If you do not keep in contact with the issuer or do not   have any activity in your account for the time period specified by state law,   your property may become subject to state unclaimed property laws and   transferred to the appropriate state. Signature(s) Guaranteed: Medallion   Guarantee Stamp THE SIGNATURE(S) SHOULD BE GUARANTEED BY AN ELIGIBLE   GUARANTOR INSTITUTION (Banks, Stockbrokers, Savings and Loan Associations and   Credit Unions) WITH MEMBERSHIP IN AN APPROVED SIGNATURE GUARANTEE MEDALLION   PROGRAM, PURSUANT TO S.E.C. RULE 17Ad-15. The following abbreviations, when   used in the inscription on the face of this certificate, shall be construed   as though they were written out in full according to applicable laws or   regulations: TEN COM - as tenants in common UNIF GIFT MIN ACT -   ............................................Custodian   ................................................ TEN ENT - as tenants by the   entireties under Uniform Gifts to Minors   Act......................................................... JT TEN - as   joint tenants with right of survivorship UNIF TRF MIN ACT -   ............................................Custodian (until age   ................................) .............................under Uniform   Transfers to Minors Act ................... Additional abbreviations may also   be used though not in the above list.