How do RNA sequence, DNA sequence, and chromatin properties regulate splicing?

How do RNA sequence, DNA sequence, and chromatin properties regulate splicing?

Recent genome-wide studies have revealed a remarkable correspondence between nucleosome positions and exon-intron boundaries, and several studies have implicated specific histone modifications in regulating alternative splicing. In addition, recent progress in cracking the 'splicing code' shows that sequence motifs carried on the nascent RNA molecule itself are sufficient to accurately predict ...

How does Tra2β protein regulate tissue-specific RNA splicing?

The splicing regulator protein Tra2β is conserved between humans and insects and is essential for mouse development. Recent identification of physiological RNA targets has started to uncover molecular targets and mechanisms of action of Tra2β. At a transcriptome-wide level, Tra2β protein binds a matrix of AGAA-rich sequences mapping frequently to exons. Particular tissue-specific alternatively ...

Non-Coding RNA: Sequence-Specific Guide for Chromatin Modification and DNA Damage Signaling

Chromatin conformation shapes the environment in which our genome is transcribed into RNA. Transcription is a source of DNA damage, thus it often occurs concomitantly to DNA damage signaling. Growing amounts of evidence suggest that different types of RNAs can, independently from their protein-coding properties, directly affect chromatin conformation, transcription and splicing, as well as prom...

Sequence-dependent elastic properties of DNA.

Harmonic elastic constants of 3-11 bp duplex DNA fragments were evaluated using four 5 ns unrestrained molecular dynamics simulation trajectories of 17 bp duplexes with explicit inclusion of solvent and counterions. All simulations were carried out with the Cornell et al. force-field and particle mesh Ewald method for long-range electrostatic interactions. The elastic constants including anisot...

Sequence heterogeneity in kinetoplast minicircle DNA of Leishmania majer