Lindblad-Toh_2011_Nature_478_476

Reference

Title : A high-resolution map of human evolutionary constraint using 29 mammals - Lindblad-Toh_2011_Nature_478_476
Author(s) : Lindblad-Toh K , Garber M , Zuk O , Lin MF , Parker BJ , Washietl S , Kheradpour P , Ernst J , Jordan G , Mauceli E , Ward LD , Lowe CB , Holloway AK , Clamp M , Gnerre S , Alfoldi J , Beal K , Chang J , Clawson H , Cuff J , Di Palma F , Fitzgerald S , Flicek P , Guttman M , Hubisz MJ , Jaffe DB , Jungreis I , Kent WJ , Kostka D , Lara M , Martins AL , Massingham T , Moltke I , Raney BJ , Rasmussen MD , Robinson J , Stark A , Vilella AJ , Wen J , Xie X , Zody MC , Baldwin J , Bloom T , Chin CW , Heiman D , Nicol R , Nusbaum C , Young S , Wilkinson J , Worley KC , Kovar CL , Muzny DM , Gibbs RA , Cree A , Dihn HH , Fowler G , Jhangiani S , Joshi V , Lee S , Lewis LR , Nazareth LV , Okwuonu G , Santibanez J , Warren WC , Mardis ER , Weinstock GM , Wilson RK , Delehaunty K , Dooling D , Fronik C , Fulton L , Fulton B , Graves T , Minx P , Sodergren E , Birney E , Margulies EH , Herrero J , Green ED , Haussler D , Siepel A , Goldman N , Pollard KS , Pedersen JS , Lander ES , Kellis M
Ref : Nature , 478 :476 , 2011
Abstract :

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering approximately 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for approximately 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.

PubMedSearch : Lindblad-Toh_2011_Nature_478_476
PubMedID: 21993624
Gene_locus related to this paper: cavpo-1plip , cavpo-2plrp , cavpo-h0v1b7 , cavpo-h0v5v8 , cavpo-h0vj36 , cavpo-lipli , rabit-1hlip , rabit-1plip , rabit-g1t6x7 , rabit-LIPH , myolu-l7n1c2 , myolu-g1pqd9 , cavpo-h0uyz6 , cavpo-h0vi56 , rabit-g1tbj4 , myolu-g1p5c0 , rabit-g1sds3 , rabit-g1sye0 , cavpo-h0v0r2 , cavpo-h0v7s5 , rabit-g1sp43 , myolu-g1p4p3 , cavpo-h0vw09 , rabit-g1ssu3 , myolu-g1pds0 , rabit-g1sic4 , cavpo-h0v2c4 , myolu-g1pg61 , myolu-g1pnb1 , myolu-g1pu06 , myolu-g1qa15 , myolu-g1qfu0 , rabit-g1sn99 , rabit-g1snq9 , rabit-g1sns7 , rabit-g1tuu8 , rabit-g1tzq7 , cavpo-h0v2i2 , cavpo-h0v2j0 , cavpo-h0vsf5 , cavpo-a0a286x8d3 , cavpo-a0a286xbr3 , cavpo-a0a286y0i8 , cavpo-a0a286y4p3 , myolu-g1q2n9 , cavpo-h0v1p4 , myolu-g1pan8 , myolu-g1paq0 , myolu-g1par4 , myolu-g1prn3 , myolu-g1q3i0 , myolu-g1q463 , myolu-g1pat6 , myolu-g1q859 , rabit-g1sul9 , rabit-g1sun0 , rabit-g1sup0 , myolu-l7n125 , myolu-g1pan2 , rabit-g1sxd0 , cavpo-h0v8j4 , rabit-d5fit0 , rabit-g1tkr5 , myolu-g1nty6 , myolu-g1p1p3 , cavpo-h0vdd5 , myolu-g1pdp2 , rabit-g1tmm5 , cavpo-h0vhq3 , myolu-g1nth4 , cavpo-h0vqx6 , rabit-g1tqr7 , myolu-g1p1e9 , cavpo-h0v8y6 , rabit-g1skt3 , myolu-g1nzg3 , cavpo-h0v5z0 , rabit-g1sgz5 , myolu-g1pkg5 , rabit-g1tmw5 , rabit-g1t134 , cavpo-a0a286x9v5 , myolu-g1qc57 , myolu-g1q061 , rabit-g1tnp4 , rabit-g1tyf7 , cavpo-h0w2w1 , rabit-g1ta36 , cavpo-h0w342 , myolu-g1q4e3 , rabit-g1sqa1 , cavpo-h0uxk7 , myolu-g1p353 , cavpo-h0vpm0 , rabit-a0a5f9cru6 , cavpo-a0a286xtc0 , myolu-g1nt22 , rabit-g1smi0 , cavpo-h0vin2 , myolu-g1q6b4 , rabit-g1tsd3 , cavpo-h0vg80 , cavpo-h0uy83 , rabit-g1ta86 , myolu-g1pa25 , cavpo-h0vls0 , cavpo-a0a286xw20 , rabit-g1sya5 , cavpo-a0a286xna1 , myolu-g1p5z6 , myolu-g1q764 , rabit-g1tbp6 , cavpo-h0vfq4

