Tatjana Sauka‐Spengler

RegVelo: gene-regulatory-informed dynamics of single cells

RegVelo integrates gene regulatory networks with dynamic modeling to predict cellular changes and perturbations, showing improved performance in cell cycle, hematopoiesis, and pancreatic development datasets.

Specific Modulation of CRISPR Transcriptional Activators through RNA-Sensing Guide RNAs in Mammalian Cells and Zebrafish Embryos

This paper introduces a method to modulate CRISPR activity in response to RNA detection using engineered guide RNAs, demonstrating functionality in mammalian cells and zebrafish embryos.

Precise engineering of chimeric antigen receptor expression levels defines T cell identity and function

This study shows that varying CAR expression levels in T cells affects their activation, function, and transcriptional identity, with optimal CAR levels preventing exhaustion.

Cell type-specific gene expression dynamics during human brain maturation

This study uses snRNA-seq and spatial transcriptomics to create a pediatric and adult brain cell atlas, identifying cell type-specific gene expression changes during human brain maturation.

Chromatin remodeller Chd7 is developmentally regulated in the neural crest by tissue-specific transcription factors

The paper identifies enhancers regulating Chd7 expression in neural crest cells and validates their function in chick embryos, revealing tissue-specific regulation of a chromatin remodeller.

Endothelial regulatory circuits control cranial neural crest migration and plasticity

The paper identifies gene regulatory circuits controlling cranial neural crest migration and plasticity using multi-omics and computational methods.

Robust CRISPR/dCas13 RNA blockers specifically perturb miRNA-target interactions and rescue type 1 myotonic dystrophy pathology

This paper develops CRISPR-Lock, a CRISPR/dCas13 RNA blocker that disrupts miRNA-target interactions and rescues DM1 pathology by correcting splicing biomarkers and reducing nuclear foci.

Re-purposing Ac/Ds transgenic system for CRISPR/dCas9 modulation of enhancers and non-coding RNAs in zebrafish

The paper adapts the Ac/Ds transposition system to enable CRISPR/dCas9 interference for studying non-coding RNAs and enhancers in zebrafish without altering genetic sequences.

Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

Segregation of neural crest specific lineage trajectories from a heterogeneous neural plate border territory only emerges at neurulation

The paper uses single-cell RNA-seq to show that neural crest lineage segregation from the neural plate border occurs at early neurulation, not gastrulation.

Distinct epicardial gene regulatory programmes drive development and regeneration of the zebrafish heart

The paper identifies distinct gene regulatory programmes in the zebrafish epicardium during development and regeneration, revealing differences from developmental programmes.

Characterising open chromatin identifies novel cis-regulatory elements important for paraxial mesoderm formation and axis extension

The paper identifies novel cis-regulatory elements involved in paraxial mesoderm formation and axis extension using chromatin accessibility and transcriptomic data from chick embryos.

Neuromesodermal progenitor origin of trunk neural crest in vivo

The paper shows that trunk neural crest in zebrafish originates from pro-neural neuromesodermal progenitors, revealing a shared origin with these progenitors and explaining their pro-neural bias.

Functional heterogeneity within the developing zebrafish epicardium

This study identifies three distinct epicardial subpopulations in developing zebrafish hearts using single-cell RNA-sequencing and reveals their unique functions in cell adhesion, migration, and leukocyte recruitment.

A genome-wide assessment of the ancestral neural crest gene regulatory network

This study analyzes the neural crest gene regulatory network in sea lampreys to identify conserved and unique elements across vertebrates.

Reconstruction of the global neural crest gene regulatory network in vivo

The paper reconstructs the global neural crest gene regulatory network in vivo using epigenomic and single-cell transcriptome data combined with genome engineering.

From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape in vivo

This study shows foxd3 acts as a pioneer factor and then switches to a repressor in neural crest cells, dynamically remodeling chromatin structure to control stemness and cell fate.

Genome And Epigenome Engineering CRISPR Toolkit For Probing In Vivo cis-Regulatory Interactions In The Chicken Embryo

The paper develops a CRISPR-based toolkit for genome and epigenome engineering in chicken embryos to study gene regulatory interactions during neural crest development.

Generation Of A Double Binary Transgenic Zebrafish Model To Study Myeloid Gene Regulation In Response To Melanocyte Transformation

The paper develops a double binary zebrafish model to study myeloid gene regulation during melanocyte transformation and melanoma initiation.

Embryonic circular RNAs at tandem duplicated genes in zebrafish present new paradigm in gene expression

The paper identifies a novel class of circular RNAs in zebrafish embryonic cells that arise from tandem duplicated genes and are enriched on polysomes.