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Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation

Pinglay, Sudarshan; Bulajić, Milica; Rahe, Dylan P; Huang, Emily; Brosh, Ran; Mamrak, Nicholas E; King, Benjamin R; German, Sergei; Cadley, John A; Rieber, Lila; Easo, Nicole; Lionnet, Timothée; Mahony, Shaun; Maurano, Matthew T; Holt, Liam J; Mazzoni, Esteban O; Boeke, Jef D
Precise Hox gene expression is crucial for embryonic patterning. Intra-Hox transcription factor binding and distal enhancer elements have emerged as the major regulatory modules controlling Hox gene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce "synthetic regulatory reconstitution," a conceptual framework for studying gene regulation, and apply it to the HoxA cluster. We synthesized and delivered variant rat HoxA clusters (130 to 170 kilobases) to an ectopic location in the mouse genome. We found that a minimal HoxA cluster recapitulated correct patterns of chromatin remodeling and transcription in response to patterning signals, whereas the addition of distal enhancers was needed for full transcriptional output. Synthetic regulatory reconstitution could provide a generalizable strategy for deciphering the regulatory logic of gene expression in complex genomes.
PMID: 35771912
ISSN: 1095-9203
CID: 5268842

A conditional counterselectable Piga knockout in mouse embryonic stem cells for advanced genome writing applications

Zhang, Weimin; Brosh, Ran; McCulloch, Laura H; Zhu, Yinan; Ashe, Hannah; Ellis, Gwen; Camellato, Brendan R; Kim, Sang Yong; Maurano, Matthew T; Boeke, Jef D
Overwriting counterselectable markers is an efficient strategy for removing wild-type DNA or replacing it with payload DNA of interest. Currently, one bottleneck of efficient genome engineering in mammals is the shortage of counterselectable (negative selection) markers that work robustly without affecting organismal developmental potential. Here, we report a conditional Piga knockout strategy that enables efficient proaerolysin-based counterselection in mouse embryonic stem cells. The conditional Piga knockout cells show similar proaerolysin resistance as full (non-conditional) Piga deletion cells, which enables the use of a PIGA transgene as a counterselectable marker for genome engineering purposes. Native Piga function is readily restored in conditional Piga knockout cells to facilitate subsequent mouse development. We also demonstrate the generality of our strategy by engineering a conditional knockout of endogenous Hprt. Taken together, our work provides a new tool for advanced mouse genome writing and mouse model establishment.
PMCID:9184564
PMID: 35692632
ISSN: 2589-0042
CID: 5282452

Results of Two Cases of Pig-to-Human Kidney Xenotransplantation [Case Report]

Montgomery, Robert A; Stern, Jeffrey M; Lonze, Bonnie E; Tatapudi, Vasishta S; Mangiola, Massimo; Wu, Ming; Weldon, Elaina; Lawson, Nikki; Deterville, Cecilia; Dieter, Rebecca A; Sullivan, Brigitte; Boulton, Gabriella; Parent, Brendan; Piper, Greta; Sommer, Philip; Cawthon, Samantha; Duggan, Erin; Ayares, David; Dandro, Amy; Fazio-Kroll, Ana; Kokkinaki, Maria; Burdorf, Lars; Lorber, Marc; Boeke, Jef D; Pass, Harvey; Keating, Brendan; Griesemer, Adam; Ali, Nicole M; Mehta, Sapna A; Stewart, Zoe A
BACKGROUND:Xenografts from genetically modified pigs have become one of the most promising solutions to the dearth of human organs available for transplantation. The challenge in this model has been hyperacute rejection. To avoid this, pigs have been bred with a knockout of the alpha-1,3-galactosyltransferase gene and with subcapsular autologous thymic tissue. METHODS:We transplanted kidneys from these genetically modified pigs into two brain-dead human recipients whose circulatory and respiratory activity was maintained on ventilators for the duration of the study. We performed serial biopsies and monitored the urine output and kinetic estimated glomerular filtration rate (eGFR) to assess renal function and xenograft rejection. RESULTS:in Recipient 2. In both recipients, the creatinine level, which had been at a steady state, decreased after implantation of the xenograft, from 1.97 to 0.82 mg per deciliter in Recipient 1 and from 1.10 to 0.57 mg per deciliter in Recipient 2. The transplanted kidneys remained pink and well-perfused, continuing to make urine throughout the study. Biopsies that were performed at 6, 24, 48, and 54 hours revealed no signs of hyperacute or antibody-mediated rejection. Hourly urine output with the xenograft was more than double the output with the native kidneys. CONCLUSIONS:Genetically modified kidney xenografts from pigs remained viable and functioning in brain-dead human recipients for 54 hours, without signs of hyperacute rejection. (Funded by Lung Biotechnology.).
PMID: 35584156
ISSN: 1533-4406
CID: 5230812

