CHROMATIN REMODELING

CHROMATIN REMODELINGMaryam AminiWinter 2012

Contents:

Chromatin RemodelingChromatin Remodeling ComplexesMechanisms of Chromatin RemodelingDisorders of Chromatin RemodelingChromatin Immunoprecipitation Sequencing

ATP-dependent chromatin remodeling, or simply chromatin remodeling, refers to dynamic changes in the structure of chromatin that occur during the life of a cell.

Introduction

A summary of the events of gene expression

At the level of transcription, chromatin remodeling determines which genes are transcribed. Alternate splicing creates different forms of a protein by combining exons in different ways. MicroRNAs bind to the 3 ends of mRNAs by complementary base pairing, blocking translation. At the level of translation, a protein must fold a certain way. Certain polypeptides must be shortened, attached to sugars, or aggregated.

4

SmartArt custom animation effects: expand and peek in(Basic)

To reproduce the SmartArt effects on this slide, do the following:On the Home tab, in the Slides group, click Layout, and then click Blank. On the Insert tab, in the Illustrations group, click SmartArt. In the Choose a SmartArt Graphic dialog box, in the left pane, click Matrix. In the Matrix pane, click Titled Matrix (second option from the left), and then click OK to insert the graphic into the slide.Select the graphic, and then click one of the arrows on the left border. In the Type your text here dialog box, enter text.On the slide, select the graphic. Under SmartArt Tools, on the Design tab, in the SmartArt Styles group, do the following: Click Change Colors, and then under Colorful click Colorful - Accent Colors (first option from the left).Click More, and then under Best Match for Document click Moderate Effect (fourth option from the left).On the Home tab, in the Font group, select Calibri from the Font list, and then select 24 from the Font Size list.On the slide, select the text in the center rounded rectangle of the graphic.On the Home tab, in the Font group, select 28 from the Font Size list, click the arrow next to Font Color, and then under Theme Colors click White, Background 1 (first row, first option from the left).Right-click the rounded rectangle in the center of the graphic, and then click Format Shape.In the Format Shape dialog box, in the left pane, click Fill, select Gradient fill in the Fill pane, and then do the following:In the Type list, select Linear.Click the button next to Direction, and then click Linear Up (second row, second option from the left).Under Gradient stops, click Add or Remove until three stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 0%.Click the button next to Color, and then under Theme Colors click White, Background 1, Darker 35% (fifth row, first option from the left).Select Stop 2 from the list, and then do the following: In the Stop position box, enter 80%.Click the button next to Color, and then under Theme Colors click White, Background 1, Darker 35% (fifth row, first option from the left).Select Stop 3 from the list, and then do the following:In the Stop position box, enter 100%.Click the button next to Color, and then under Theme Colors click White, Background 1, Darker 15% (third row, first option from the left).

To reproduce the animation effects on this slide, do the following:On the Animations tab, in the Animations group, click Custom Animation.On the slide, select the graphic. In the Custom Animation task pane, do the following: Click Add Effect, point to Entrance, and then click More Effects. In the Add Entrance Effect dialog box, under Subtle, click Expand. Under Modify: Expand, in the Speed list, select Fast.Also in the Custom Animation task pane, select the expand effect. Click the arrow to the right of the expand effect, and then click Effect Options. In the Expand dialog box, on the SmartArt Animation tab, in the Group graphic list, select One by one.Also in the Custom Animation task pane, click the double arrow under the expand effect to expand the contents of the list of effects.Press and hold CTRL, and then select all five expand effects in the Custom Animation pane. Under Modify: Expand, in the Start list, select With Previous.Press and hold CTRL, select the second, third, fourth, and fifth expand effects in the Custom Animation pane, and then do the following:Under Modify: Expand, click Change, point to Entrance, and then click More Effects. In the Change Entrance Effect dialog box, under Basic, click Peek In, and then click OK.Under Modify: Peek In, in the Speed list, select Fast.Also in the Custom Animation task pane, do the following:Select the second expand effect. Under Modify: Peek In, in the Start list, select After Previous.Select the third expand effect. Under Modify: Peek In, in the Direction list, select From Left.Select the fourth expand effect. Under Modify: Peek In, in the Direction list, select From Right.Select the fifth expand effect. Under Modify: Peek In, in the Direction list, select From Top.

