Several macromolecular machines collaborate to produce eukaryotic messenger RNA. RNA
polymerase II (Pol II) translocates along genes that are up to millions of base pairs in length …

RNA splicing, an essential part of eukaryotic pre-messenger RNA processing, can be
simultaneous with transcription by RNA polymerase II. Here, we compare and review …

The functional consequences of alternative splicing on altering the transcription rate have
been the subject of intensive study in mammalian cells but less is known about effects of …

The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns
that must be spliced out for proper gene expression. Each intron contains three obligate …

Experimental detection of RNA splicing branchpoints is difficult. To date, high-confidence
experimental annotations exist for 18% of 3′ splice sites in the human genome. We …

RNA and protein components of the spliceosome work together to identify the 5΄ splice site,
the 3΄ splice site, and the branchsite (BS) of nascent pre-mRNA. SF3b1 plays a key role in …

Tools to understand how the spliceosome functions in vivo have lagged behind advances in
the structural biology of the spliceosome. Here, methods are described to globally profile …

Deciphering how nucleotides in genomes encode regulatory instructions and molecular
machines is a long-standing goal in biology. DNA language models (LMs) implicitly capture …

Background Cellular non‐coding RNAs are extensively modified post‐transcriptionally, with
more than 100 chemically distinct nucleotides identified to date. In the past five years, new …

The fidelity of splice site selection is critical for proper gene expression. In particular, proper
recognition of 3′-splice site (3′ SS) sequences by the spliceosome is challenging …