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Felsenfeld, Gary, and Mark Groudine. "Controlling the double helix." Nature 421.6921 (2003): 448-453.

Groudine, Mark, and Harold Weintraub. "Propagation of globin DNAase I-hypersensitive sites in absence of factors required for induction: a possible mechanism for determination." Cell 30.1 (1982): 131-139.

Weintraub, Harold, and Mark Groudine. "Chromosomal subunits in active genes have an altered conformation." Science 193.4256 (1976): 848-856.

Weintraub, Harold. "Tissue-specific gene expression and chromatin structure." Harvey lectures 79 (1983): 217.

Classics: Amazing Ideas and Clear Thinking!

My unofficial digital library….

https://rajapakse.lab.medicine.umich.edu/papers/digital-library

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Human Embryonic Stem cell

E

H

2 μm

d = 7 μm

E = Euchromatin, H = Heterochromatin

Felsenfeld G, Groudine M. 2003. Controlling the double helix. Nature 421:448–53

Interphase

Mitosis

The human genome is made up of 3 billion base pairs, on 23 chromosome pairs

that contain over 20,000 genes

3 Billion letters and 2 meters long (37.2 trillion cells)

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Inactive loci at the nuclear periphery are relocalized to the center, coinciding with their activation.

Inactive

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Inactive loci at the nuclear periphery are relocalized to the

center, coinciding with their activation.

Active

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β-globin pol II

Formation of Red Blood Cells

globin

pol II

Spatial Dynamics

Co-localization

No

Yes

E

L

E

L

E = Early cells

L= Late cells

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Hi-C: Genome-wide Chromosome Conformation Capture

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Hi-C

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Chromosome Conformation Capture

Hi-C: All-All

=

Contact Matrix

3C: One-One

4C: One-Many

5C: Many-Many

Intra-chromosomal contacts

Inter-chromosomal

contacts

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Genome-wide Chromosome Conformation Capture (Hi-C)

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Hi-C

No locus-specific primers!

*

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Hi-C

A

50

0

reads/Mb²

Intensity =

# of Reads

Intra-chromosomal contacts

Chromosome 8

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Hi-C

A

B

A

50

0

reads/Mb²

Intensity =

# of Reads

Chromosome 8

Intra-chromosomal contacts

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Hi-C

A

C

B

A

50

0

reads/Mb²

Intensity =

# of Reads

Chromosome 8

Intra-chromosomal contacts

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Intra-chromosome

Inter-chromosome

Hi-C: Genome-wide

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The Whole Genome

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(1880 x 1880)

Active

Inactive

Mixed

LOC100

TTC29

ZNF827

SLC10A7

PROM1

FGFBP2

FGFBP1

CD38

LSM6

POU4F2

CLOCK

SRD5A3

TMEM165

8

16

24

32

40

48

56

0

-1

-0.5

0.5

1

1.5

2

-1.5

-1

-0.5

0

0.5

1

1.5

2

2.5

Time (h)

Function (RPKM)

Here only static information is shown

Gene expression over time

Our Work

Chen H, Chen J, Muir LA, Ronquist S, Meixner W, Ljungman M, Ried T, Smale S, Rajapakse I. "Functional Organization of the Human 4D Nucleome. " Proceedings of the National Academy of Sciences 112.26 (2015): 8002-8007.

Fig. 1. Topologically associating domain (TAD) and corresponding gene expression dynamics of Chr 4. (A) Mean RNA-seq counts (RPKM) of binned genes. (B) Fiedler vector computed from the normalized Hi-C matrix. Red bins are the genes associated with the positive Fiedler vector entries, and green bins are the genes associated with negative Fiedler vector entries. (C) Hi-C matrix of Chr 4 with activity of identified TADs annotated by colored boxes on the diagonal. Active (green), inactive (blue), or mixed (black) TADs contain genes that are all actively transcribed, repressed, or a mix of both, respectively. (D1) Left, fragment read contact map of an inactive TAD with genes annotated by color; Right, no detectable transcripts from any genes in this TAD over time, with individual genes colored corresponding to the left maps. (D2) Left, fragment read contact map of an active TAD; Right, active transcription of all genes in this TAD over time. (D3) Left, fragment read contact map of a mixed TAD; Right, expression patterns of its genes are both active and inactive over time. Dashed green lines on the maps indicate Hind-III cutting sites.

