Browsing by Author "Aryee, Martin"

Now showing items 1-17 of 17

    • Augmenting and Directing Robust, Long-Range CRISPR-Mediated Activation in Human Cells 

      Tak, Y. Esther; Horng, Joy E.; Perry, Nicholas T.; Schultz, Hayley; Iyer, Sowmya; Yao, Qiuming; Zou, Luli S.; Aryee, Martin; Pinello, Luca; Joung, Keith (Springer Science and Business Media LLC, 2021-08-05)
      Epigenetic editing is an emerging technology that uses artificial transcription factors (aTFs) to regulate expression of a target gene. Although human genes can be robustly upregulated by targeting aTFs to promoters, the ...

    • A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression 

      Guintivano, Jerry; Aryee, Martin J.; Kaminsky, Zachary A. (Landes Bioscience, 2013)
      Brain cellular heterogeneity may bias cell type specific DNA methylation patterns, influencing findings in psychiatric epigenetic studies. We performed fluorescence activated cell sorting (FACS) of neuronal nuclei and ...

    • Coverage recommendations for methylation analysis by whole genome bisulfite sequencing 

      Ziller, Michael J.; Hansen, Kasper D.; Meissner, Alexander; Aryee, Martin J. (2014)
      Whole genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling but the associated high sequencing costs continue to limit its widespread application. We utilized several high coverage reference data ...

    • CRISPR DNA Base Editors With Reduced RNA Off-Target and Self-Editing Activities 

      Grünewald, Julian; Zhou, Ronghao; Iyer, Sowmya; Lareau, Caleb; Garcia, Sara; Aryee, Martin; Joung, Keith (Springer Science and Business Media LLC, 2019-09)
      Cytosine or adenine base editors (CBEs or ABEs) can introduce specific DNA C-to-T or A-to-G alterations1,2,3,4. However, we recently demonstrated that they can also induce transcriptome-wide guide-RNA-independent editing ...

    • Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing 

      Tsai, Shengdar Q.; Wyvekens, Nicolas; Khayter, Cyd; Foden, Jennifer A.; Thapar, Vishal; Reyon, Deepak; Goodwin, Mathew J.; Aryee, Martin J.; Joung, J. Keith (2014)
      Monomeric CRISPR-Cas9 nucleases are widely used for targeted genome editing but can induce unwanted off-target mutations with high frequencies. Here we describe dimeric RNA-guided FokI Nucleases (RFNs) that recognize ...

    • Droplet-Based Combinatorial Indexing for Massive-Scale Single-Cell Chromatin Accessibility 

      Lareau, Caleb A.; Duarte, Fabiana; Chew, Jennifer G.; Kartha, Vinay; Burkett, Zach D.; Kohlway, Andrew S.; Pokholok, Dmitry; Aryee, Martin; Steemers, Frank J.; Lebofsky, Ronald; Buenrostro, Jason (Springer Science and Business Media LLC, 2019-06-24)
      Recent technical advancements have facilitated the mapping of epigenomes at single-cell resolution; however, the throughput and quality of these methods have limited their widespread adoption. Here we describe a high-quality ...

    • A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing 

      Grünewald, Julian; Zhou, Ronghao; Lareau, Caleb A.; Garcia, Sara P.; Iyer, Sowmya; Miller, Bret R.; Langner, Lukas M.; Hsu, Jonathan Y.; Aryee, Martin; Joung, J. Keith (Springer Science and Business Media LLC, 2020-06-01)

    • Engineered CRISPR-Cas9 nucleases with altered PAM specificities 

      Kleinstiver, Benjamin P.; Prew, Michelle S.; Tsai, Shengdar Q.; Topkar, Ved; Nguyen, Nhu T.; Zheng, Zongli; Gonzales, Andrew P.W.; Li, Zhuyun; Peterson, Randall T.; Yeh, Jing-Ruey Joanna; Aryee, Martin J.; Joung, J. Keith (2015)
      Although CRISPR-Cas9 nucleases are widely used for genome editing1, 2, the range of sequences that Cas9 can recognize is constrained by the need for a specific protospacer adjacent motif (PAM)3–6. As a result, it can often ...

    • Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia 

      Gaiti, Federico; Chaligne, Ronan; Brand, Ryan M.; Kothen-Hill, Steven; Schulman, Rafael C.; Grigorev, Kirill; Risso, Davide; Kim, Kyu-Tae; Pastore, Alessandro; Huang, Kevin Y.; Alonso, Alicia; Sheridan, Caroline; Omans, Nathaniel D.; Biederstedt, Evan; Clement, Kendell; Wang, Lili; Felsenfeld, Joshua A.; Bhavsar, Erica B.; Allan, John N.; Furman, Richard; Meissner, Alexander; Landau, Dan A.; Gu, Hongcang; Aryee, Martin; Gnirke, Andreas; Wu, Catherine (Springer Science and Business Media LLC, 2019-05-15)

    • Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells 

      Shareef, Sarah; Bevill, Samantha; Raman, Ayush; Aryee, Martin; van Galen, Peter; Hovestadt, Volker; Bernstein, Bradley (Springer Science and Business Media LLC, 2021-05-06)
      The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast numbers of ...

    • Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells 

      Kleinstiver, Benjamin P.; Tsai, Shengdar Q.; Prew, Michelle S.; Nguyen, Nhu T.; Welch, Moira M.; Lopez, Jose M.; McCaw, Zachary R.; Aryee, Martin J.; Joung, J. Keith (2016)
      The activities and genome-wide specificities of CRISPR-Cas Cpf1 nucleases1 are not well defined. We show that two Cpf1 nucleases from Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium ND2006 (AsCpf1 and LbCpf1, ...

    • GUIDE-Seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases 

      Tsai, Shengdar Q.; Zheng, Zongli; Nguyen, Nhu T.; Liebers, Matthew; Topkar, Ved V.; Thapar, Vishal; Wyvekens, Nicolas; Khayter, Cyd; Iafrate, A. John; Le, Long P.; Aryee, Martin J.; Joung, J. Keith (2014)
      CRISPR RNA-guided nucleases (RGNs) are widely used genome-editing reagents, but methods to delineate their genome-wide off-target cleavage activities have been lacking. Here we describe an approach for global detection of ...

    • High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis 

      Gomez-Cabrero, David; Almgren, Malin; Sjöholm, Louise K.; Hensvold, Aase H.; Ringh, Mikael V.; Tryggvadottir, Rakel; Kere, Juha; Scheynius, Annika; Acevedo, Nathalie; Reinius, Lovisa; Taub, Margaret A.; Montano, Carolina; Aryee, Martin J.; Feinberg, Jason I.; Feinberg, Andrew P.; Tegnér, Jesper; Klareskog, Lars; Catrina, Anca I.; Ekström, Tomas J. (BioMed Central, 2016)
      Background: Twin studies are powerful models to elucidate epigenetic modifications resulting from gene–environment interactions. Yet, commonly a limited number of clinical twin samples are available, leading to an underpowered ...

    • Identification of direction in gene networks from expression and methylation 

      Simcha, David M; Younes, Laurent; Aryee, Martin J; Geman, Donald (BioMed Central, 2013)
      Background: Reverse-engineering gene regulatory networks from expression data is difficult, especially without temporal measurements or interventional experiments. In particular, the causal direction of an edge is generally ...

    • Interrogation of human hematopoiesis at single-cell and single-variant resolution 

      Ulirsch, Jacob; Lareau, Caleb A.; Bao, Erik L.; Ludwig, Leif S.; Guo, Michael H.; Benner, Christian; Satpathy, Ansuman T.; Kartha, Vinay; Salem, Rany M.; Hirschhorn, Joel; Finucane, Hilary; Aryee, Martin; Buenrostro, Jason; Sankaran, Vijay (Springer Science and Business Media LLC, 2019-03-11)
      Widespread linkage disequilibrium and incomplete annotation of cell-to-cell state variation represent substantial challenges to elucidating mechanisms of trait-associated genetic variation. Here, we perform genetic ...

    • Smart-RRBS for single-cell methylome and transcriptome analysis 

      Gu, Hongcang; Raman, Ayush T.; Wang, Xiaoxue; Gaiti, Federico; Chaligne, Ronan; Mohammad, Arman W.; Arczewska, Aleksandra; Smith, Zachary D.; Landau, Dan A.; Aryee, Martin; Meissner, Alexander; Gnirke, Andreas; Raman, Ayush (Springer Science and Business Media LLC, 2021-07-09)

    • Transcriptome-Wide Off-Target RNA Editing Induced by CRISPR-Guided DNA Base Editors 

      Grünewald, Julian; Zhou, Ronghao; Garcia, Sara; Iyer, Sowmya; Lareau, Caleb; Aryee, Martin; Joung, Keith (Springer Science and Business Media LLC, 2019-04-17)
      CRISPR-Cas base editor technology enables targeted nucleotide alterations and is being rapidly deployed for research and potential therapeutic applications. The most widely used base editors induce DNA cytosine (C) deamination ...