A genome-wide interactome of DNA-associated proteins in the human liver

Ramaker, Ryne C.; Savic, Daniel; Hardigan, Andrew A.; Newberry, Kimberly M.; Cooper, Gregory M.; Myers, R

doi:10.1101/gr.222083.117

Cited by 12 publications

(14 citation statements)

References 70 publications

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“…Furthermore, the allele-specificity of DAP associations is not considered by our analysis. Few allele-specific analyses have been conducted on a large number of DAPs in the same cell line or tissue, but some evidence exists that DAPs may favor a single allele in the context of allelic sequence variation (Ramaker et al 2017;Reddy et al 2012).…”

Section: Discussionmentioning

confidence: 99%

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Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

Ramaker

Hardigan

Goh

et al. 2019

Preprint

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DNA associated proteins (DAPs) regulate gene expression by binding to regulatory loci such as enhancers or promoters. An understanding of how DAPs cooperate at regulatory loci is essential to deciphering how these regions contribute to normal development and disease. In this study, we aggregated publicly available ChIP-seq data from 469 human DNA-associated proteins assayed in three cell lines and integrated these data with an orthogonal dataset of 352 non-redundant, in vitro-derived motifs mapped to the genome within DNase hypersensitivity footprints in an effort to characterize regions of the genome that have exceptionally high numbers of DAP associations. We subsequently performed a massively parallel mutagenesis assay to discover the key sequence elements driving transcriptional activity at these loci and explored plausible biological mechanisms underlying their formation. We establish a generalizable definition for High Occupancy Target (HOT) loci and identify putative driver DAP motifs, including HNF4A, SP1, SP5, and ETV4, that are highly prevalent and exhibit sequence conservation at HOT loci. We also found the number of DAP associations is positively associated with evidence of regulatory activity and, by systematically mutating 245 HOT loci in our massively parallel reporter assay, localize regulatory activity in these loci to a central core region that is dependent on the motif sequences of our previously nominated driver DAPs. In sum, our work leverages the increasingly large number of DAP motif and ChIP-seq data publicly available to explore how DAP associations contribute to genome-wide transcriptional regulation. 3 provided an increasingly rich set of clues to the locations and physical connections among such elements. Nevertheless, these biochemical signatures cannot yet accurately predict the presence or amount of regulatory activity of the underlying DNA. There are many known and suspected reasons for this difficulty, including the relative strength, number of interacting partners, and redundancy of each element, each of which may modulate a locus' contribution to the native expression level(s) of its respective target gene(s) in a manner difficult to predict without direct experimentation (Roadmap Epigenomics Consortium 2015; The ENCODE Project Consortium 2007Sanyal et al. 2012). In this manuscript, we present evidence that the total number of DNA-associated proteins (DAPs) that associate with a locus can act as a quantitative predictor of the locus' regulatory activity and that the activities of loci with large numbers of DAP associations can be disrupted in a predictable manner by altering subsets of putative "driver motifs".Classically, regulatory loci are thought to be discriminately bound by a small subset of expressed transcription factors in a manner governed by each factor's DNA sequence preference, and additional proteins are recruited through specific protein-protein interactions (Mitchell and Tjian 1989). However, this model is becoming incongruent with observed DAP

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Section: Discussionmentioning

confidence: 99%

“…Predicted mutation effects were determined using the lsgkm analysis suite in a manner previously described (Lee 2016;Ramaker et al 2017). Briefly, genome sequence was obtained in FASTA format for each HepG2 DAP narrow peak using the bedtools getfasta command.…”

Section: Starr-seq Data Processing and Analysismentioning

confidence: 99%

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

Ramaker

Hardigan

Goh

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

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“…When analyzing data from rare disease cohorts, knowing if potentially pathogenic variants are in cis or trans is necessary for interpreting the impact of these variants. Additionally, haplotype information is necessary for understanding allele specific impacts on gene expression (Ramaker et al 2017). In addition to the value that haplotype information can bring to interpreting variation data, studies also show that this information can be critical for variant identification, particularly for SVs that are heterozygous in a sample (Huddleston and Eichler 2016).…”

Section: Introductionmentioning

confidence: 99%

Resolving the Full Spectrum of Human Genome Variation using Linked-Reads

Marks

Garcia

Barrio

et al. 2017

Preprint

157

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Large-scale population based analyses coupled with advances in technology have demonstrated that the human genome is more diverse than originally thought. To date, this diversity has largely been uncovered using short read whole genome sequencing. However, standard short-read approaches, used primarily due to accuracy, throughput and costs, fail to give a complete picture of a genome. They struggle to identify large, balanced structural events, cannot access repetitive regions of the genome and fail to resolve the human genome into its two haplotypes. Here we describe an approach that retains long range information while harnessing the advantages of short reads. Starting from only~ ng of DNA, we produce barcoded short read libraries. The use of novel informatic approaches allows for the barcoded short reads to be associated with the long molecules of origin producing a novel datatype known as 'Linked-Reads'. This approach allows for simultaneous detection of small and large variants from a single Linked-Read library. We have previously demonstrated the utility of whole genome Linked-Reads (lrWGS) for performing diploid, de novo assembly of individual genomes (Weisenfeld et al. ). In this manuscript, weshow the advantages of Linked-Reads over standard short read approaches for reference based analysis. We demonstrate the ability of Linked-Reads to reconstruct megabase scale haplotypes and to recover parts of the genome that are typically inaccessible to short reads, including phenotypically important genes such as STRC, SMN and SMN . We demonstrate the ability of both lrWGS and Linked-Read Whole Exome Sequencing (lrWES) to identify complex structural variations, including balanced events, single exon deletions, and single exon duplications. The data presented here show that Linked-Reads provide a scalable approach for comprehensive genome analysis that is not possible using short reads alone.

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“…Haplotype phasing is the process of determining the sequences of genetic variants that cooccur along an intact maternal or paternal homologous chromosome [3,4]. Haplotype information is crucial for performing linkage analysis, association studies, population, and clinical genetic studies and also for allele specific impacts on gene expression [3,5]. Haplotype information are also critical for identifying heterozygous structural variants (SVs) [6].…”

Section: Introductionmentioning

confidence: 99%

A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle

Srikanth

Park

Lim

et al. 2020

Genes

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Until recently, genome-scale phasing was limited due to the short read sizes of sequence data. Though the use of long-read sequencing can overcome this limitation, they require extensive error correction. The emergence of technologies such as 10X genomics linked read sequencing and Hi-C which uses short-read sequencers along with library preparation protocols that facilitates long-read assemblies have greatly reduced the complexities of genome scale phasing. Moreover, it is possible to accurately assemble phased genome of individual samples using these methods. Therefore, in this study, we compared three phasing strategies which included two sample preparation methods along with the Long Ranger pipeline of 10X genomics and HapCut2 software, namely 10X-LG, 10X-HapCut2, and HiC-HapCut2 and assessed their performance and accuracy. We found that the 10X-LG had the best phasing performance amongst the method analyzed. They had the highest phasing rate (89.6%), longest adjusted N50 (1.24 Mb), and lowest switch error rate (0.07%). Moreover, the phasing accuracy and yield of the 10X-LG stayed over 90% for distances up to 4 Mb and 550 Kb respectively, which were considerably higher than 10X-HapCut2 and Hi-C Hapcut2. The results of this study will serve as a good reference for future benchmarking studies and also for reference-based imputation in Hanwoo.

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A genome-wide interactome of DNA-associated proteins in the human liver

Cited by 12 publications

References 70 publications

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

Resolving the Full Spectrum of Human Genome Variation using Linked-Reads

A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle

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