The transcription-related DNA damage response was analyzed on a genome-wide scale with great spatial and temporal resolution. Upon UV irradiation, a slowdown of transcript elongation and restriction of gene activity to the promoter-proximal ∼25 kb is observed. This is associated with a shift from expression of long mRNAs to shorter isoforms, incorporating alternative last exons (ALEs) that are ...

The smooth/skeletal muscle beta-tropomyosin gene contains an additional exon (exon 1') which is located between exons 2 and 3 and which is used to generate a 1.3-kb transcript expressed in undifferentiated muscle as well as nonmuscle cells. This mRNA, besides exon 1', corresponds to exons 3, 4, 5, 6A, 7, 8, and 9B of the gene and codes for a 247-amino acid low molecular weight tropomyosin. Exon...

A genomic clone for the rat liver gap junction protein (connexin-32) was isolated and characterized by restriction enzyme mapping and sequence analysis. While the complete coding sequence is contained within one uninterrupted block, the 5'-untranslated region of the transcript contains a 6.1 kb intron. Both S1 nuclease protection and primer extension assays indicate multiple transcription start...

Non-coding RNA GAS5 (growth arrest-specific transcript 5) is a 5'-TOP (5'-terminal oligopyrimidine tract) RNA, whose translation, and consequently also stability, is controlled by the mTOR (mammalian target of rapamycin) pathway. GAS5 was identified by functional expression cloning and is necessary and sufficient for normal growth arrest in both leukaemic and untransformed human T-lymphocytes. ...

ANRIL (antisense non-coding RNA in the INK4 locus), located at the 9p21.3 locus, has been known to be closely associated with the risk of coronary artery disease (CAD). To date, studies of the 9p21.3 variants on CAD risk mainly focus on the non-coding region of ANRIL. However, the biological significance of the variants on ANRIL promoter and exons is still unknown. Here we investigate whether t...

Two forms of NADH-cytochrome b5 reductase are produced from one gene: a myristylated membrane-bound enzyme, expressed in all tissues, and a soluble, erythrocyte-specific, isoform. The two forms are identical in a large cytoplasmic domain (Mr approximately 30,000) and differ at the NH2-terminus, which, in the membrane form, is responsible for binding to the bilayer, and which contains the myrist...

MOTIVATION Long non-coding RNAs (lncRNAs) resemble protein-coding mRNAs but do not encode proteins. Most lncRNAs are under lower sequence constraints than protein-coding genes and lack conserved secondary structures, making it hard to predict them computationally. RESULTS We introduce an approach to predict spliced lncRNAs in vertebrate genomes combining comparative genomics and machine learn...

The calcitonin/calcitonin gene-related peptide gene expresses two different mRNAs by tissue-specific alternative processing. The calcitonin mRNA is produced in thyroid C cells by splicing of the first three exons to the fourth polyadenylated exon. It encodes a protein precursor containing an amino-terminal peptide, calcitonin, and a carboxyl-terminal peptide (CCP I). Calcitonin gene-related pep...

Previous studies have shown that infection of Prochlorococcus MED4 by the cyanophage P-SSP7 leads to increased transcript levels of host endoribonuclease (RNase) E. However, it has remained enigmatic whether this is part of a host defense mechanism to degrade phage messenger RNA (mRNA) or whether this single-strand RNA-specific RNase is utilized by the phage. Here we describe a hitherto unknown...