Documente Academic
Documente Profesional
Documente Cultură
Samuel D. Perli,* Cheryl H. Cui,* Timothy K. Lu† magnitude of stgRNA activity. We showed
that computationally designed stgRNAs that
contain longer SDSs of length 30, 40, and 70
INTRODUCTION: Technologies that enable expression of stgRNA or Cas9 to biological nucleotides are able to accumulate muta-
the longitudinal tracking and recording of events of interest, one could then record the tions over longer durations of time. We dem-
molecular events into genomic DNA would be duration and/or intensity of such events in onstrated the analog nature of mSCRIBE by
useful for the detailed monitoring of cellular the form of accumulated mutations at the building a tumor necrosis factor–a (TNFa)–
C
Cas9 endonuclease activity toward the stgRNA’s
ellular behavior is dynamic, responsive, and Cellular Recorders Integrating Biological Events own DNA locus. After a double-strand DNA break
regulated by the integration of multiple (mSCRIBE), an analog memory system that en- is introduced in the SDS-encoding region and
molecular signals. Biological memory devi- ables the recording of cellular events within human repaired via the NHEJ repair pathway, the
ces that can record regulatory events would cell populations in the form of DNA mutations. resulting de novo mutated stgRNA locus should
be useful tools for investigating cellular mSCRIBE uses self-targeting guide RNAs (stgRNAs) continue to be transcribed as a mutated version
behavior over the course of a biological process that direct clustered regularly interspaced short of the original stgRNA and participate in another
and furthering our understanding of signaling dy- palindromic repeats–associated (CRISPR-Cas) ac- cycle of self-targeting mutagenesis. Multiple cycles
namics within cellular niches. Earlier genera- tivity to repeatedly mutagenize the DNA loci that of transcription followed by cleavage and error-
tions of biological memory devices relied on encodes the stgRNAs (7). During the course of review prone repair should occur, resulting in a contin-
digital switching between two or multiple quasi- of this work, systems with similar principles have uous, self-evolving Cas9-stgRNA system (Fig. 1A).
stable states based on active transcription and been proposed (8, 9). Although these systems use We hypothesized that by biologically linking the
translation of proteins (1–3). However, such sys- Cas9 to record information in DNA, they pursue activity of this system with regulatory events of
tems do not maintain their memory after the different applications, such as lineage tracing and interest, mSCRIBE can serve as a memory device
cells are disruptively harvested. Encoding tran- generating barcodes, to specifically tag multiple that records information in the form of DNA
sient cellular events into genomic DNA memory cells simultaneously. In contrast, we use our plat- mutations. We analyzed the sequence evolution
by using DNA recombinases enables the storage form to build memory devices capable of record- dynamics of stgRNAs containing 20-, 30-, and
of heritable biological information even after gene ing analog biological activity into mammalian cells 40-nucleotide SDSs and created a population-
regulation is disrupted (4, 5). The capacity and both in vitro and in vivo. based recording metric that conveys information
scalability of these memory devices are limited The Streptococcus pyogenes Cas9 system from about the duration and/or intensity of stgRNA
by the number of orthogonal regulatory elements the CRISPR-Cas family is an effective genome- activity.
