Little ROCK is a ROCK1 pseudogene expressed in human smooth muscle cells.
BACKGROUND
Sequencing of the human genome has identified numerous chromosome copy number additions and subtractions that include stable partial gene duplications and pseudogenes that when not properly annotated can interfere with genetic analysis. As an example of this problem, an evolutionary chromosome event in the primate ancestral chromosome 18 produced a partial duplication and inversion of rho-associated protein kinase 1 (ROCK1 -18q11.1, 33 exons) in the subtelomeric region of the p arm of chromosome 18 detectable only in humans. ROCK1 and the partial gene copy, which the gene databases also currently call ROCK1, include non-unique single nucleotide polymorphisms (SNPs).


RESULTS
Here, we characterize this partial gene copy of the human ROCK1, termed Little ROCK, located at 18p11.32. Little ROCK includes five exons, four of which share 99% identity with the terminal four exons of ROCK1 and one of which is unique to Little ROCK. In human while ROCK1 is expressed in many organs, Little ROCK expression is restricted to vascular smooth muscle cell (VSMC) lines and organs rich in smooth muscle. The single nucleotide polymorphism database (dbSNP) lists multiple variants contained in the region shared by ROCK1 and Little ROCK. Using gene and cDNA sequence analysis we clarified the origins of two non-synonymous SNPs annotated in the genome to actually be fixed differences between the ROCK1 and the Little ROCK gene sequences. Two additional coding SNPs were valid polymorphisms selectively within Little ROCK. Little ROCK-Green Fluorescent fusion proteins were highly unstable and degraded by the ubiquitin-proteasome system in vitro.


CONCLUSIONS
In this report we have characterized Little ROCK (ROCK1P1), a human expressed pseudogene derived from partial duplication of ROCK1. The large number of pseudogenes in the human genome creates significant genetic diversity. Our findings emphasize the importance of taking into consideration pseudogenes in all candidate gene and genome-wide association studies, as well as the need for complete annotation of human pseudogenome.
Montefusco
Maria Claudia
MC
Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Boston, MA 02111, USA.
Merlo
Kristen
K
Bryan
Crystal D
CD
Surks
Howard K
HK
Reis
Steven E
SE
Mendelsohn
Michael E
ME
Huggins
Gordon S
GS
D001483:Base Sequence; D002887:Chromosomes, Human, Pair 18; D020440:Gene Duplication; D006801:Humans; D008969:Molecular Sequence Data; D009130:Muscle, Smooth / Q000378:metabolism*; D009131:Muscle, Smooth, Vascular / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D011544:Pseudogenes; D016415:Sequence Alignment; D054460:rho-Associated Kinases / Q000235:genetics* / Q000378:metabolism
C515851:ROCK1 protein, human; D054460:rho-Associated Kinases
Nucleic Acids Res. 2009 Jan;37(Database issue):D738-43
18957444
Am J Med. 2007 Nov;120(11):960-7
17976423
Blood. 1999 May 15;93(10):3408-17
10233893
J Neurosci. 1999 Sep 15;19(18):7711-20
10479675
Nature. 2005 Sep 22;437(7058):551-5
16177791
Mol Cell Biol. 2003 Jul;23(14):5043-55
12832488
Nature. 1997 Oct 30;389(6654):990-4
9353125
Nat Genet. 2009 Jun;41(6):666-76
19430483
J Biol Chem. 2002 Apr 12;277(15):12680-8
11815607
Nature. 2008 May 22;453(7194):539-43
18404146
J Cardiovasc Pharmacol. 2002 Nov;40(5):751-61
12409984
Nature. 2006 Nov 23;444(7118):444-54
17122850
Am J Physiol. 1999 Jul;277(1):L106-12
10409236
J Biol Chem. 1996 Sep 20;271(38):23022-8
8798490
Nat Rev Mol Cell Biol. 2003 Jun;4(6):446-56
12778124
Biochem Biophys Res Commun. 2000 Aug 11;274(3):825-30
10924361
Science. 2002 Dec 6;298(5600):1912-34
12471243
J Hum Hypertens. 2008 Jul;22(7):512-5
18418400
Biochem J. 2002 Jul 1;365(Pt 1):79-87
11931630
J Biol Chem. 2002 Jan 4;277(1):725-34
11673466
Mol Biol Evol. 2008 Dec;25(12):2601-13
18791038
Hypertension. 2006 May;47(5):937-47
16585408
J Clin Invest. 2005 Apr;115(4):840-4
15841174
Science. 1999 Aug 6;285(5429):895-8
10436159
Hum Genet. 2004 Jul;115(2):116-22
15133654
J Biol Chem. 1999 Dec 24;274(52):37385-90
10601309
Curr Opin Genet Dev. 2004 Aug;14(4):328-35
15261647
Circulation. 2002 Apr 2;105(13):1545-7
11927519
Genomics. 2004 Mar;83(3):493-501
14962675
Nature. 2008 May 22;453(7194):534-8
18404147
BMC Bioinformatics. 2005 Dec 01;6 Suppl 4:S20
16351747
FEBS Lett. 2000 Jun 23;475(3):197-200
10869555
Nature. 2003 May 1;423(6935):91-6
12721631
Am J Physiol Cell Physiol. 2006 Mar;290(3):C661-8
16469861
EMBO J. 1996 Apr 15;15(8):1885-93
8617235
Cell. 1994 Sep 9;78(5):773-85
8087845
FEBS Lett. 1996 Aug 26;392(2):189-93
8772201