Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression

Nikki R Kong; Mahmoud A Bassal; Hong Kee Tan; Jesse V Kurland; Kol Jia Yong; John J Young; Yang Yang; Fudong Li; Jonathan D Lee; Yue Liu; Chan-Shuo Wu; Alicia Stein; Hongbo R Luo; Leslie E Silberstein; Martha L Bulyk; Daniel G Tenen; Li Chai

doi:10.1016/j.celrep.2020.108574

Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression

Cell Rep. 2021 Jan 5;34(1):108574. doi: 10.1016/j.celrep.2020.108574.

Authors

Nikki R Kong¹, Mahmoud A Bassal², Hong Kee Tan³, Jesse V Kurland⁴, Kol Jia Yong⁵, John J Young⁶, Yang Yang⁷, Fudong Li⁷, Jonathan D Lee⁸, Yue Liu¹, Chan-Shuo Wu⁹, Alicia Stein¹⁰, Hongbo R Luo¹¹, Leslie E Silberstein¹¹, Martha L Bulyk¹², Daniel G Tenen¹³, Li Chai¹⁴

Affiliations

¹ Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA.
² Harvard Stem Cell Institute, Boston, MA 02115, USA; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
³ Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117599, Singapore.
⁴ Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
⁵ Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Biochemistry, Yoon Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.
⁶ Department of Biology, Simmons University, Boston, MA 02115, USA.
⁷ Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China.
⁸ Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.
⁹ Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
¹⁰ Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
¹¹ Joint Program in Transfusion Medicine, Department of Laboratory Medicne, Children's Hospital Boston, Boston, MA 02115, USA.
¹² Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
¹³ Harvard Stem Cell Institute, Boston, MA 02115, USA; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore. Electronic address: daniel.tenen@nus.edu.sg.
¹⁴ Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA. Electronic address: lchai@bwh.harvard.edu.

Abstract

The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, downregulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive therapeutic target. However, whether SALL4 binds DNA directly to regulate gene expression is unclear, and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and cleavage under targets and release using nuclease (CUT&RUN) experiments, we identify and validate the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA sequencing (RNA-seq) analyses after SALL4 knockdown, we discover hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of histone 3 lysine 9-specific demethylases (KDMs). Taken together, these results elucidate the mechanism of SALL4 DNA binding and reveal pathways and molecules to target in SALL4-dependent tumors.

Keywords: CUT&RUN; KDM; SALL4; heterochromatin; liver cancer; protein binding microarray; transcription.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Amino Acid Motifs
Amino Acid Sequence
Carcinoma, Hepatocellular / genetics
Carcinoma, Hepatocellular / metabolism*
Cell Line, Tumor
DNA-Binding Proteins / genetics
DNA-Binding Proteins / metabolism*
Embryonic Stem Cells / metabolism*
Gene Expression Regulation, Neoplastic*
Gene Knockdown Techniques
HEK293 Cells
HeLa Cells
Histone Demethylases / genetics
Histone Demethylases / metabolism*
Humans
Liver Neoplasms / genetics
Liver Neoplasms / metabolism
Protein Array Analysis
Protein Binding
Sequence Analysis, RNA
Transcription Factors / genetics
Transcription Factors / metabolism*
Zinc Fingers*

Substances

DNA-Binding Proteins
SALL4 protein, human
Transcription Factors
Histone Demethylases

Abstract

Publication types

MeSH terms

Substances

Grants and funding