(such as transcription factors and recombinases) engineering enzyme that catalyzes double-strand
that can reliably function together. Furthermore, breaks and generates mutations at DNA loci tar- Modifying a sgRNA-expressing
because they are restricted to a small number of geted by a small guide RNA (sgRNA) (11–13). Nor- DNA locus to include a PAM renders
digital states, they cannot record dynamic (ana- mal sgRNAs are composed of a 20-nucleotide (nt) it self-targeting
log) biological information, such as the magnitude specificity determining sequence (SDS), which We built multiple variants of a S. pyogenes sgRNA-
or duration of a cellular event. We recently dem- specifies the DNA sequence to be targeted and encoding DNA sequence with a 5′-GGG-3′ PAM
onstrated a population-based technology for ge- is immediately followed by an 80-nt scaffold located immediately downstream of the region
nomically encoded analog memory in Escherichia sequence, which associates the sgRNA with Cas9. encoding the 20-nt SDS and tested them for their
coli based on dynamic genome editing with ret- In addition to sequence homology with the ability to generate mutations at their own DNA
rons (6). Here, we present Mammalian Synthetic SDS, targeted DNA sequences must possess a locus. Human embryonic kidney (HEK) 293T–
protospacer-adjacent motif (PAM) (5′-NGG-3′) derived stable cell lines were built to express
1
Synthetic Biology Group, MIT Synthetic Biology Center, immediately adjacent to their 3′-end in order either the wild-type (WT) or each of the variant
Massachusetts Institute of Technology (MIT), Cambridge, MA
02139, USA. 2Research Laboratory of Electronics, MIT,
to be bound by the Cas9-sgRNA complex and sgRNAs shown in Fig. 1B (table S2, constructs
Cambridge, MA 02139, USA. 3Department of Electrical cleaved (14). When a double-strand break is 1 to 6, and Materials and methods). Plasmids en-
Engineering and Computer Science, MIT, Cambridge, MA introduced in the target DNA locus in the ge- coding either spCas9 (table S2, construct 7) or
02139, USA. 4Harvard-MIT Division of Health Sciences and nome, the break is repaired through either ho- monomeric yellow fluorescent protein (mYFP)
Technology, Cambridge, MA 02139, USA. 5Department of
Biological Engineering, MIT, Cambridge, MA 02139, USA.
mologous recombination (when a repair template (negative control) driven by the cytomegalovirus
*These authors contributed equally to this work. †Corresponding is provided) or error-prone nonhomologous end promoter (CMVp) were transfected into cells stab-
author. Email: timlu@mit.edu joining (NHEJ) DNA repair mechanisms, resulting ly expressing the depicted sgRNAs, and the sgRNA
loci were inspected for mutagenesis by using T7 A49 position) of the mod2 sgRNA variant and ing either Cas9 (table S2, construct 7) or mYFP
endonuclease I (T7 E1) assays 4 days after trans- observed robust mutagenesis at the modified driven by the CMV promoter. Genomic DNA was
fection. A straightforward variant sgRNA (mod1) sgRNA locus (Fig. 1B). Additional variant sgRNAs harvested from the cells at either 24 or 96 hours
with guanine substitutions at the U23 and U24 (mod3, mod4, and mod5) did not exhibit notice- after transfection and subjected to targeted poly-
positions did not exhibit any noticeable self- able self-targeting activity. Thus, the mod2 sgRNA merase chain reaction (PCR) amplification of the
targeting activity. We speculated that this was due was hereafter referred to and used as the stgRNA region encoding the stgRNAs. The PCR ampli-
to the presence of bulky guanine and adenine architecture. cons were either sequenced with MiSeq or cloned
residues facing each other in the stem region, We further characterized the mutagenesis pat- into E. coli for Sanger sequencing of individual
resulting in a destablized secondary structure. tern of the stgRNA by sequencing the DNA locus bacterial colonies (fig. S1). We found that cells
Thus, we encoded compensatory adenine-to- encoding it. A HEK 293T cell line expressing the transfected with the Cas9-expressing plasmid ex-
cytosine mutations within the stem region (A48, stgRNA was transfected with a plasmid express- hibited enhanced mutation frequencies in the
stgRNA loci, and those frequencies increased over using high-throughput sequencing, we inspected tions occurring at specific base pair positions. We
time, compared with cells transfected with the the mutated sequences generated by stgRNAs to calculated the percentage of those that contained
control mYFP-expressing plasmid (Fig. 1C). By determine the probability of insertions or dele- insertions or deletions at each base pair position
among all mutated sequences (Fig. 1D). We ob- would be shortened over time with repeated self- 20-nt SDSs might contain undesirable secondary