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Hypergraphs and Pore-C

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Hypergraphs

Email data: summarizes which of the five users were involved in the three emails.

A hypergraph is a generalizations of graph in which a hyperedge can join any number of nodes

Hypergraph can represent multidimensional relationships unambiguously, e.g. not sure if Carl, Dan, and Ed participated in the same email in the graph model

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Hypergraphs

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Multi-way Interactions in the Human Genome

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B Lymphocyte

Fibroblast

Whole Genome

25 Mb Loci

Intra and inter

Intra only

Inter only

1

2

3

...

X

Chromosomes

1

2

3

...

X

Chromosomes

Genome-Wide Multi-Way Contacts

Degree

Genome-wide Patterning

Figure 4: Genome-wide patterning of multi-way contacts. Incidence matrix visualization of the top 10 most common multi-way contacts per chromosome. Matrices are constructed at 25 Mb resolution for both fibroblasts (V1-V4) and B lymphocytes. Specifically, 5 intra-chromosomal and 5 inter-chromosomal multi-way contacts were identified for each chromosome with no repeated contacts. If 5 unique intra-chromosomal multi-way contacts are not possible in a chromosome, they are supplemented with additional inter-chromosomal contacts. Vertical lines represent multi-way contacts, nodes indicate the corresponding locus’ participation in a multi-way contact, and color-coded rows delineate chromosomes. Highlighted boxes indicate example intra-chromosomal contacts (red), inter-chromosomal contacts (magenta), and combinations of intra- and inter-chromosomal contacts (blue). Multi-way contacts of specific regions are compared between cell types by connecting highlighted boxes with black dashed lines, emphasizing similarities and differences between fibroblasts and B lymphocytes. Normalized degree of loci participating in the top 10 most common multi-way contacts for each chromosome in fibroblast and B-lymphocytes are shown on the left. Red dashed lines indicate the mean degree for fibroblasts and B lymphocytes (top and bottom, respectively). Genomic loci that do not participate in the top 10 most common multi-way contacts for fibroblasts or B lymphocytes were removed from their respective incidence and degree plots. Multi-way contacts were determined in 25 Mb resolution after noise reduction (Supplementary Materials \ref{}).

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Data-driven Identification of Transcription Factories (clusters)

Figure 6: Data-driven identification of transcription factories. (A) A 5 kb region before and after each locus in a Pore-C read (between red dashed lines) is queried for chromatin accessibility and RNA Pol II binding (ATAC-seq and ChIP-seq, respectively) to identify “label”. Multi-way contacts between “label” are indicative of potential transcription clusters. Gene expression (RNA-seq, E₁ for gene 1 and E₂ for gene 2, respectively) and transcription factor binding sites (TF₁ and TF₂) are integrated to determine potential coexpression and coregulation within multi-way contacts with multiple genes. Transcription factor binding sites are queried +/- 5 kb from the gene’s transcription start site (Materials and Methods). (B) Pipeline for extracting transcription clusters (Supplementary Materials X). Genes are colored based on the overlapping Pore-C locus, and the extended line from each gene represents the 5 kb flanking region used to query transcription factor binding sites. (C) Schematic representation of a transcription cluster.

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Data-driven Identification of Transcription Factories (clusters)

Figure 6: Data-driven identification of transcription factories. (A) A 5 kb region before and after each locus in a Pore-C read (between red dashed lines) is queried for chromatin accessibility and RNA Pol II binding (ATAC-seq and ChIP-seq, respectively) to identify “label”. Multi-way contacts between “label” are indicative of potential transcription clusters. Gene expression (RNA-seq, E₁ for gene 1 and E₂ for gene 2, respectively) and transcription factor binding sites (TF₁ and TF₂) are integrated to determine potential coexpression and coregulation within multi-way contacts with multiple genes. Transcription factor binding sites are queried +/- 5 kb from the gene’s transcription start site (Materials and Methods). (B) Pipeline for extracting transcription clusters (Supplementary Materials X). Genes are colored based on the overlapping Pore-C locus, and the extended line from each gene represents the 5 kb flanking region used to query transcription factor binding sites. (C) Schematic representation of a transcription cluster.

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Dynamical Data

Dynamical System

Time

. . .

Structure

Function

4D Nucleome

The relationship between genome Structure and Function over Time is referred to as the 4D Nucleome (4DN). Output of this relationship is a PHENOTYPE

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4D Nucleome