Transcriptional neighborhoods regulate transcript isoform lengths and expression levels

Brooks, Aaron N; Hughes, Amanda L; Clauder-Münster, Sandra; Mitchell, Leslie A; Boeke, Jef D; Steinmetz, Lars M
Sequence features of genes and their flanking regulatory regions are determinants of RNA transcript isoform expression and have been used as context-independent plug-and-play modules in synthetic biology. However, genetic context-including the adjacent transcriptional environment-also influences transcript isoform expression levels and boundaries. We used synthetic yeast strains with stochastically repositioned genes to systematically disentangle the effects of sequence and context. Profiling 120 million full-length transcript molecules across 612 genomic perturbations, we observed sequence-independent alterations to gene expression levels and transcript isoform boundaries that were influenced by neighboring transcription. We identified features of transcriptional context that could predict these alterations and used these features to engineer a synthetic circuit where transcript length was controlled by neighboring transcription. This demonstrates how positional context can be leveraged in synthetic genome engineering.
PMID: 35239377
ISSN: 1095-9203
CID: 5174602

LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint

McKerrow, Wilson; Wang, Xuya; Mendez-Dorantes, Carlos; Mita, Paolo; Cao, Song; Grivainis, Mark; Ding, Li; LaCava, John; Burns, Kathleen H; Boeke, Jef D; Fenyö, David
Retrotransposons are genomic DNA sequences that copy themselves to new genomic locations via RNA intermediates; LINE-1 is the only active and autonomous retrotransposon in the human genome. The mobility of LINE-1 is largely repressed in somatic tissues but is derepressed in many cancers, where LINE-1 retrotransposition is correlated with p53 mutation and copy number alteration (CNA). In cell lines, inducing LINE-1 expression can cause double-strand breaks (DSBs) and replication stress. Reanalyzing multiomic data from breast, ovarian, endometrial, and colon cancers, we confirmed correlations between LINE-1 expression, p53 mutation status, and CNA. We observed a consistent correlation between LINE-1 expression and the abundance of DNA replication complex components, indicating that LINE-1 may also induce replication stress in human tumors. In endometrial cancer, high-quality phosphoproteomic data allowed us to identify the DSB-induced ATM-MRN-SMC S phase checkpoint pathway as the primary DNA damage response (DDR) pathway associated with LINE-1 expression. Induction of LINE-1 expression in an in vitro model led to increased phosphorylation of MRN complex member RAD50, suggesting that LINE-1 directly activates this pathway.
PMCID:8872788
PMID: 35169076
ISSN: 1091-6490
CID: 5167442