served higher rates of deletions as compared with targeting activity, ultimately rendering them inef- structures that result in loss of activity. Therefore,
insertions at each nucleotide position. Moreover, fective because of loss of the PAM or shortened we computationally designed stgRNAs that were
an elevated percentage of mutated sequences ex- SDS. To enable multiple cycles of self-targeting predicted to maintain the scaffold fold of sgRNAs
hibited deletions consecutively spanning nucleo- activity, we designed stgRNAs that are made up of without undesirable secondary structures, such
tide positions 13 to 17 for this specific stgRNA longer SDSs. We initially built a cell line express- as stem loops and pseudoknots within the SDS
(20nt-1). We later carried out a more thorough ing a stgRNA containing a randomly chosen 30-nt (Materials and methods). Stable cell lines encod-
analysis into the sequence evolution patterns of SDS (table S2, construct 8) but did not detect ing stgRNAs containing these computationally
stgRNAs. noticeable self-targeting activity when the cell line designed 30-, 40-, and 70-nt SDS (table S2, con-
Given our observation that deletions are pre- was transfected with a plasmid expressing Cas9. structs 9 to 11) were transfected with a plasmid
ferred over insertions, we suspected that stgRNAs We speculated that stgRNAs with longer than expressing Cas9 driven by the CMV promoter. T7
E1 assays of PCR-amplified genomic DNA dem- the cells were RFP+/GFP– or RFP–/GFP+, which infections resulted in ~60,000 successfully trans-
onstrated robust indel formation in the respec- were sorted into Gen1:RFP and Gen1:GFP popu- duced cells per well. For each stgRNA library,
tive stgRNA loci (Fig. 1E). lations, respectively (Fig. 2, C and D), and <0.3% eight cell samples were collected at time points
cells expressed both GFP and RFP. We cultured spaced ~48 hours apart until day 16 (Fig. 3B). All
stgRNA-encoding loci undergo multiple the Gen1:RFP and Gen1:GFP cells for 7 days, samples from eight different time points across
rounds of self-targeted mutagenesis resulting in Gen2R and Gen2G populations, re- the six different libraries were pooled together
We sought to demonstrate that the stgRNA- spectively. We then subjected the Gen2R and and sequenced via NextSeq (Illumina, San Diego,
encoding DNA locus in individual cells undergoes Gen2G populations to a second round of FACS. CA). After aligning the next-generation sequenc-
multiple rounds of self-targeted mutagenesis. To For cells with the stgRNA MBTR, a subpopulation ing reads to reference DNA sequences (Materials
track genomic mutations in single cells over time, of Gen2R cells toggled into being GFP-positive, and methods), 16-bp barcodes that were observed
we developed a mutation-based toggling reporter and similarly, a subpopulation of Gen2G cells across all the time points and the corresponding
(MBTR) system that generates distinct fluores- toggled into being RFP-positive. In contrast, cells upstream stgRNA sequences were identified (fig.
cence outputs based on indel sizes at the stgRNA- containing the non–self-targeting MBTR with S4A). For each of the stgRNA libraries, we found
encoding locus, which was inspired by a design a regular sgRNA maintained their original flu- >104 distinct 16-bp barcoded loci that were ob-
previously described for tracking DNA mutagen- orescence signals with no appreciable toggling served across all of the eight time points (fig.
esis outcomes (15). Downstream of a CMV pro- behavior observed with FACS analysis (Fig. 2, C S4B). The aligned stgRNA sequence variants were
moter and a canonical ATG start codon, we and D). The toggling of fluorescence output ob- represented with words composed of a four-letter
embedded the mutation detection region (MDR), served in UBCp-Cas9 cells transduced with the alphabet: At each base pair position, the stgRNA
which consists of a modified U6 promoter fol- stgRNA MBTR suggests that repeated mutagen- sequence was represented by either M, I, X, or D,
lowed by a stgRNA locus. The MDR was imme- esis, resulting in multiple frameshifts in the MDR, which stand for match, insertion, mismatch, or
diately followed by out-of-frame green (GFP) and occurred at the stgRNA locus within single cells. deletion, respectively (fig. S4, C and D, and Mate-
activity can result in specific and consistent mu- the 20nt-2 stgRNA, which saturated to ~100% animals. We adapted a well-established acute in-
tations. We also analyzed whether any of stgRNA by 10 days, we observed nonsaturating and flammation model involving repetitive intraperi-
