Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features.

Three-dimensional (3D) chromatin structure has been shown to play a role in regulating gene transcription during biological transitions. Although our understanding of loop formation and maintenance is rapidly improving, much less is known about the mechanisms driving changes in looping and the impact of differential looping on gene transcription. One limitation has been a lack of well-powered differential looping data sets. To address this, we conducted a deeply sequenced Hi-C time course of megakaryocyte development comprising four biological replicates and 6 billion reads per time point. Statistical analysis revealed 1503 differential loops. Gained loop anchors were enriched for AP-1 occupancy and were characterized by large increases in histone H3K27ac (over 11-fold) but relatively small increases in CTCF and RAD21 binding (1.26- and 1.23-fold, respectively). Linear modeling revealed that changes in histone H3K27ac, chromatin accessibility, and JUN binding were better correlated with changes in looping than RAD21 and almost as well correlated as CTCF. Changes to epigenetic features between-rather than at-boundaries were highly predictive of changes in looping. Together these data suggest that although CTCF and RAD21 may be the core machinery dictating where loops form, other features (both at the anchors and within the loop boundaries) may play a larger role than previously anticipated in determining the relative loop strength across cell types and conditions.

Inefficient splicing of long non-coding RNAs is associated with higher transcript complexity in human and mouse.

Recent reports show that long non-coding RNAs (lncRNAs) have inefficient splicing and fewer alternative splice variants than mRNAs. Here, we have explored the efficiency of lncRNAs and mRNAs in producing various splice variants, given the number of exons in humans and mice. Intriguingly, lncRNAs produce more splice variants per exon, referred to as Transcript Complexity, than mRNAs. Most lncRNA splice variants are the product of the alternative last exon and exon skipping. LncRNAs and mRNAs with higher transcript complexity have shorter intron lengths. Longer exon length and GC/AG at 5'/3' splice sites are associated with higher transcript complexity in lncRNAs. Lastly, our results indicate that inefficient splicing of lncRNAs may facilitate multiple introns splicing and, thus, more spliced products per exon.

CaTCH: Calculating transcript complexity of human genes.

The findings based on whole transcriptome sequencing suggest that alternative splicing occurs in approximately 95% of human multi-exon genes, thus, playing a crucial role in promoting proteome diversity. According to the latest GENCODE annotations, most genes have less than four transcripts, positively correlating with the number of exons. Thus, it is more accurate to measure the splice variant efficiency of a gene with respect to the number of exons, which is a measure of Transcript Complexity (TC). In addition to that, the theoretical number of transcripts is substantially higher than the actual number of transcripts produced by Alternative Splicing Events, and the features restricting this phenomenon need to be explored. In this method, we have extracted the data of various features contributing to TC from different databases. Linear regression is used to identify the determinant features and to train and test the model of TC. The results indicate that exon length is the determining feature of TC, followed by coding potential, presence of chromatin signature, and 5' splice site dinucleotide, all of which negatively affect a gene's TC, except exon length. To further classify the genes based on TC, random forest is used to identify the determinant features.•The splicing efficiency of a gene can be inferred by the transcript complexity, which is the number of transcripts per exon.•CaTCH is a linear regression-based model to calculate the transcript complexity of human genes, which can be calculated from the exon length, coding potentiality, presence of chromatin signature/s, and 5' splice site dinucleotide.