Sirt6 regulates lifespan in Drosophila melanogaster

Taylor, Jackson R; Wood, Jason G; Mizerak, Evan; Hinthorn, Samuel; Liu, Julianna; Finn, Matthew; Gordon, Sarah; Zingas, Louis; Chang, Chengyi; Klein, Mark A; Denu, John M; Gorbunova, Vera; Seluanov, Andrei; Boeke, Jef D; Sedivy, John M; Helfand, Stephen L
Sirt6 is a multifunctional enzyme that regulates diverse cellular processes such as metabolism, DNA repair, and aging. Overexpressing Sirt6 extends lifespan in mice, but the underlying cellular mechanisms are unclear. Drosophila melanogaster are an excellent model to study genetic regulation of lifespan; however, despite extensive study in mammals, very little is known about Sirt6 function in flies. Here, we characterized the Drosophila ortholog of Sirt6, dSirt6, and examined its role in regulating longevity; dSirt6 is a nuclear and chromatin-associated protein with NAD+-dependent histone deacetylase activity. dSirt6 overexpression (OE) in flies produces robust lifespan extension in both sexes, while reducing dSirt6 levels shortens lifespan. dSirt6 OE flies have normal food consumption and fertility but increased resistance to oxidative stress and reduced protein synthesis rates. Transcriptomic analyses reveal that dSirt6 OE reduces expression of genes involved in ribosome biogenesis, including many dMyc target genes. dSirt6 OE partially rescues many effects of dMyc OE, including increased nuclear size, up-regulation of ribosome biogenesis genes, and lifespan shortening. Last, dMyc haploinsufficiency does not convey additional lifespan extension to dSirt6 OE flies, suggesting dSirt6 OE is upstream of dMyc in regulating lifespan. Our results provide insight into the mechanisms by which Sirt6 OE leads to longer lifespan.
PMID: 35091469
ISSN: 1091-6490
CID: 5154992

Immune and Genome Engineering as the Future of Transplantable Tissue

Elisseeff, Jennifer; Badylak, Stephen F; Boeke, Jef D
PMID: 34936741
ISSN: 1533-4406
CID: 5103942

Unbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9

Briggs, Erica M; Mita, Paolo; Sun, Xiaoji; Ha, Susan; Vasilyev, Nikita; Leopold, Zev R; Nudler, Evgeny; Boeke, Jef D; Logan, Susan K
BACKGROUND:The autonomous retroelement Long Interspersed Element-1 (LINE-1) mobilizes though a copy and paste mechanism using an RNA intermediate (retrotransposition). Throughout human evolution, around 500,000 LINE-1 sequences have accumulated in the genome. Most of these sequences belong to ancestral LINE-1 subfamilies, including L1PA2-L1PA7, and can no longer mobilize. Only a small fraction of LINE-1 sequences, approximately 80 to 100 copies belonging to the L1Hs subfamily, are complete and still capable of retrotransposition. While silenced in most cells, many questions remain regarding LINE-1 dysregulation in cancer cells. RESULTS:Here, we optimized CRISPR Cas9 gRNAs to specifically target the regulatory sequence of the L1Hs 5'UTR promoter. We identified three gRNAs that were more specific to L1Hs, with limited binding to older LINE-1 sequences (L1PA2-L1PA7). We also adapted the C-BERST method (dCas9-APEX2 Biotinylation at genomic Elements by Restricted Spatial Tagging) to identify LINE-1 transcriptional regulators in cancer cells. Our LINE-1 C-BERST screen revealed both known and novel LINE-1 transcriptional regulators, including CTCF, YY1 and DUSP1. CONCLUSION/CONCLUSIONS:Our optimization and evaluation of gRNA specificity and application of the C-BERST method creates a tool for studying the regulatory mechanisms of LINE-1 in cancer. Further, we identified the dual specificity protein phosphatase, DUSP1, as a novel regulator of LINE-1 transcription.
PMCID:8381588
PMID: 34425899
ISSN: 1759-8753
CID: 5018102