Related information

Gene_locus cavpo-1plip    cavpo-2plrp    cavpo-h0v1b7    cavpo-h0v5v8    cavpo-h0vj36    cavpo-lipli    rabit-1hlip    rabit-1plip    rabit-g1t6x7    rabit-LIPH    myolu-l7n1c2    myolu-g1pqd9    cavpo-h0uyz6    cavpo-h0vi56    rabit-g1tbj4    myolu-g1p5c0    rabit-g1sds3    rabit-g1sye0    cavpo-h0v0r2    cavpo-h0v7s5    rabit-g1sp43    myolu-g1p4p3    cavpo-h0vw09    rabit-g1ssu3    myolu-g1pds0    rabit-g1sic4    cavpo-h0v2c4    myolu-g1pg61    myolu-g1pnb1    myolu-g1pu06    myolu-g1qa15    myolu-g1qfu0    rabit-g1sn99    rabit-g1snq9    rabit-g1sns7    rabit-g1tuu8    rabit-g1tzq7    cavpo-h0v2i2    cavpo-h0v2j0    cavpo-h0vsf5    cavpo-a0a286x8d3    cavpo-a0a286xbr3    cavpo-a0a286y0i8    cavpo-a0a286y4p3    myolu-g1q2n9    cavpo-h0v1p4    myolu-g1pan8    myolu-g1paq0    myolu-g1par4    myolu-g1prn3    myolu-g1q3i0    myolu-g1q463    myolu-g1pat6    myolu-g1q859    rabit-g1sul9    rabit-g1sun0    rabit-g1sup0    myolu-l7n125    myolu-g1pan2    rabit-g1sxd0    cavpo-h0v8j4    rabit-d5fit0    rabit-g1tkr5    myolu-g1nty6    myolu-g1p1p3    cavpo-h0vdd5    myolu-g1pdp2    rabit-g1tmm5    cavpo-h0vhq3    myolu-g1nth4    cavpo-h0vqx6    rabit-g1tqr7    myolu-g1p1e9    cavpo-h0v8y6    rabit-g1skt3    myolu-g1nzg3    cavpo-h0v5z0    rabit-g1sgz5    myolu-g1pkg5    rabit-g1tmw5    rabit-g1t134    cavpo-a0a286x9v5    myolu-g1qc57    myolu-g1q061    rabit-g1tnp4    rabit-g1tyf7    cavpo-h0w2w1    rabit-g1ta36    cavpo-h0w342    myolu-g1q4e3    rabit-g1sqa1    cavpo-h0uxk7    myolu-g1p353    cavpo-h0vpm0    rabit-a0a5f9cru6    cavpo-a0a286xtc0    myolu-g1nt22    rabit-g1smi0    cavpo-h0vin2    myolu-g1q6b4    rabit-g1tsd3    cavpo-h0vg80    cavpo-h0uy83    rabit-g1ta86    myolu-g1pa25    cavpo-h0vls0    cavpo-a0a286xw20    rabit-g1sya5    cavpo-a0a286xna1    myolu-g1p5z6    myolu-g1q764    rabit-g1tbp6    cavpo-h0vfq4
Gene_locus_frgt rabit-g1u944    myolu-g1q7t6    cavpo-h0vlc7    myolu-g1p1q8    cavpo-h0uzy9    cavpo-a0a286xaf4    cavpo-a0a286xhi2    cavpo-a0a286xjr3    cavpo-a0a286xy73    myolu-g1q9n7    myolu-g1nzb2    cavpo-h0vpw2

Citations formats

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alfoldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M (2011)
A high-resolution map of human evolutionary constraint using 29 mammals
Nature 478 :476

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alfoldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M (2011)
Nature 478 :476