variants might contain direct homology to human steadily increasing responses of the metric for toneal injection of lipopolysaccharide (LPS) in
genomic DNA. In fig. S5C, we present homology all stgRNAs over the entire 16-day experimen- mice (18). Immune cells that sense LPS release
analysis for the top 100 most frequent 30nt-1 tation period. On the basis of the rate of in- tumor necrosis factor a (TNFa), which is a potent
stgRNA variants. We found that only one of the crease of the percent mutated stgRNA (percent activator of the NF-kB pathway (19). The activa-
top 100 stgRNA variants (35th most frequent mutated stgRNA/time), stgRNAs encoding SDSs tion of the NF-kB pathway plays an important
variant) had perfect homology to genomic DNA of longer length should have a greater capacity role in coordinating responses to inflammation
(an intronic region), whereas most of the variants to maintain a steady increase in the recording (20). To sense the activation of the NF-kB path-
differed from the DNA by at least 2 bp in their metric for longer durations of time and thus way, we built a construct containing a NF-kB–
SDS. Hence, the DNA locus encoding each stgRNA should be more suitable for longer-term record- responsive promoter driving the expression of
variant was the most likely targeted sequence ing applications. the RFP mKate2 (table S2, construct 32) and
for the majority of the 30nt-1 stgRNA variants. We also conducted a time course experiment stably integrated it into HEK 293T cells. We
Given our observation that stgRNAs may have with regular sgRNAs targeting a DNA target observed a >50-fold increase in expression
characteristic sequence evolution patterns, we sequence so as to test their ability to serve as levels when these cells were exposed to TNFa
sought to infer the likelihood of a stgRNA locus memory registers (fig. S7). We used sgRNAs en- in vitro (fig. S9, A, B, and C). Next, we implanted
transitioning from any given sequence variant coding the same 20nt-1, 30nt-2, and 40nt-1 SDSs these cells into the flanks of athymic nude mice
to another variant owing to self-targeted muta- tested in Fig. 3F (table S2, constructs 25 to 27) (female nu/nu). After implanted cells reached a
genesis. We computed such likelihoods in the and found that unlike stgRNA loci, sgRNA target palpable volume, we performed intraperito-
form of a transition probability matrix, which loci quickly saturate the percent mutated sequence neal injection of LPS and observed robust
captures the probability of a sequence variant metric and exhibit restricted linear ranges. mKate2 expression (fig. S9D) and elevated TNFa
While generating data for Figs. 3F and 4E, each stgRNA cleavage event would result in a the DNA constructs used in this work are
we used PCR to amplify the stgRNA loci from defined mutation, rather than a range of muta- listed in Table S2 and their plasmid maps are
~30,000 cells and then calculated the percent tions. Among NHEJ repair mechanisms, recent available at www.rle.mit.edu/sbg/resources/
mutated stgRNA metric as a readout of genomic studies have identified a more error-prone repair stgRNA.
memory. However, access to tissues or biological pathway, termed alternative NHEJ (aNHEJ). To
samples could be limited in certain in vivo con- enhance the controllability of mutations that T7 Endonuclease I (T7 E1) assay and
texts. To investigate the sensitivity of our stgRNA- arise over time, small-molecule inhibitors of Sanger sequencing
encoded memory when the input biological aNHEJ components, including ligase III and Unless otherwise stated, cells used for T7 E1 as-
material is restricted, we sampled 1:100 dilutions PARP1, could be used (27, 28). The systematic says were grown in 24-well plates with 200,000
of the genomic DNA extracted from the TNFa- engineering and characterization of a larger cells per well. Genomic DNA from respective cell
treated inflammation-recording cells in Fig. 4E library of stgRNA sequences could also help to lines containing stgRNA or the sgRNA loci was
(which corresponds to ~300 cells) in triplicate identify memory registers that are more effi- extracted using the QuickExtract DNA extraction
followed by PCR amplification, sequencing, and cient than the ones tested here. solution (Epicentre). Genomic PCR was performed
calculation of the percent mutated stgRNA met- Moreover, because our system generates a using the KAPA-HiFi polymerase (KAPA biosys-
ric (fig. S10). We found very little deviation be- diverse set of stgRNA variants during the self- tems) using the primers:
tween the percent mutated sgRNA metric between mutagenesis process, it is difficult to predict JP1710 – GCAGAGATCCAGTTTGGGGGGTTC-
samples with ~300 cells versus those from ~30,000 and eliminate potential off-target effects that CGCGCAC and JP1711 – CCCGGTAGAATTCCTC-
