Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

Content

• This repository contains the source code and datasets used in the manuscript titled "Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression," published in eLife (DOI: [doi.org/10.7554/eLife.89001]). These resources support the analyses of human-specific long non-coding RNAs (lncRNAs), their evolutionary significance, and their distinct regulatory effects on gene expression. The repository is structured into data and code folders to facilitate accessibility, reproducibility, and further research.

Data folders

• LncRNA_orthologs: Contains processed datasets on orthologs of GENCODE-annotated human lncRNAs across 16 mammalian species, derived from the LongMan database (http://www.gaemons.net/LongMan). Based on these orthologous relationships, human-specific lncRNAs can be identified.
• Favored_mutations: Includes datasets on favored and hitchhiking mutations, sourced from the PopTradeOff database (http://www.gaemons.net/PopFMIntro). This file holds filtered mutation profiles, variant annotations, and statistical summaries employed to assess selective pressures on DNA binding sites of lncRNAs and transcription factors (TFs).

Code folders

• fasim-LongTarget: The source code for the fasim-LongTarget program, including scripts for predicting lncRNA binding sites and regulatory targets.
• eGRAM: Contains the source code for the eGRAM program, featuring modules for analyzing gene regulatory associations modulated by lncRNAs.

eGRAM is implemented in Python, while LongTarget is written in C++. For detailed usage instructions, installation guidelines, and dependency requirements, please refer to the README.md file in the root directory.