RNA-seq analysis of gene expression regulated by CRAMP1

Proper histone gene expression is critical for cell viability and maintenance of genomic integrity. Multiple histone genes are organized into three genomic loci encode replication-coupled core and linker histones. Histone gene expression and transcript processing are orchestrated in the histone locus body (HLB) within the nucleus. We identified human CRAMP1 as a selective regulator of the linker histone H1 expression. CRAMP1 was recruited to the HLB in RPE1hTERT cells. Affinity purification showed that CRAMP1 physically associates with the HLB component GON4L (also known as YARP). We demonstrated that the PAH domains of GON4L interact with CRAMP1. CRAMP1 disruption resulted in a loss of histone H1 expression and a reduction in H1 protein levels. CRAMP1 occupies unmethylated promoters of replication-coupled linker histone genes that reside within the histone locus body and replication-independent histone H1 loci, which reside in a region of the genome without other histone genes. Together, these data identify CRAMP1 as a novel and selective regulator of histone H1 gene expression. Overall design: To evelaute the gene exprseion changes that occur dependent on CRAMP1 activity we created HEK293T cells thata contain a degraon tag at the endogenous locus. RNA-seq was conducted following degradation of CRAMP1 by dTAG addition at defined times.