Kaessmann Lab
@kaessmannlab.bsky.social
Our research group is interested in the molecular and cellular origins and evolution of vertebrate organs. Tweets by Henrik, usually in the name of our group.
home.kaessmannlab.org
home.kaessmannlab.org
Thanks so much Rob!
October 17, 2025 at 8:05 AM
Thanks so much Rob!
Our study presents the first comprehensive, cell type-resolved analysis of TE regulatory co-option across primate evolution, revealing how TEs contribute to species-specific regulatory divergence and phenotypic evolution.
October 16, 2025 at 10:01 PM
Our study presents the first comprehensive, cell type-resolved analysis of TE regulatory co-option across primate evolution, revealing how TEs contribute to species-specific regulatory divergence and phenotypic evolution.
Species-specific accessible HERVL copies contribute to divergent gene expression patterns – including elevated expression of neurodevelopmentally relevant genes such as C9orf72 and MGST2 in humans.
October 16, 2025 at 10:01 PM
Species-specific accessible HERVL copies contribute to divergent gene expression patterns – including elevated expression of neurodevelopmentally relevant genes such as C9orf72 and MGST2 in humans.
Comparative analysis across primates and mouse show that although the regulatory potential for HERVL co-option is conserved, different HERVL copies become accessible in each species, creating lineage-specific regulatory landscapes.
October 16, 2025 at 10:01 PM
Comparative analysis across primates and mouse show that although the regulatory potential for HERVL co-option is conserved, different HERVL copies become accessible in each species, creating lineage-specific regulatory landscapes.
Accessibility of individual HERVL copies is governed by two complementary factors: the preservation of transcription factor binding motifs and positioning within active chromatin neighborhoods.
October 16, 2025 at 10:01 PM
Accessibility of individual HERVL copies is governed by two complementary factors: the preservation of transcription factor binding motifs and positioning within active chromatin neighborhoods.
Luciferase reporter assays using consensus sequences of HERVL and related TEs demonstrated that HERVL specifically exhibits enhancer activity in primary cultures of mouse granule cells.
October 16, 2025 at 10:01 PM
Luciferase reporter assays using consensus sequences of HERVL and related TEs demonstrated that HERVL specifically exhibits enhancer activity in primary cultures of mouse granule cells.
We discovered that HERVLs – primate-specific retrotransposons – are preferentially co-opted as regulatory elements in cerebellar granule cells and other rhombic lip-derived neuroblasts in the pons and medulla, facilitated by the presence of sequences that resemble ATOH1 and NFI binding motifs.
October 16, 2025 at 10:01 PM
We discovered that HERVLs – primate-specific retrotransposons – are preferentially co-opted as regulatory elements in cerebellar granule cells and other rhombic lip-derived neuroblasts in the pons and medulla, facilitated by the presence of sequences that resemble ATOH1 and NFI binding motifs.
Our deep learning-based pipeline systematically screened TE fragments for regulatory potential, and identified 17 TE subfamilies whose ancestral sequences contain cis-regulatory motifs that resemble those found in elements accessible in cerebellar cells.
October 16, 2025 at 10:01 PM
Our deep learning-based pipeline systematically screened TE fragments for regulatory potential, and identified 17 TE subfamilies whose ancestral sequences contain cis-regulatory motifs that resemble those found in elements accessible in cerebellar cells.
We found that TEs are significantly enriched in species- and cell type-specific elements – particularly in later-developing, less constrained cell types. This pattern is further supported by datasets spanning multiple human organs across development.
October 16, 2025 at 10:01 PM
We found that TEs are significantly enriched in species- and cell type-specific elements – particularly in later-developing, less constrained cell types. This pattern is further supported by datasets spanning multiple human organs across development.
By combining comprehensive single-cell multiomics atlases of mammalian cerebellum development with deep learning-based modeling of enhancer grammar, we systematically investigated how TEs contribute to gene regulatory programs across developing cerebellar cell types.
October 16, 2025 at 10:01 PM
By combining comprehensive single-cell multiomics atlases of mammalian cerebellum development with deep learning-based modeling of enhancer grammar, we systematically investigated how TEs contribute to gene regulatory programs across developing cerebellar cell types.
However, their contribution to mammalian organ development at the cellular level has remained largely unexplored, owing to the lack of cell type-resolved datasets and suitable analytical frameworks.
October 16, 2025 at 10:01 PM
However, their contribution to mammalian organ development at the cellular level has remained largely unexplored, owing to the lack of cell type-resolved datasets and suitable analytical frameworks.
