CTCF regulates NELF, DSIF and P-TEFb recruitment during transcription

Clélia Laitem,Justyna Zaborowska,Michael Tellier,Yuki Yamaguchi,Qingfu Cao,Sylvain Egloff,Hiroshi Handa,Shona Murphy

doi:10.1080/21541264.2015.1095269

Abstract

CTCF is a versatile transcription factor with well-established roles in chromatin organization and insulator function. Recent findings also implicate CTCF in the control of elongation by RNA polymerase (RNAP) II. Here we show that CTCF knockdown abrogates RNAP II pausing at the early elongation checkpoint of c-myc by affecting recruitment of DRB-sensitivity-inducing factor (DSIF). CTCF knockdown also causes a termination defect on the U2 snRNA genes (U2), by affecting recruitment of negative elongation factor (NELF). In addition, CTCF is required for recruitment of positive elongation factor b (P-TEFb), which phosphorylates NELF, DSIF, and Ser2 of the RNAP II CTD to activate elongation of transcription of c-myc and recognition of the snRNA gene-specific 3’ box RNA processing signal. These findings implicate CTCF in a complex network of protein:protein/protein:DNA interactions and assign a key role to CTCF in controlling RNAP II transcription through the elongation checkpoint of the protein-coding c-myc and the termination site of the non-coding U2, by regulating the recruitment and/or activity of key players in these processes.

Highlights

CCCTC binding factor (CTCF) is a highly conserved and ubiquitously-expressed transcription factor, which regulates gene expression and organizes chromatin structure.[1]
SiRNA-mediated knockdown (KD) of CTCF was used to assess its function in expression of the protooncogene c-myc, as a model of a protein-coding gene where CTCF binds at an early elongation checkpoint and represses expression.[7]
CTCF binds to a site between C5 and C45 downstream from the P2 promoter 7 and previous studies have shown that RNA polymerase (RNAP) II pauses between C17 and C52 and that a region upstream of C47 was sufficient to confer promoter proximal pausing.[49,50]

Summary

Introduction

CCCTC binding factor (CTCF) is a highly conserved and ubiquitously-expressed transcription factor, which regulates gene expression and organizes chromatin structure.[1] It is a critical factor for various cellular processes, including growth, proliferation, differentiation, and apoptosis in mammalian cells,[2,3] and homozygous CTCF knockout mice exhibit early embryonic lethality prior to implantation.[4]. CTCF binding sites are important elements of insulators, which block communication between adjacent regulatory elements and prevent spreading of heterochromatin.[1,5,6] CTCF acts at the level of transcription mainly as a repressor, for example at the c-myc, pax-6, and chicken lysozyme genes.[7,8,9]. El-Kady and Klenova[13] suggest that phosphorylation converts CTCF from a repressor to an activator

Methods

Results

Conclusion