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Rabin, A.

Publications and source records attributed to Rabin, A..

2 recordsLinked to original sources
bioRxiv2019

A comprehensive pipeline for accurate annotation and quantification of circRNAs

Identification and quantification of circular RNAs (circRNAs) depends strongly on the utilized computational pipeline. Here we describe an integrative approach for accurate annotation and quantification of circRNAs. First, we utilize several circRNA-identification pipelines to annotate circRNAs in a given organism. Second, we build a short sequence index that is used to search the unaligned RNA-seq reads. Our approach allows full annotation of circRNAs with fewer false positives and negatives than any individual pipeline or combination of them. Moreover, our approach is more sensitive than any individual pipeline and allows more accurate quantification and larger number of differentially expressed circRNAs.

bioinformatics↗
bioRxiv2017

Evolution of chalcone isomerase from a non-catalytic ancestor

The emergence of catalysis in a non-catalytic protein scaffold is a rare, unexplored event. Chalcone isomerase (CHI), a key enzyme in plant flavonoid biosynthesis, is presumed to have evolved from a non-enzymatic ancestor related to the widely-distributed fatty-acid binding proteins (FAPs) and a plant protein family with no isomerase activity (CHILs for \"CHI-like\"). Ancestral inference confirmed that CHI evolved from a protein lacking isomerase activity. We also identified four alternative founder mutations, i.e. mutations that individually instated activity, including a mutation that is not phylogenetically traceable. Despite strong epistasis in other cases of protein evolution, CHIs laboratory reconstructed mutational trajectory shows weak epistasis. Thus, enantioselective CHI activity can readily emerge despite a catalytically inactive starting point. X-ray crystallography, NMR, and MD simulations reveal reshaping of the active site toward a productive substrate-binding mode and repositioning of the catalytic arginine that was inherited from the ancestral fatty-acid binding proteins.

biochemistry↗