axelvisel - Network

Congratulations again to Rinaldo, Susan, John, Alex and Rinaldo, John and Alex and thank you for making us part of this study! 14/14Here is...

Congratulations again to Rinaldo, Susan, John, Alex and Rinaldo, John and Alex and thank you for making us part of this study! 14/14

Here is the link to the paper again:
https://authors.elsevier.com/sd/article/S1534-5807(24)00603-8

🌱 Taken together, this work adds to understanding of brain development and may offer paths toward new ways to treat disorders linked to...

🌱 Taken together, this work adds to understanding of brain development and may offer paths toward new ways to treat disorders linked to GABAergic neurons. It also highlights the complexity of the regulatory code underlying developmental processes. 13/14

Integrating this result with the previous knowledge about the processes of cell migration and differentiation processes in the basal ganglia...

Integrating this result with the previous knowledge about the processes of cell migration and differentiation processes in the basal ganglia provides insights into how these TFs (and combinations thereof) direct the process. 12/14

By combining these results with single-cell transcriptome and chromatin accessibility data from developing basal ganglia, it became possible...

By combining these results with single-cell transcriptome and chromatin accessibility data from developing basal ganglia, it became possible to associate modules, defined by specific sets of TF, with subtypes of differentiation neurons. 11/14

Among these clusters of different modules, the D_1 cluster stands out in two ways: These regulatory sequences are unusually densely occupied...

Among these clusters of different modules, the D_1 cluster stands out in two ways: These regulatory sequences are unusually densely occupied by many of the relevant TFs, and they tend to be extremely well conserved in evolution. 10/14

Intriguingly, the study identified regulatory “modules,” which are sets of regulatory sequences that bind common sets of the same...

Intriguingly, the study identified regulatory “modules,” which are sets of regulatory sequences that bind common sets of the same transcription factors and are responsible for distinct pathways of GABAergic differentiation. 9/14

In transgenic mouse reporter assays, these enhancers drive highly reproducible reporter expression to specific subregions of the developing...

In transgenic mouse reporter assays, these enhancers drive highly reproducible reporter expression to specific subregions of the developing basal ganglia. 8/14

Using ChIP-seq of relevant TFs and chromatin interaction assays, the study maps out over 27,000 regulatory elements (most of them distal,...

Using ChIP-seq of relevant TFs and chromatin interaction assays, the study maps out over 27,000 regulatory elements (most of them distal, i.e., enhancers) that are active during GABAergic neuron development. 7/14

The new paper focuses on transcription factors (TFs), special molecules that turn genes on or off, guiding cells to become specific types,...

The new paper focuses on transcription factors (TFs), special molecules that turn genes on or off, guiding cells to become specific types, like GABAergic neurons. 6/14

🔬 Why is it important to understand how these neurons are made? Issues with GABAergic neurons have been linked to neurological conditions...

🔬 Why is it important to understand how these neurons are made? Issues with GABAergic neurons have been linked to neurological conditions like epilepsy, schizophrenia, and anxiety. By learning how they’re formed, we can better understand these conditions and develop treatments. 5/14

Where do GABAergic neurons come from? They’re created during early brain development in an area called the basal ganglia, a part of the...

Where do GABAergic neurons come from? They’re created during early brain development in an area called the basal ganglia, a part of the brain that controls movement and behavior. 4/14

🧠 Seriously, what are GABAergic neurons? These cells play a critical role in keeping our brain balanced by slowing down activity. They...

🧠 Seriously, what are GABAergic neurons? These cells play a critical role in keeping our brain balanced by slowing down activity. They use a neurotransmitter called GABA to calm things down, preventing overstimulation. This balance is essential for functions like movement and mood regulation! 3/14

GABBA GABBA HEY!!!The paper looks at how specific brain cells—GABAergic neurons—are created and how different transcription factors work...

GABBA GABBA HEY!!!

The paper looks at how specific brain cells—GABAergic neurons—are created and how different transcription factors work together to help form these cells. 2/14

🧵 Paper alert: How do different transcription factors work together to help form GABAergic neurons in the brain?The work was led by...

🧵 Paper alert: How do different transcription factors work together to help form GABAergic neurons in the brain?

The work was led by Rinaldo Catta-Preta, Susan Lindtner, John Rubenstein, and Alex Nord (we were a minor part of it) - time for a thread nonetheless! 1/14

https://authors.elsevier.com/sd/article/S1534-5807(24)00603-8

Again, here is the link to the paper (10/10)https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae940/7848837@LBNLBioSci...

Again, here is the link to the paper (10/10)

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae940/7848837

@LBNLBioSci @berkeleylab

If you want to try it out yourself: https://enhancer.lbl.govPlease let us know what you think – we just released this and would be happy...

If you want to try it out yourself:
https://enhancer.lbl.gov
Please let us know what you think – we just released this and would be happy to consider any suggestion for further improvement. 9/10

In terms of content, the largest numbers of tissue-specific enhancers are available for brain, limb, and heart tissues. But enhancers for...

In terms of content, the largest numbers of tissue-specific enhancers are available for brain, limb, and heart tissues. But enhancers for many of the other organ systems are available, too. 8/10

In terms of new features, a noteworthy addition are side-by-side Allelic comparisons! We’ve incorporated hundreds of manually curated...

In terms of new features, a noteworthy addition are side-by-side Allelic comparisons! We’ve incorporated hundreds of manually curated comparisons for alleles, e.g., specific human pathogenic and synthetic variants. Such comparisons are essential for understanding variant impact in developmental contexts. 7/10 #GenomicVariants

Here is how these four levels relate to the experimental design 6/10

Here is how these four levels relate to the experimental design 6/10

The experimental data is organized across four levels: loci, elements, experiments, and embryos. This hierarchical structure allows tracking...

The experimental data is organized across four levels: loci, elements, experiments, and embryos. This hierarchical structure allows tracking and easy access to complex experimental data. 5/10 #Bioinformatics #DatabaseDesign