If any current PhD student is interested in a Postdoc position applying computational methods (including machine learning) to study the evolution of nucleotide content in human genes, please contact me.

For some context this is the average nucleotide content of human genes with five exons:

EXACTLY. Call a spade a spade!

That U-rich introns promote expression makes sense - U is naturally enriched in human introns. Here's the average nucleotide content across all human genes with exactly 5 exons (yellow exons, white introns).

For the record:

Let's see what happens when the tariffs go up tomorrow.

The #1 reason the US could never absorb Canada.

Every few years a catastrophe happens and I remember it all being described in John McPhee's The Control of Nature. In relation to the wild fires, McPhee describes these in the third part of the book called "Los Angeles vs the San Gabriel Mountains".

TC incubator door handle version 4.0.

My last gift to the lab for 2024!

I was this years old when I realized that the version of Mingus Ah Um that I had been listening to for all these years was the edited short version where the songs were all shorted, some by as many as 3 minutes. Listening to the original recordings is like meeting an old friend for the first time.

Just arrived.

I hate it when part of an essential lab equipment apparatus breaks. Fortunately, we have a 3D printer.

(I finally replaced that broken door handle on our tissue culture incubator.)

We had previously documented that intact 5’ splice sites target mRNAs (aka IPA transcripts) to nuclear speckles soon after they are made. Now we show that m6A is required to transfer these IPAs to YTH-bodies, a nuclear structure that resides next to the nuclear speckle.

By performing m6A-Seq (Me-RIP-Seq) we found that natural IPA transcripts have a low level of m6A deposition (1-6 modifications), above what is present in size/level-matched exons. Interestingly, fewer IPAs tended to have a high level of m6A modifications (>12) when matched to the same controls.

We then found that reporter mRNAs that were engineered to contain unused 5’ splice site motifs, needed to be m6A modified, and required the m6A methyl-transferase METTL3 and YTHDC1/2, to be retained in the nucleus.

We found that ZFC3H1 and YTHDC1 interact with one another and with U1-70K (so likely the U1 snRNP).

In fission yeast the PAXT complex functions with Mmi1 to retain and degrade unspliced mRNAs, ncRNAs and TE-derived RNAs. Mmi1 has a YTH domain, which in vertebrates binds to N-6-methyladenosine (m6A). We thus investigated whether the YTHDC1/2 proteins act with ZFC3H1 to retain IPA transcripts.

When mRNAs are misprocessed they often leave splicing signals behind. For example, certain pre-mRNAs have cryptic 3’ cleavage/polyadenylation sites in their introns. If these are used, they form inronic polyadenylated (IPA) transcripts.

Post a perfect album from the 90s that isn’t Nirvana, Pearl Jam, Soundgarden, or Alice in Chains.