Guohao Liang - Academia.edu (original) (raw)

Papers by Guohao Liang

Research paper thumbnail of Dynamics and functional roles of splicing factor autoregulation

Cell Reports, Jun 1, 2022

Research paper thumbnail of Cost-efficient boundary-free surface patterning achieves high effective-throughput of time-lapse microscopy experiments

bioRxiv (Cold Spring Harbor Laboratory), Apr 28, 2022

Time-lapse microscopy plays critical roles in the studies of cellular dynamics. However, setting ... more Time-lapse microscopy plays critical roles in the studies of cellular dynamics. However, setting up a time-lapse movie experiments is not only laborious but also with low output, mainly due to the cell-losing problem (i.e., cells moving out of limited field of view), especially in a long-time recording. To overcome this issue, we have designed a cost-efficient way that enables cell patterning on the imaging surfaces without any physical boundaries. Using mouse embryonic stem cells as an example system, we have demonstrated that our boundary-free patterned surface solves the cell-losing problem without disturbing their cellular phenotype. Statistically, the presented system increases the effective-throughput of timelapse microscopy experiments by an order of magnitude.

Research paper thumbnail of Molecular recording of sequential cellular events into DNA

bioRxiv (Cold Spring Harbor Laboratory), Nov 7, 2021

Research paper thumbnail of Cost-efficient boundary-free surface patterning achieves high effective-throughput of time-lapse microscopy experiments

Time-lapse microscopy plays critical roles in the studies of cellular dynamics. However, to set u... more Time-lapse microscopy plays critical roles in the studies of cellular dynamics. However, to set up a time-lapse movie experiments is not only laborious but also with low output, mainly due to the cell-losing problem (i.e., cell moving out of limited field of view), especially in a long time recording. To overcome these issues, we have designed a cost-efficient way that enables cell patterning on the imaging surfaces without any physical boundaries. Using mouse embryonic stem cells as an example system, we have demonstrated that our boundary-free patterned surface solves the cell-losing problem without disturbing their cellular phenotype. Statistically, the presented system increases the effective-throughput of time-lapse microscopy experiments by order of magnitude.

Research paper thumbnail of Dynamics and Functional Roles of Splicing Factor Autoregulation

SSRN Electronic Journal, 2021

Research paper thumbnail of Molecular recording of sequential cellular events into DNA

SummaryGenetically encoded DNA recorders noninvasively convert transient biological events into d... more SummaryGenetically encoded DNA recorders noninvasively convert transient biological events into durable mutations in a cell’s genome, allowing for the later reconstruction of cellular experiences using high-throughput DNA sequencing1. Existing DNA recorders have achieved high-information recording2–14, durable recording3,5–10,13,15–18, prolonged recording over multiple timescales3,5,8,10, multiplexed recording of several user-selected signals5–8,18, and temporally resolved signal recording5–8,18, but not all at the same time. We present a DNA recorder called peCHYRON (prime editing19 Cell HistorY Recording by Ordered iNsertion) that does. In peCHYRON, prime editor guide RNAs19 (pegRNAs) insert a variable triplet DNA sequence alongside a constant propagation sequence that deactivates the previous and activates the next step of insertion. This process results in the sequential accumulation of regularly spaced insertion mutations at a synthetic locus. Accumulated insertions are permane...

Research paper thumbnail of Lineage tracing and analog recording in mammalian cells by single-site DNA writing

Nature Chemical Biology, 2021

Studying cellular and developmental processes in complex multicellular organisms can require the ... more Studying cellular and developmental processes in complex multicellular organisms can require the non-destructive observation of thousands to billions of cells deep within an animal. DNA recorders address the staggering difficulty of this task by converting transient cellular experiences into mutations at defined genomic sites that can be sequenced later in high throughput. However, existing recorders act primarily by erasing DNA. This is problematic because, in the limit of progressive erasure, no record remains. We present a DNA recorder called CHYRON (Cell History Recording by Ordered Insertion) that acts primarily by writing new DNA through the repeated insertion of random nucleotides at a single locus in temporal order. To achieve in vivo DNA writing, CHYRON combines Cas9, a homing guide RNA and the template-independent DNA polymerase terminal deoxynucleotidyl transferase. We successfully applied CHYRON as an evolving lineage tracer and as a recorder of user-selected cellular stimuli. CHYRON (Cell History Recording by Ordered Insertion) enables DNA recording of cellular states and lineage reconstruction by Cas9-targeted insertions of random nucleotides by terminal deoxynucleotidyl transferase.