TEs make up nearly half of the human genome and have long been hypothesized to drive gene expression innovation through their capacity to rewire regulatory networks.
October 16, 2025 at 10:01 PM
TEs make up nearly half of the human genome and have long been hypothesized to drive gene expression innovation through their capacity to rewire regulatory networks.
In that study, we traced evolutionary history of human cis-regulatory elements (CREs) and highlighted many candidate CRE innovations from single-nucleotide substitutions or small insertions and deletions (indels). But what about TEs?
October 16, 2025 at 10:01 PM
In that study, we traced evolutionary history of human cis-regulatory elements (CREs) and highlighted many candidate CRE innovations from single-nucleotide substitutions or small insertions and deletions (indels). But what about TEs?
In our previous study (www.biorxiv.org/content/10.1...), we investigated gene regulatory evolution in mammalian cerebellum development using sequence-based deep-learning models and comparative genomics.
October 16, 2025 at 10:01 PM
In our previous study (www.biorxiv.org/content/10.1...), we investigated gene regulatory evolution in mammalian cerebellum development using sequence-based deep-learning models and comparative genomics.
We discovered that HERVLs – primate-specific retrotransposons – are preferentially co-opted as regulatory elements in cerebellar granule cells and other rhombic lip-derived neuroblasts in the pons and medulla, facilitated by the presence of sequences that resemble ATOH1 and NFI binding motifs.
October 16, 2025 at 9:54 PM
We discovered that HERVLs – primate-specific retrotransposons – are preferentially co-opted as regulatory elements in cerebellar granule cells and other rhombic lip-derived neuroblasts in the pons and medulla, facilitated by the presence of sequences that resemble ATOH1 and NFI binding motifs.
Our deep learning-based pipeline systematically screened TE fragments for regulatory potential, and identified 17 TE subfamilies whose ancestral sequences contain cis-regulatory motifs that resemble those found in elements accessible in cerebellar cells.
October 16, 2025 at 9:54 PM
Our deep learning-based pipeline systematically screened TE fragments for regulatory potential, and identified 17 TE subfamilies whose ancestral sequences contain cis-regulatory motifs that resemble those found in elements accessible in cerebellar cells.
We found that TEs are significantly enriched in species- and cell type-specific elements – particularly in later-developing, less constrained cell types. This pattern is further supported by datasets spanning multiple human organs across development.
October 16, 2025 at 9:54 PM
We found that TEs are significantly enriched in species- and cell type-specific elements – particularly in later-developing, less constrained cell types. This pattern is further supported by datasets spanning multiple human organs across development.
By combining comprehensive single-cell multiomics atlases of mammalian cerebellum development with deep learning-based modeling of enhancer grammar, we systematically investigated how TEs contribute to gene regulatory programs across developing cerebellar cell types.
October 16, 2025 at 9:54 PM
By combining comprehensive single-cell multiomics atlases of mammalian cerebellum development with deep learning-based modeling of enhancer grammar, we systematically investigated how TEs contribute to gene regulatory programs across developing cerebellar cell types.
However, their contribution to mammalian organ development at the cellular level has remained largely unexplored, owing to the lack of cell type-resolved datasets and suitable analytical frameworks.
October 16, 2025 at 9:54 PM
However, their contribution to mammalian organ development at the cellular level has remained largely unexplored, owing to the lack of cell type-resolved datasets and suitable analytical frameworks.
TEs make up nearly half of the human genome and have long been hypothesized to drive gene expression innovation through their capacity to rewire regulatory networks.
October 16, 2025 at 9:54 PM
TEs make up nearly half of the human genome and have long been hypothesized to drive gene expression innovation through their capacity to rewire regulatory networks.
In that study, we traced evolutionary history of human cis-regulatory elements (CREs) and highlighted many candidate CRE innovations from single-nucleotide substitutions or small insertions and deletions (indels). But what about TEs?
October 16, 2025 at 9:54 PM
In that study, we traced evolutionary history of human cis-regulatory elements (CREs) and highlighted many candidate CRE innovations from single-nucleotide substitutions or small insertions and deletions (indels). But what about TEs?
In our previous study (www.biorxiv.org/content/10.1...), we investigated gene regulatory evolution in mammalian cerebellum development using sequence-based deep-learning models and comparative genomics.
October 16, 2025 at 9:54 PM
In our previous study (www.biorxiv.org/content/10.1...), we investigated gene regulatory evolution in mammalian cerebellum development using sequence-based deep-learning models and comparative genomics.
Thanks a lot James!
October 15, 2025 at 6:21 PM
Thanks a lot James!