Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
Margulies
Elliott H
EH
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. elliott@nhgri.nih.gov
Cooper
Gregory M
GM
Asimenos
George
G
Thomas
Daryl J
DJ
Dewey
Colin N
CN
Siepel
Adam
A
Birney
Ewan
E
Keefe
Damian
D
Schwartz
Ariel S
AS
Hou
Minmei
M
Taylor
James
J
Nikolaev
Sergey
S
Montoya-Burgos
Juan I
JI
Löytynoja
Ari
A
Whelan
Simon
S
Pardi
Fabio
F
Massingham
Tim
T
Brown
James B
JB
Bickel
Peter
P
Holmes
Ian
I
Mullikin
James C
JC
Ureta-Vidal
Abel
A
Paten
Benedict
B
Stone
Eric A
EA
Rosenbloom
Kate R
KR
Kent
W James
WJ
Bouffard
Gerard G
GG
Guan
Xiaobin
X
Hansen
Nancy F
NF
Idol
Jacquelyn R
JR
Maduro
Valerie V B
VV
Maskeri
Baishali
B
McDowell
Jennifer C
JC
Park
Morgan
M
Thomas
Pamela J
PJ
Young
Alice C
AC
Blakesley
Robert W
RW
Muzny
Donna M
DM
Sodergren
Erica
E
Wheeler
David A
DA
Worley
Kim C
KC
Jiang
Huaiyang
H
Weinstock
George M
GM
Gibbs
Richard A
RA
Graves
Tina
T
Fulton
Robert
R
Mardis
Elaine R
ER
Wilson
Richard K
RK
Clamp
Michele
M
Cuff
James
J
Gnerre
Sante
S
Jaffe
David B
DB
Chang
Jean L
JL
Lindblad-Toh
Kerstin
K
Lander
Eric S
ES
Hinrichs
Angie
A
Trumbower
Heather
H
Clawson
Hiram
H
Zweig
Ann
A
Kuhn
Robert M
RM
Barber
Galt
G
Harte
Rachel
R
Karolchik
Donna
D
Field
Matthew A
MA
Moore
Richard A
RA
Matthewson
Carrie A
CA
Schein
Jacqueline E
JE
Marra
Marco A
MA
Antonarakis
Stylianos E
SE
Batzoglou
Serafim
S
Goldman
Nick
N
Hardison
Ross
R
Haussler
David
D
Miller
Webb
W
Pachter
Lior
L
Green
Eric D
ED
Sidow
Arend
A
D000818:Animals; D019143:Evolution, Molecular; D015894:Genome, Human; D016045:Human Genome Project; D006801:Humans; D008322:Mammals / Q000235:genetics*; D016366:Open Reading Frames; D010802:Phylogeny; D016415:Sequence Alignment