INSIGHTS | P E R S P E C T I V E S
GENOMICS
A master regulator of regeneration
Study of panther worm reveals a pioneer transcription factor that regulates regeneration
By Michael Alonge1 and
Michael C. Schatz1,2,3
H
ofstenia miamia, commonly called
the three-banded panther worm, is
a small flatworm that can be found
along the shores of the Caribbean
and other warm waters. It is known
for its impressive regenerative capa-
bilities, including the ability to regenerate
any body part within a few days of ampu-
tation. Previous reports identified some of
the molecular signals used to coordinate
regeneration (1), although the specific
genes and gene networks that regulate this
response were unknown. On page 1191 of
this issue, Gehrke et al. (2) developed an
impressive collection of genomic resources
for the species, including extensive DNA,
RNA, and chromatin accessibility data to
promote H. miamia as a new model sys-
tem for studying regeneration. Using these
data, they identify early growth response
(Egr), which encodes a candidate pioneer
transcription factor responsible for regu-
lating the molecular regenerating response
to wounding.
In eukaryotic cells, meters of genomic
DNA are tightly packed into protein-DNA
structures called chromatin. The extent of
DNA compaction or accessibility in chro-
matin facilitates cell type–specific gene
regulation by physically blocking or per-
mitting regulatory DNA binding proteins,
called transcription factors. Pioneer fac-
tors are a class of transcription factors
that are unique in their ability to indepen-
dently and initially bind their DNA target
sequences in “silent” compacted chroma-
tin. Through actively establishing DNA ac-
cessibility, recruiting other transcription
factors, and/or triggering local epigenetic
changes, pioneer factor binding can prime
genes for positive or negative regulation
(3). The first pioneer factors, forkhead box
protein A (FoxA) and GATA binding factor
4 (Gata4), were identified in studies of the
serum albumin gene Alb1 during mouse
hepatic differentiation (4). Although it was
previously known that these transcription
factors were recruited early for Alb1 tran-
1
Department of Computer Science, Johns Hopkins University,
Baltimore, MD, USA. 2Department of Biology, Johns Hopkins
University, Baltimore, MD, USA. 3Cold Spring Harbor Laboratory,
Cold Spring Harbor, NY, USA. Email: mschatz@cs.jhu.edu
1152 15 MARCH 2019 • VOL 363 ISSUE 6432
scription, it was shown that they could
independently bind and open compacted
chromatin at this locus in vitro (5). Several
additional pioneer factors have since been
identified by studying local chromatin ac-
cessibility and epigenetic dynamics, such
as histone modifications or DNA methyla-
tion, across key stages of cell development.
As more pioneer factors are discovered in
diverse systems, their characterization will
be crucial for understanding cell fate and
reprogramming, as they have the capa-
bility to initiate transcription of develop-
mentally silenced genes. For example, the
expression of certain pioneer factors has
been demonstrated to transdifferentiate fi-
broblasts into functional neurons (6), and
mutations of FoxA pioneer factors play an
important role in many cancers by altering
Genomics of regeneration
in Hofstenia miamia
Chromatin accessibility and gene expression data
collected post-amputation in H. miamia suggest
that the early growth response (Egr) transcription
factor (TF) is a pioneer factor that can bind to
closed chromatin, rearrange nucleosomes to allow
transcription, and thereby activate the expression
of genes needed for regeneration.
H. miamia
Amputate
Bind Pioneer factor
Egr
Nucleosome
Rearrange Recruitment of additional TFs
TF
Egr TF
Activate Wound response gene expression
TF
Egr TF
Regeneration
Published by AAAS
the epigenetic landscape needed for nor-
mal gene regulation (7).
Owing to the lack of a reference genome
for H. miamia, Gehrke et al. assembled
and annotated a reference genome to en-
able genome-wide research of whole-body
regeneration. Importantly, their approach
of combining high-throughput short-read
DNA sequencing with long-range chroma-
tin conformation mapping data using the
“Chicago” protocol (8) led to a chromo-
some-scale assembly with more than 90%
Downloaded from http://science.sciencemag.org/ on March 14, 2019
of the genes assembled along with their
flanking regulatory sequences. This level
of assembly quality was crucial to iden-
tifying transcription factor binding sites
and studying chromatin architecture. This
work also highlights the recent advances
in modern genome assembly technology,
which allow researchers to quickly produce
relatively inexpensive yet highly accurate
reference assemblies of uncharacterized
eukaryotic species (9).
The availability of a high-quality ref-
erence genome opened the door to ex-
periments to uncover the gene regulatory
networks involved in whole-body regen-
eration. Gehrke et al. collected chromatin
accessibility data (ATAC-seq, or assay for
transposase-accessible chromatin using
sequencing) (10) and gene expression data
(RNA-seq) from regenerating cells at mul-
tiple time points following amputation.
The results showed that Egr binding was
strongly associated with chromatin accessi-
bility during regeneration and that Egr was
also the most significantly up-regulated
gene early in wounded cells. Gehrke et al.
performed focused experiments to demon-
strate that Egr is a master regulator of a
gene regulatory network for whole-body
regeneration composed of at least 61 genes.
Further analysis showed that Egr has pio-
neer factor–like properties, especially the
rapid and complete transition from closed
to open chromatin states near Egr binding
sites during regeneration (11) (see the fig-
GRAPHIC: VERONICA FALCONIERI/SCIENCE
ure). Additionally, using ATAC-seq follow-
ing amputation in the planarian Schmidtea
mediterranea, a classic model system for
regeneration (12), they showed a simi-
lar chromatin response near Egr binding
sites. This finding suggests that the regen-
eration response to amputation and the
pioneer factor activity for Egr originated
in the common ancestor of H. miamia and
sciencemag.org SCIENCE
S. mediterranea some ~550 million years
ago and potentially will be present in other
bilaterians such as humans.
The study by Gehrke et al. presents sev-
eral avenues for future research. With H.
