Shao-shan Carol Huang

Functions of natural genome and epigenome variation in gene expression regulation, computational analysis of cis-regulatory elements and gene regulatory neworks

A long-term goal of my lab is to understand how naturally occurring genetic and epigenetic variation in the genome gives rise to genome-wide variation in transcription factor-DNA interactions, and how these variation collectively alter the regulatory networks in the cell. To this end we are utilizing both “dry”- and “wet”-lab genomics methods to investigate the effect of natural variation in protein-DNA interaction using the diverse genomes and epigenomes of natural strains (accessions) of Arabidopsis thaliana as model. We developed the DNA affinity purification-sequencing (DAP-seq) technique that allows efficient and accurate mapping of genome-wide binding sites in endogenous genome context for hundreds of transcription factors. Using DAP-seq we are systematically characterizing the variation in genome-wide transcription factor binding sites across multiple accessions, between coding variants of transcription factors, and between variable transcription factor complexes. We are creating computational models to analyze the experimentally determined binding site variation to understand the contributions from sequence and non-sequence features of endogenous genomic DNA, providing important baseline datasets for studying in vivo binding variation. In collaboration with multiple groups we are applying DAP-seq to agriculturally and ecologically important plants including maize, grapevine, and poplars.

• Mentoring Faculty, PhD program in Developmental Genetics, NYU School of Medicine
• Affiliate Faculty, Center for Data Science, New York University

Genomics & Systems Biology

1. Potentials of single-cell genomics in deciphering cellular phenotypes.
   Shojaee A, Saavedra M, Huang SC.
   Curr Opin Plant Biol. 2021 Jun 8;63:102059. doi: 10.1016/j.pbi.2021.102059. Online ahead of print.
   PMID: 34116424
2. Big Data to the Bench: Transcriptome Analysis for Undergraduates.
   Procko C, Morrison S, Dunar C, Mills S, Maldonado B, Cockrum C, Peters NE, Huang SC, Chory J.
   CBE Life Sci Educ. 2019 Jun;18(2):ar19. doi: 10.1187/cbe.18-08-0161. PMID: 31074696
3. Mapping genome-wide transcription-factor binding sites using DAP-seq.
   Bartlett A, O'Malley RC, Huang SC, Galli M, Nery JR, Gallavotti A, Ecker JR.
   Nat Protoc. 2017 Aug;12(8):1659-1672. doi: 10.1038/nprot.2017.055. Epub 2017 Jul 20. PMID: 28726847 
4. A transcription factor hierarchy defines an environmental stress response network.
   Song L, Huang SC, Wise A, Castanon R, Nery JR, Chen H, Watanabe M, Thomas J, Bar-Joseph Z, Ecker JR.
   Science. 2016 Nov 4;354(6312):aag1550. doi: 10.1126/science.aag1550.
   PMID: 27811239
5. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.
   O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR.
   Cell. 2016 Sep 8;166(6):1598. doi: 10.1016/j.cell.2016.08.063. Epub 2016 Sep 8.
   PMID: 27610578
6. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.
   Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O'Neil R, O'Malley RC, Quarless DX; 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR.
   Cell. 2016 Jul 14;166(2):492-505. doi: 10.1016/j.cell.2016.06.044.
   PMID: 27419873