The role of retrotransposable elements in ageing and age-associated diseases

Gorbunova, Vera; Seluanov, Andrei; Mita, Paolo; McKerrow, Wilson; Fenyö, David; Boeke, Jef D; Linker, Sara B; Gage, Fred H; Kreiling, Jill A; Petrashen, Anna P; Woodham, Trenton A; Taylor, Jackson R; Helfand, Stephen L; Sedivy, John M
The genomes of virtually all organisms contain repetitive sequences that are generated by the activity of transposable elements (transposons). Transposons are mobile genetic elements that can move from one genomic location to another; in this process, they amplify and increase their presence in genomes, sometimes to very high copy numbers. In this Review we discuss new evidence and ideas that the activity of retrotransposons, a major subgroup of transposons overall, influences and even promotes the process of ageing and age-related diseases in complex metazoan organisms, including humans. Retrotransposons have been coevolving with their host genomes since the dawn of life. This relationship has been largely competitive, and transposons have earned epithets such as 'junk DNA' and 'molecular parasites'. Much of our knowledge of the evolution of retrotransposons reflects their activity in the germline and is evident from genome sequence data. Recent research has provided a wealth of information on the activity of retrotransposons in somatic tissues during an individual lifespan, the molecular mechanisms that underlie this activity, and the manner in which these processes intersect with our own physiology, health and well-being.
PMID: 34349292
ISSN: 1476-4687
CID: 4990022

Transposon insertion profiling by sequencing (TIPseq) identifies novel LINE-1 insertions in human sperm [Meeting Abstract]

Berteli, T; Wang, F; McKerrow, W; Navarro, P; Fenyo, D; Boeke, J; Kohlrausch, F; Keefe, D
Study question: Do human sperm contain novel LINE-1 insertions and are they affected by paternal age? Summary answer: Human sperm contain novel LINE-1 insertions. Their location or number are not affected by paternal age. What is known already: LINE-1 comprises 17% of the human genome and some LINE-1s are the only autonomous retrotransposons in humans. Retrotransposons influence genomic instability and/or regulation if new retrotransposition events disrupt coding or regulatory regions in the host genome. Demethylation during germ cell development de-represses retrotransposons. Advanced paternal age is associated with genomic instability. Previously we showed that sperm LINE-1 copy number decreases with paternal age. We hypothesize that human sperm exhibit De novo retrotransposition and that sperm from older men contain increased novel LINE-1 insertions. Study design, size, duration: Cross-sectional case-control study with semen samples collected between February to July 2020. Participants/materials, setting, methods: Normospermic sperm samples (n=10; 5 <35 years old and 5 >=45 years old) obtained from consenting men undergoing IVF at NYU Fertility Center were submitted to a novel method, single cell Transposon Insertion Profiling by Sequencing (scTIPseq) to identify and map LINE-1 insertions in human sperm. TIPseqHunter, a custom bioinformatics pipeline, compared the architecture of sperm LINE-1 to known LINE-1 insertions from the European database of human specific LINE-1 (L1Hs) retrotransposon insertions in humans (euL1db). Main results and the role of chance: TIPseq identified 17 novel insertions in sperm, 8 from older (>= 45 years) and 9 in younger men (<35 years). New insertions were mainly intergenic or intronic, including AC007402 (2/10), TMEM163 (2/7), CTTNBP2NL (3/5), AC107023 (3/3), TMC2 (2/19), MacroD2 (2/6), RAB3C (3/4), LINC02664 (1/1), AC079052 (2/3) and AC017091 (4/4). One novel insertion (<35 years old) hits a known regulatory element. Only one sample (>= 45 years old) did not exhibit any new insertion. The location or number of novel insertions did not differ by paternal age. Limitations, reasons for caution: The small sample-size and use of normospermic specimens limit interpretation of paternal age effect on LINE-1. Besides, the novel insertions could be polymorphic sites that have low allele frequency and thus have not yet been described. Wider implications of the findings: This study for the first time reports novel LINE-1 insertions in human sperm, demonstrating that scTIPseq method is a feasible technique, and identifying new contributions to genetic diversity in the human germ line. Further studies are needed to evaluate the impact of these insertions on sperm function
EMBASE:637630355
ISSN: 1460-2350
CID: 5240962