is organized for hydrolysis in the targeting complex structures (fig. S11). The higher-order Get3
oligomers that form during oxidative stress (28)
are structurally and functionally distinct.
The structure of the Get3-TA substrate targeting
complex illustrates a common strategy for binding to hydrophobic cargo. Like Get3, the signal
sequence–binding subunit of SRP (SRP54) captures
substrates within a hydrophobic, methionine-rich
groove presented on a helical scaffold (26, 27, 29).
These scaffolds provide a large and intrinsically
dynamic binding site that is not appreciably ordered by substrate capture. This likely confers
the ability of Get3 and SRP54 to bind a variety of
hydrophobic sequences—an essential property of
both targeting systems. It will be of interest to
determine whether these principles are shared
by other TMD-binding factors, including SGTA
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We thank S. Shao for help with assay development; S. Koide
for the phage library; S. Sidhu for the sAB expression vector;
M. Kivlen for plasmids; F. Bezanilla, E. Perozo ,and J. Piccirilli
for instrumentation; members of the Keenan, Hegde, and
Kossiakoff labs for support; and the NE-CAT (24-ID-C) beamline
staff at Advanced Photon Source for technical assistance.
NE-CAT is supported by NIH grant P41 GM103403 and U.S.
Department of Energy contract DE-AC02-06CH11357. Additional
support was from the UK Medical Research Council
(MC_UP_A022_1007 to R.S.H.), the NIH (U01 GM094588 and
U54 GM087519 to A.A.K.; R01 GM086487 to R.J.K.), and the
Searle Funds at The Chicago Community Trust for the Chicago
Biomedical Consortium (to A.A.K. and R.J.K.). The Protein
Data Bank (PDB) accession codes are 4XTR (Pep12), 4XVU (Nyv1),
and 4XWO (Sec22).
Materials and Methods
Figs. S1 to S12
23 September 2014; accepted 30 January 2015
Evolutionary changes in promoter
and enhancer activity during
Steven K. Reilly,1* Jun Yin,1 Albert E. Ayoub,2,3 Deena Emera,1 Jing Leng,1,4†
Justin Cotney,1 Richard Sarro,1 Pasko Rakic,2,3 James P. Noonan1,2,4‡
Human higher cognition is attributed to the evolutionary expansion and elaboration of the
human cerebral cortex. However, the genetic mechanisms contributing to these developmental
changes are poorly understood. We used comparative epigenetic profiling of human, rhesus
macaque, and mouse corticogenesis to identify promoters and enhancers that have gained
activity in humans. These gains are significantly enriched in modules of coexpressed genes in
the cortex that function in neuronal proliferation, migration, and cortical-map organization.
Gain-enriched modules also showed correlated gene expression patterns and similar
transcription factor binding site enrichments in promoters and enhancers, suggesting that they
are connected by common regulatory mechanisms. Our results reveal coordinated patterns of
potential regulatory changes associated with conserved developmental processes during
corticogenesis, providing insight into human cortical evolution.
The massive expansion and functional elab- oration of the neocortex underlies the ad- vanced cognitive abilities of humans (1). Although the overall process of cortico- genesis is broadly conserved across mammals, humans exhibit differences that emerge
within the first 12 weeks of gestation. Among
these are an increased duration of neurogenesis, increases in the number and diversity of
progenitors, modification of neuronal migration, and introduction of new connections among
functional areas (2, 3). The genetic changes responsible for these evolutionary novelties are
Changes in gene regulation are hypothesized
to be a major source of evolutionary innovation
during development (1, 3, 4). Critical events in
corticogenesis, including the specification of cortical areas and differentiation of cortical layers,
rely on the precise control of gene expression (4).
The evolution of distinctly human cortical features required changes in many of these early
developmental processes, which may have been
driven by modifications in the gene regulatory
programs that govern them. However, identifying such regulatory changes and linking them to
relevant biological processes has proven to be
challenging. Previous efforts have relied on comparative genomics or on gene expression comparisons at later developmental and adult stages
(5–7). Further progress has been hindered by the
lack of genome-wide maps of regulatory function
Genome-wide profiling of posttranslational
histone modifications associated with regulatory functions has been used to compare regulatory element activities across species (8–12).
In this work, we profiled H3K27ac and H3K4me2
to map active promoters and enhancers during
human, rhesus macaque, and mouse corticogenesis, as well as to identify increases in their activity
in humans. We examined biological replicates of
whole human cortex at 7 postconception weeks
(p.c.w.) and 8.5 p.c.w. and primitive frontal and
occipital tissues from 12 p.c.w. (Fig. 1A). These
stages span the appearance of the transient embryonic zones that generate cortical neurons from
the deep to the superficial layers, when distinctly
human features of the cortex begin to emerge
1Department of Genetics, Yale School of Medicine, New Haven,
CT 06510, USA. 2Kavli Institute for Neuroscience, Yale School of
Medicine, New Haven, CT 06510, USA. 3Department of
Neurobiology, Yale School of Medicine, New Haven, CT 06510,
USA. 4Program in Computational Biology and Bioinformatics,
Yale University, New Haven, CT 06511, USA.
* These authors contributed equally to this work. †Present address:
Illumina, 499 Illinois Street, San Francisco, CA 94158, USA.
‡Corresponding author. E-mail: email@example.com