Research paper thumbnail of Ordered insertional mutagenesis at a single genomic site enables lineage tracing and analog recording in mammalian cells

The study of intricate cellular and developmental processes in the context of complex multicellul... more The study of intricate cellular and developmental processes in the context of complex multicellular organisms is difficult because it can require the non-destructive observation of thousands, millions, or even billions of cells deep within an animal. To address this difficulty, several groups have recently reported CRISPR-based DNA recorders that convert transient cellular experiences and processes into changes in the genome, which can then be read by sequencing in high-throughput. However, existing DNA recorders act primarily by erasing DNA: they use the random accumulation of CRISPR-induced deletions to record information. This is problematic because in the limit of progressive deletion, no record remains. Here, we present a new type of DNA recorder that acts primarily by writing new DNA. Our system, called CHYRON (Cell HistorY Recording by Ordered iNsertion), inserts random nucleotides at a single locus in temporal order in vivo and can be applied as an evolving lineage tracer as well as a recorder of user-selected cellular stimuli. As a lineage tracer, CHYRON allowed us to perfectly reconstruct the population lineage relationships among 16 groups of human cells descended from four starting groups that were subject to a series of splitting steps. In this experiment, CHYRON progressively wrote and retained base insertions in 20% percent of cells where the average amount written was 8.4 bp (~14.5 bits), reflecting high information content and density. As a stimulus recorder, we showed that when the CHYRON machinery was placed under the control of a stress-responsive promoter, the frequency and length of writing reflected the dose and duration of the stress. We believe CHYRON represents a conceptual advance in DNA recording technologies where writing rather than erasing becomes the primary mode of information accumulation. With further engineering of CHYRON's components to increase writing efficiency, CHYRON should lead to single-cell-resolution recording of lineage and other information through long periods of time in complex animals or tumors, advancing the pursuit of a full picture of mammalian development.

Research paper thumbnail of Dynamics and functional roles of splicing factor autoregulation

Cell Reports, Jun 1, 2022

Research paper thumbnail of Cost-efficient boundary-free surface patterning achieves high effective-throughput of time-lapse microscopy experiments

bioRxiv (Cold Spring Harbor Laboratory), Apr 28, 2022

Time-lapse microscopy plays critical roles in the studies of cellular dynamics. However, setting ... more Time-lapse microscopy plays critical roles in the studies of cellular dynamics. However, setting up a time-lapse movie experiments is not only laborious but also with low output, mainly due to the cell-losing problem (i.e., cells moving out of limited field of view), especially in a long-time recording. To overcome this issue, we have designed a cost-efficient way that enables cell patterning on the imaging surfaces without any physical boundaries. Using mouse embryonic stem cells as an example system, we have demonstrated that our boundary-free patterned surface solves the cell-losing problem without disturbing their cellular phenotype. Statistically, the presented system increases the effective-throughput of timelapse microscopy experiments by an order of magnitude.

Research paper thumbnail of Molecular recording of sequential cellular events into DNA

bioRxiv (Cold Spring Harbor Laboratory), Nov 7, 2021

Research paper thumbnail of Cost-efficient boundary-free surface patterning achieves high effective-throughput of time-lapse microscopy experiments

Time-lapse microscopy plays critical roles in the studies of cellular dynamics. However, to set u... more Time-lapse microscopy plays critical roles in the studies of cellular dynamics. However, to set up a time-lapse movie experiments is not only laborious but also with low output, mainly due to the cell-losing problem (i.e., cell moving out of limited field of view), especially in a long time recording. To overcome these issues, we have designed a cost-efficient way that enables cell patterning on the imaging surfaces without any physical boundaries. Using mouse embryonic stem cells as an example system, we have demonstrated that our boundary-free patterned surface solves the cell-losing problem without disturbing their cellular phenotype. Statistically, the presented system increases the effective-throughput of time-lapse microscopy experiments by order of magnitude.