cells. We hypothesize that this tight correspon- may arise even if the original stgRNA can be GACGTCTAATGCCAAC at 65°C for 30s and 25s/
dence is due to stgRNA evolution toward very designed for minimal off-target effects. As an cycle extension at 72°C for 29 cycles. Purified
few, dominating sequence variants, as was ob- alternative, we could fuse deactivated Cas9 PCR DNA was then used in the T7 Endonuclease
served in Fig. 3D and fig. S5B. (dCas9) to DNA cleavage domains such as single- I (T7 E1) assays. Specifically, 400 ng of PCR DNA
particles encoding the 30nt-1 stgRNA locus at (Gen2R:RFP, Gen2R:GFP, Gen2G:RFP and Gen2G: code in the immediately preceding time point
0.3 multiplicity of infection (MOI) to build GFP) was collected, PCR amplified and Sanger that had the minimum Hamming distance to the
inflammation-recording cells. Cell lines used to sequenced after bacterial cloning. See Fig. 2 and daughter sequence variant was assigned as the
test stgRNA activity were built by infecting HEK fig. S3. parent. Since the presence of an intact PAM is an
293T cells with lentiviral particles encoding con- absolute requirement for self-targeting capability
structs 1 through 6 (table S2) and selecting for Next-generation sequencing and alignment of stgRNAs, only the sequence variants that con-
successfully transduced cells with 300 mg/mL hy- Genomic DNA from respective cell lines was ex- tained an intact PAM were considered as poten-
gromycin. The cell line used to test inducible and tracted using QuickExtract (Epicenter) and ampli- tial parents. Many parent-daughter associations
multiplexed recording with doxycycline and IPTG fied using sequence specific primers containing were computed across all the barcodes and time
was built by infecting UBCp-Cas9 cells with Illumina adapter sequences P5 – AATGATACGG- points, resulting in an overall count for each spe-
lentiviral particles encoding a DNA construct CGACCACCGAGATCTACAC and P7 – CAAGCA- cific parent-daughter association. Finally, the
that expresses TetR and LacI constitutively (table GAAGACGGCATACGAGAT as primer overhangs. counts were normalized such that the total like-
S2, construct 28) followed by selection with Multiple PCR samples were multiplexed together lihood of transitioning from each parent to all
200 mg/mL zeocin for seven days. and sequenced on a single flow cell using 8 bp possible daughters would sum to one. The Ham-
multiplexing barcodes incorporated via reverse ming distance metric between two sequence var-
Design of longer stgRNAs primers. The barcode library stgRNA samples in iants in the MIXD format was calculated by
Longer stgRNAs were designed using the Vien- Fig. 3 were split into two groups and sequenced assigning a distance score for each base pair
naRNA package (36). Specifically, the RNAfold on the NextSeq platform (resulting in 154 and 178 position. Specifically, if only one of the sequence
software was used to generate SDSs that retain million reads) while the 20nt-1 stgRNA samples variants being compared had an insertion at a
the native structure of the guide RNA handle and in Fig. 1, the regular sgRNA samples in fig. S7, particular base pair position, then the score for
no secondary structures in the SDS encoding TNFa dosage and time course characterization that position is assigned 2. In all other cases, the
induction and PCR amplified genomic DNA was 9. R. Kalhor, P. Mali, G. M. Church, Rapidly evolving homing zinc-finger nuclease for the selective degradation of
subject to T7 E1 assays. See Fig. 4, A and B. CRISPR barcodes. bioRxiv 10.1101/055863 (2016); available at mutated human mitochondrial DNA. Nucleic Acids Res. 36,
http://biorxiv.org/content/early/2016/05/27/055863.abstract. 3926–3938 (2008). doi: 10.1093/nar/gkn313;
In vivo inflammation model 10. M. Jinek et al., RNA-programmed genome editing in human pmid: 18511461
cells. eLife 2, e00471–e00471 (2013). doi: 10.7554/ 30. A. C. Komor, Y. B. Kim, M. S. Packer, J. A. Zuris, D. R. Liu,
Four to six weeks old female athymic nude mice eLife.00471; pmid: 23386978 Programmable editing of a target base in genomic DNA
(strain nu/nu) were obtained from the rodent 11. L. Cong et al., Multiplex genome engineering using CRISPR/ without double-stranded DNA cleavage. Nature 533, 420–424
Cas systems. Science 339, 819–823 (2013). doi: 10.1126/ (2016). doi: 10.1038/nature17946; pmid: 27096365
breeding colony at Charles River Laboratory. science.1231143; pmid: 23287718 31. R. J. Klose, A. P. Bird, Genomic DNA methylation: The mark
They were specific pathogen free and main- 12. P. Mali et al., RNA-guided human genome engineering via Cas9. and its mediators. Trends Biochem. Sci. 31, 89–97 (2006).