To reproduce the background effects on this slide, do the following:Right-click the slide background area, and then click Format Background. In the Format Background dialog box, click Fill in the left pane, select Gradient fill in the Fill pane, and then do the following:In the Type list, select Radial.Click the button next to Direction, and then click From Corner (second option from the left).Under Gradient stops, click Add or Remove until two stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 0%.Click the button next to Color, and then under Theme Colors click White, Background 1 (first row, first option from the left).Select Stop 2 from the list, and then do the following: In the Stop position box, enter 100%.Click the button next to Color, and then under Theme Colors click White, Background 1, Darker 15% (third row, first option from the left).

Chromatin Remodeling Complexes Alter the Positions and Compositions of NucleosomesA key role of some transcriptional activators is to orchestrate changes in chromatin structure from the closed to the open conformation by altering Nucleosomes.

One way to change chromatin structure is through ATP dependent chromatin remodeling.

All remodeling complexes have a catalytic ATPase subunit that is similar to other motor proteins, called DNA translocases , that move along the DNA.

SmartArt custom animation effects: basic radial(Intermediate)

To reproduce the SmartArt on this slide, do the following:On the Home tab, in the Slides group, click Layout, and then click Blank. On the Insert tab, in the Illustrations group, click SmartArt. In the Choose a SmartArt Graphic dialog box, in the left pane, click Relationship. In the Relationship pane, click Basic Radial (sixth row, second option from the left), and then click OK to insert the graphic into the slide. On the slide, select the SmartArt graphic, and then click one of the arrows on the left border. In the Type your text here dialog box, in the top level bullet, enter the text for the center circle of the graphic. In the second-level bullets, enter the text for all the other shapes in the SmartArt graphic. With the SmartArt graphic still selected, on the Design tab, in the Themes group, click Colors, and then select Median. Under SmartArt Tools, on the Format tab, in the Size group, do the following:In the Shape Height box, enter 5. In the Shape Width box, enter 7.5.Under SmartArt Tools, on the Design tab, in the SmartArt Styles group, click SmartArt Styles, and then under Best Match for Document select Intense Effect (fifth option from the left).On the Home tab, in the Font group, click the button next to Font Color, and then under Theme Colors select Black, Text 1 (first row, second option from the left). On the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click 3-D Format in the left pane, and in the 3-D Format pane, under Surface, do the following:In the Material list, under Special Effect, select Soft Edge (first row, second option from the left).In the Lighting list, under Neutral, select Harsh (first row, fourth option from the left).In the Angle box, enter 30.Press and hold CTRL, and select all five shapes in the SmartArt graphic. On the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Shadow in the left pane. In the Shadow pane, in the Presets list, under Outer select Offset Bottom (first row, second option from the left), and then do the following:In the Transparency box, enter 65%.In the Size box, enter 103%.In the Blur box, enter 9 pt.In the Angle box, enter 90.In the Distance box, enter 3 pt.

