Winston Timp

Finally, in CA1 engram (Fos+) neurons, we found upregulated isoforms (Egr1-201, Junb-201, Arpc2-201) and downregulated isoforms (Plp1-201). Notably, Arpc2-201—a learning-linked cytoskeletal isoform—suggests structural remodeling during engram activation.

For example Baiap2; which encodes an abundant scaffolding protein (Irsp53) in the postsynaptic density. We observed no differential expression, only differential splicing, resulting in loss of the C-terminal PDZ binding motif, needed for postsynaptic density localization.

We generated single-cell long-read hippocampal data from 17 total mice subjected to one of three contextual experiences: Fear-conditioned (C+), Unconditioned (U+), or Naive (N). 20% of experience-variable isoforms arise from genes with no detectable difference at the gene level.

Using @10xgenomics.bsky.social Genomics and @nanoporetech.com sequencing, we generated the first single-cell long-read dataset of the mouse hippocampus. For example, S100a16, a calcium-binding protein, has cell-type alternative isoforms undetectable with standard 10X 3’ short-read data:

Single-cell long-read sequencing of the experience-induced transcriptome Neural activity drives transcriptional events that are critical for learning. Activity-induced transcript isoform expression and alternative splicing are cell-type specific events typically obscured b...

We are excited to announce our most recent preprint “Single-cell long-read sequencing of the experience-induced transcriptome” (www.biorxiv.org/content/10.1...) led by @sheridan in collaboration with Richard Huganir. A few highlights:

I think 5kb, 10kb, 25kb, 50kb and 100kb personally.

Here's the White House's proposed reorganization of NIH institutes & budgets. Details in: www.hhs.gov/sites/defaul...

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).

myloasm-docs.github.io

Complete sequencing of ape genomes - Nature Complete sequences of chromosomes telomere-to-telomere from chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang provide a comprehensive and valuable resource for future evol...

Telomere-to-telomere genome sequences of six ape species: chimpanzee, bonobo, gorilla, Bornean & Sumatran orangutan, & siamang! Invaluable resource for future evolutionary studies of humans & our closest living relatives. Kateryna Makova, @aphillippy.bsky.social, Evan Eichler & co in @nature.com.🙌🧬🧪

Long reads such as @nanoporetech.com or @pacbio.bsky.social can provide insights into epigenetic. We
@yileifu.bsky.social & @timp0.bsky.social )summarize the latest #Bioinformatics approaches & why this matters! Out now @natrevgenet.bsky.social at:
bit.ly/4cjxUtl
@bcmhouston.bsky.social @jhu.edu

We summarized state-of-the-art computational methods for DNA methylation analysis using long-read sequencing, covering everything from base calling to sample-level, cell-type-level, and even population-scale analysis. Huge thanks to @sedlazeck.bsky.social and @timp0.bsky.social for this great work!

Biology of Genomes Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

The abstract deadline for Biology of Genomes is a month away. We hope to see you there!

meetings.cshl.edu/meetings.asp...