tained on sterilized water and animal food. All Science 339, 823–826 (2013). doi: 10.1126/science.1232033; doi: 10.1016/j.tibs.2005.12.008; pmid: 16403636
animals were maintained and used in accord- pmid: 23287722 32. M. L. Maeder et al., Targeted DNA demethylation and activation
13. L. Nissim, S. D. Perli, A. Fridkin, P. Perez-Pinera, T. K. Lu, of endogenous genes using programmable TALE-TET1 fusion
ance with the guidelines of the Institutional Multiplexed and programmable regulation of gene networks proteins. Nat. Biotechnol. 31, 1137–1142 (2013). doi: 10.1038/
Animal Care and Use Committee. Sample sizes with an integrated RNA and CRISPR/Cas toolkit in human cells. nbt.2726; pmid: 24108092
of the study were estimated based according to Mol. Cell. 54, 698–710 (2014) doi: 10.1016/j. 33. J. H. Lee et al., Highly multiplexed subcellular RNA sequencing
in vivo pilot studies and in vitro studies on the molcel.2014.04.022; pmid: 24837679 in situ. Science 343, 1360–1363 (2014). doi: 10.1126/
14. C. Anders, O. Niewoehner, A. Duerst, M. Jinek, Structural basis science.1250212; pmid: 24578530
expected variance between animals and assay of PAM-dependent target DNA recognition by the Cas9 34. C. Lois, E. J. Hong, S. Pease, E. J. Brown, D. Baltimore,
sensitivity (32). Inflammation-recording cells were endonuclease. Nature 513, 569–573 (2014). doi: 10.1038/ Germline transmission and tissue-specific expression of
suspended in matrigel (Corning, NY) in 1:1 ratio nature13579; pmid: 25079318 transgenes delivered by lentiviral vectors. Science 295,
with cell growth media. 2 x106 cells were im- 15. M. T. Certo et al., Tracking genome engineering outcome at 868–872 (2002). doi: 10.1126/science.1067081;
individual DNA breakpoints. Nat. Methods 8, 671–676 (2011). pmid: 11786607
planted subcutaneously in the flank regions of doi: 10.1038/nmeth.1648; pmid: 21743461 35. R. Lorenz et al., ViennaRNA Package 2.0. Algorithms Mol. Biol.
mice. Animals were randomly assigned into 16. M. J. Herold, J. van den Brandt, J. Seibler, H. M. Reichardt, 6, 26 (2011). doi: 10.1186/1748-7188-6-26;
experimental groups after tumor implantation Inducible and reversible gene silencing by stable integration of pmid: 22115189
SUPPLEMENTARY http://science.sciencemag.org/content/suppl/2016/08/17/science.aag0511.DC1
MATERIALS
REFERENCES This article cites 36 articles, 14 of which you can access for free
http://science.sciencemag.org/content/353/6304/aag0511#BIBL
PERMISSIONS http://www.sciencemag.org/help/reprints-and-permissions
Science (print ISSN 0036-8075; online ISSN 1095-9203) is published by the American Association for the Advancement of
Science, 1200 New York Avenue NW, Washington, DC 20005. 2017 © The Authors, some rights reserved; exclusive
licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. The title
Science is a registered trademark of AAAS.