Prediction of Gene Activity in Early B Cell Development Based on an Integrative Multi-Omics Analysis.

Mohammad Heydarian

doi:10.4172/jpb.1000302

Abstract

An increasingly common method for predicting gene activity is genome-wide chromatin immuno-precipitation of ‘active’ chromatin modifications followed by massively parallel sequencing (ChIP-seq). In order to understand better the relationship between developmentally regulated chromatin landscapes and regulation of early B cell development, we determined how differentially active promoter regions were able to predict relative RNA and protein levels at the pre-pro-B and pro-B stages. Herein, we describe a novel ChIP-seq quantification method (cRPKM) to identify active promoters and a multi-omics approach that compares promoter chromatin status with ongoing active transcription (GRO-seq), steady state mRNA (RNA-seq), inferred mRNA stability, and relative proteome abundance measurements (iTRAQ). We demonstrate that active chromatin modifications at promoters are good indicators of transcription and steady state mRNA levels. Moreover, we found that promoters with active chromatin modifications exclusively in one of these cell states frequently predicted the differential abundance of proteins. However, we found that many genes whose promoters have non-differential but active chromatin modifications also displayed changes in abundance of their cognate proteins. As expected, this large class of developmentally and differentially regulated proteins that was uncoupled from chromatin status used mostly post-transcriptional mechanisms. Strikingly, the most differentially abundant protein in our B-cell development system, 2410004B18Rik, was regulated by a post-transcriptional mechanism, which further analyses indicated was mediated by a micro-RNA. These data highlight how this integrated multi-omics data set can be a useful resource in uncovering regulatory mechanisms. This data can be accessed at: https://usegalaxy.org/u/thereddylab/p/prediction-of-gene-activity-based-on-an-integrative-multi-omics-analysis

Highlights

Murine B cell development is a leading developmental system for the analysis of gene-regulatory networks that orchestrate cell fate ‘choice’ and lineage commitment [1,2,3]
We note that other studies have indicated that promoter activity status does not necessarily indicate a change in steady state RNA [18,19], we propose to expand on these previous studies by systematically investigating how well correlated differential promoter chromatin state is with concordant differential ongoing transcription and steady state mRNA levels, as well as differential protein levels
Since we observed that certain populations of genes could have such dramatic cell type specific differential between steady state mRNA levels and ongoing transcription levels, we explored the global relationship between our predicted promoter classes and mRNA stability— asking if promoter status may somehow be linked to this type of post-transcriptional regulation

Summary

Introduction

Murine B cell development is a leading developmental system for the analysis of gene-regulatory networks that orchestrate cell fate ‘choice’ and lineage commitment [1,2,3]. Published work suggests that B lymphocytes develop from lymphoid-primed multi-potent progenitors (LMPPs) in the bone marrow that give rise to myeloid progeny such as macrophages and granulocytes [3,4]. Restriction of these LMPPs to the B lineage (B cell specification) is controlled by the coordinate activity of a number of transcription factors, including E2a (Tcf3 [transcription factor 3]) and Ebf (early B-cell factor 1) which regulate, among other things, rearrangement of the immunoglobulin heavy chain (Igh) locus and pre-B cell receptor expression (Figure 1) [5,6,7]. Rag (Recombination Activating Gene) proteins are necessary for recombination of immunoglobulin genes, and deletion of Rag or Rag leads to a complete block of Igh rearrangement and a developmental

Methods

Results

Conclusion