miamia, additional genomic studies are
needed to fully characterize the role of
Egr, such as examining chromatin bind-
ing across different cell types and phases
of regeneration. Additional biochemical
studies are also needed to determine the
specific mechanisms used by Egr to open
compacted chromatin and if this can be
done completely independently of any
other factors. Beyond H. miamia, this
experimental design can be followed in
other highly regenerative species, such as
Macrostomum lignano (13), that have or-
thologs of Egr to discover additional pio-
neer factors. Notably, orthologs of Egr are
known to play an important role in human
biology, including regulating a variety of
growth factors and tumor suppressors (14),
although there are no reports of it as a pio-
neer factor. This work is also a testament
to how modern genome sequencing and
functional genomics techniques present
“This work also highlights the
recent advances in moderm
genome assembly technology,
which allow researchers to
quickly produce...reference
assemblies...”
an opportunity for studying the molecular
biology of non–model species. Researchers
should be encouraged to explore broadly
across species and then attack the molecu-
lar mechanisms of their phenotypes using
all the experimental and computational
tools available. j
REFERENCES AND NOTES
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Reddien, Curr. Biol. 24, 1107 (2014).
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10.1126/science.aaw6258
SCIENCE sciencemag.org
ANCIENT DNA
Toward a clearer view into
human prehistory
An ancient DNA study highlights ancient population
patterns on the Iberian Peninsula
By Marc Vander Linden
N
early a decade has passed since the
first ancient genome of a human was
sequenced. Since then, rapidly increas-
ing numbers of such sequences have
revealed the complex role of admixture
in human societies and evolution. Ad-
mixture is especially evident in studies sam-
pling a given area over the long term, such as
those reported on page 1230 of this issue by
Olalde et al. (1) for the Iberian Peninsula. The
authors report changes in the direction of
gene flow between this region and neighbor-
ing ones through time and how these changes
relate to cultural history. Given that this and
other studies rely upon increasing datasets,
it is worth considering the balance between
knowledge gained and the practicalities and
ethics of destructive sampling.
Olalde et al. retraced events that shaped ge-
nomic variation in the Iberian Peninsula, in-
cluding a more complex population structure
of the last foragers than previously thought
and a possible total replacement of the lo-
cal male population by people with Steppe
ancestry during the Bronze Age, a pattern
comparable to that seen in Bronze Age Brit-
ain (2). They also document gene flow from
North Africa and the eastern Mediterranean
during Classical and Medieval periods, thus
echoing known historical processes. Other
identified events are perhaps less expected,
such as the presence of a Northern African
genomic component during the Chalcolithic
period, also identified by another team (1, 3).
The archaeological community has had
a mixed reaction to ancient DNA research.
Some are delighted by its revolutionary pros-
pects, because ancient DNA allows scientists
to identify processes directly that can other-
wise only be inferred, especially migrations
(4). Others have pointed out that biological
relatedness cannot be conflated with social
or cultural identities (5). Many archaeolo-
gists have questioned how much can be con-
cluded from limited numbers of ancient DNA
samples that are unevenly distributed across
time and space. Although geneticists stress
Department of Archaeology, University of Cambridge,
Cambridge, UK. Email: mv297@cam.ac.uk
Published by AAAS
that each sample provides a wealth of in-
formation about entire past lineages, recent
research on the European Bell Beaker phe-
nomenon demonstrates that more than 200
samples were required to start encapsulating,
in genomic terms, the complexity of the past
evident in archaeological data (2).
Yet, it is naïve to assume that more data
Downloaded from http://science.sciencemag.org/ on March 14, 2019
are always necessary. Ancient DNA research
involves the destructive sampling of a finite
resource, and it is therefore imperative to
evaluate the cost to irreplaceable resources
and the benefits of knowledge gained. Given
the self-acknowledged backlog of unpub-
lished samples already generated by certain
laboratories [(6), p. 16], cynics might be
tempted to call for a temporary embargo on
destructive analyses until we have learned
how or whether the samples in the queue have
changed the state of knowledge, whether new
questions have arisen, and what further data
might be helpful to advance the field.
As with any destructive technique and
given the cost of ancient DNA sequencing,
simultaneous sampling for additional infor-
mation should be undertaken systematically.
For example, many samples are radiocarbon
dated, but others are not, including those re-
ported by Olalde et al. Aside from mitigating
sample destruction, there are analytical ad-
vantages to iterative sampling. By combining
ancient DNA sequencing with stable isotope
and material culture studies, Knipper et al.
showed that most Early Bronze Age women
in the Lech valley (southern Germany) were
nonlocal, whereas the men were mostly lo-
cal, and that maternal lineages diversified
over time. These multiple patterns point to
women marrying outside their original so-
cial group, following strict rules adopted
over several generations (7). Amorim et al.
reported how two Early Medieval cemeteries
from Hungary and Northern Italy were orga-
nized around biological kinship, with genetic
differences echoed in diet, mobility patterns,
and the deposition of grave goods, suggesting
complex family and social systems (8).
It is worth remembering that different se-
quencing techniques—such as targeted sin-
gle-nucleotide polymorphism, whole-genome
capture, and shotgun sequencing—differ in
costs, scientific outputs, and how much en-
15 MARCH 2019 • VOL 363 ISSUE 6432 1153
A master regulator of regeneration
Michael Alonge and Michael C. Schatz

Science 363 (6432), 1152-1153.

DOI: 10.1126/science.aaw6258

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