Research paper thumbnail of Dynamics and Functional Roles of Splicing Factor Autoregulation

SSRN Electronic Journal, 2021

Research paper thumbnail of Molecular recording of sequential cellular events into DNA

SummaryGenetically encoded DNA recorders noninvasively convert transient biological events into d... more SummaryGenetically encoded DNA recorders noninvasively convert transient biological events into durable mutations in a cell’s genome, allowing for the later reconstruction of cellular experiences using high-throughput DNA sequencing1. Existing DNA recorders have achieved high-information recording2–14, durable recording3,5–10,13,15–18, prolonged recording over multiple timescales3,5,8,10, multiplexed recording of several user-selected signals5–8,18, and temporally resolved signal recording5–8,18, but not all at the same time. We present a DNA recorder called peCHYRON (prime editing19 Cell HistorY Recording by Ordered iNsertion) that does. In peCHYRON, prime editor guide RNAs19 (pegRNAs) insert a variable triplet DNA sequence alongside a constant propagation sequence that deactivates the previous and activates the next step of insertion. This process results in the sequential accumulation of regularly spaced insertion mutations at a synthetic locus. Accumulated insertions are permane...

Research paper thumbnail of Lineage tracing and analog recording in mammalian cells by single-site DNA writing

Nature Chemical Biology, 2021

Studying cellular and developmental processes in complex multicellular organisms can require the ... more Studying cellular and developmental processes in complex multicellular organisms can require the non-destructive observation of thousands to billions of cells deep within an animal. DNA recorders address the staggering difficulty of this task by converting transient cellular experiences into mutations at defined genomic sites that can be sequenced later in high throughput. However, existing recorders act primarily by erasing DNA. This is problematic because, in the limit of progressive erasure, no record remains. We present a DNA recorder called CHYRON (Cell History Recording by Ordered Insertion) that acts primarily by writing new DNA through the repeated insertion of random nucleotides at a single locus in temporal order. To achieve in vivo DNA writing, CHYRON combines Cas9, a homing guide RNA and the template-independent DNA polymerase terminal deoxynucleotidyl transferase. We successfully applied CHYRON as an evolving lineage tracer and as a recorder of user-selected cellular stimuli. CHYRON (Cell History Recording by Ordered Insertion) enables DNA recording of cellular states and lineage reconstruction by Cas9-targeted insertions of random nucleotides by terminal deoxynucleotidyl transferase.

Research paper thumbnail of Ordered insertional mutagenesis at a single genomic site enables lineage tracing and analog recording in mammalian cells

The study of intricate cellular and developmental processes in the context of complex multicellul... more The study of intricate cellular and developmental processes in the context of complex multicellular organisms is difficult because it can require the non-destructive observation of thousands, millions, or even billions of cells deep within an animal. To address this difficulty, several groups have recently reported CRISPR-based DNA recorders that convert transient cellular experiences and processes into changes in the genome, which can then be read by sequencing in high-throughput. However, existing DNA recorders act primarily by erasing DNA: they use the random accumulation of CRISPR-induced deletions to record information. This is problematic because in the limit of progressive deletion, no record remains. Here, we present a new type of DNA recorder that acts primarily by writing new DNA. Our system, called CHYRON (Cell HistorY Recording by Ordered iNsertion), inserts random nucleotides at a single locus in temporal order in vivo and can be applied as an evolving lineage tracer as well as a recorder of user-selected cellular stimuli. As a lineage tracer, CHYRON allowed us to perfectly reconstruct the population lineage relationships among 16 groups of human cells descended from four starting groups that were subject to a series of splitting steps. In this experiment, CHYRON progressively wrote and retained base insertions in 20% percent of cells where the average amount written was 8.4 bp (~14.5 bits), reflecting high information content and density. As a stimulus recorder, we showed that when the CHYRON machinery was placed under the control of a stress-responsive promoter, the frequency and length of writing reflected the dose and duration of the stress. We believe CHYRON represents a conceptual advance in DNA recording technologies where writing rather than erasing becomes the primary mode of information accumulation. With further engineering of CHYRON's components to increase writing efficiency, CHYRON should lead to single-cell-resolution recording of lineage and other information through long periods of time in complex animals or tumors, advancing the pursuit of a full picture of mammalian development.