GostCertificateRequest request = new GostCertificateRequest(JCSP.PROVIDER_NAME);
request.setKeyUsage(KeyUsage.SIGN_DEFAULT);
request.setPublicKeyInfo(keyPair.getPublic());
request.setSubjectInfo(new X500Name("CN=Иванов Иван Иванович,OU=IT отдел,O=ООО Рога и Копыта,C=RU,L=Новосибирск,ST=Новосибирская область,E=inavov@mail.ru,INN=1234567890,СНИЛС=12345678901,ОГРН=1234567890123"));

GeneralNames generalNames = new GeneralNames();
Asn1UTF8String surnameAsn1String = new Asn1UTF8String("Сидоров Василий Петрович");
Asn1BerEncodeBuffer surnameAsn1Buffer = new Asn1BerEncodeBuffer();
surnameAsn1String.encode(surnameAsn1Buffer);
OtherName surname = new OtherName(new ObjectIdentifier("2.5.4.4"), surnameAsn1Buffer.getMsgCopy());
SubjectAlternativeNameExtension subjectAlternativeNameExtension = new SubjectAlternativeNameExtension(generalNames);
ByteArrayOutputStream subjectAlternativeNameExtensionStream = new ByteArrayOutputStream();
subjectAlternativeNameExtension.encode(subjectAlternativeNameExtensionStream);
request.addExtension(new Extension(
    new Asn1ObjectIdentifier(new int[]{2, 5, 29, 17}),
    new Asn1OctetString(subjectAlternativeNameExtensionStream.toByteArray())));

request.encodeAndSign(keyPair.getPrivate(), JCP.GOST_SIGN_2012_256_NAME);