To reproduce the SmartArt effects on this slide, do the following:On the slide, select the center circle in the SmartArt graphic, and then on the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click 3-D Format in the left pane, and in the 3-D Format pane do the following:Under Bevel, in the Top list, under Bevel, select Circle (first row, first option from the left).Also under Bevel, to the right of the Top list, in the Width box, enter 24 pt. Also under Bevel, to the right of the Top list, in the Height box, enter 12 pt.On the slide, select the top circle in the SmartArt graphic, and then on the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Fill in the left pane, and in the Fill pane do the following:Click Solid fill.Click the button next to Color, and then under Theme Colors select Orange, Accent 2 (first row, sixth option from the left).Also in the Format Shape dialog box, click 3-D Format in the left pane, and in the 3-D Format pane do the following:Under Bevel, in the Top list, under Bevel, select Circle (first row, first option from the left).Also under Bevel, to the right of the Top list, in the Width box, enter 20 pt. Also under Bevel, to the right of the Top list, in the Height box, enter 15 pt.Press and hold SHIFT, and then on the top circle, drag a corner adjustment handle toward the center to decrease the size.On the Home tab, in the Font group, in the Font Size box, enter 20.Drag the top circle approximately 0.5 to the right.Select the right circle in the SmartArt graphic, and then on the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Fill in the left pane, and in the Fill pane do the following:Click Solid fill.Click the button next to Color, and then under Theme Colors click Gold, Accent 4 (first row, eighth option from the left).Also in the Format Shape dialog box, click 3-D Format in the left pane, and in the 3-D Format pane do the following:Under Bevel, in the Top list, under Bevel, select Circle (first row, first option from the left).Also under Bevel, to the right of the Top list, in the Width box, enter 24 pt. Also under Bevel, to the right of the Top list, in the Height box, enter 12 pt.Press and hold SHIFT, and then on the right circle, drag a corner adjustment handle toward the center to decrease the size.On the Home tab, in the Font group, in the Font Size box, enter 28 pt.Drag the right circle slightly toward the right corner of the slide.One the slide, select the bottom circle in the SmartArt graphic, and then on the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Fill in the left pane, and in the Fill pane do the following:Click Solid fill.Click the button next to Color, and then under Theme Colors click Green, Accent 5 (first row, ninth option from the left)Also in the Format Shape dialog box, click 3-D Format in the left pane, and in the 3-D Format pane do the following:Under Bevel, in the Top list, select Circle (first row, first option from the left).Also under Bevel, to the right of the Top list, in the Width box enter 24 pt. Also under Bevel, to the right of the Top list, in the Height box enter 12 pt.Press and hold SHIFT, and then on the bottom circle, drag a corner adjustment handle away from the center to increase the size.On the Home tab, in the Font group, in the Font Size box, enter 28.On the slide, select the left circle in the SmartArt graphic, and then on the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Fill in the left pane, and in the Fill pane do the following:Click Solid fill.In the Color list, under Theme Colors select Olive Green, Accent 3 (first row, seventh option from the left).Also in the Format Shape dialog box, click 3-D Format in the left pane, and in the 3-D Format pane do the following:Under Bevel, in the Top list, under Bevel, select Circle (first row, first option from the left).Also under Bevel, to the right of the Top list, in the Width box, enter 30 pt. Also under Bevel, to the right of the Top list, in the Height box, enter 30 pt.Press and hold SHIFT, and then on the left circle, drag a corner adjustment handle toward the center to decrease the size.On the Home tab, in the Font group, in the Font Size box, enter 40, and then click Bold.Drag the top circle slightly toward the bottom of the slide.

To reproduce the line effects on this slide, do the following:Press and hold CTRL, and then select each of the four lines connecting the circles in the SmartArt graphic. On the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Line Color in the left pane, select Gradient line in the Line Color pane, and then do the following:In the Type list, select Linear.In the Direction list, select Linear Right (first row, fourth option from the left).Under Gradient stops, click Add or Remove until two stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 0%.Click the button next to Color, and then under Theme Colors click Black, Text 1 (first row, second option from the left). Select Stop 2 from the list, and then do the following: In the Stop position box, enter 100%.Click the button next to Color, and then under Theme Colors click Black, Text 1 (first row, second option from the left). In the Transparency box, enter 100%.Also in the Format Shape dialog box, click Line Style in the left pane, and in the Line Style pane do the following:In the Width box, enter 3.5 pt.In the Dash type list, select Round Dot (second option from the top).

To reproduce the animation effects on this slide, do the following:On the Animation tab, in the Animations group, click Custom Animation. On the slide, select the SmartArt graphic, and then in the Custom Animation task pane, to the following:Click Add Effect, point to Entrance, and select More Effects. In the Add Entrance Effect dialog box, under Moderate, select Zoom.Click the arrow to the right of the zoom entrance effect, and then select Effect Options. In the Zoom dialog box, do the following:On the Effect tab, in the Zoom list, select In from Screen Center.On the Timing tab, in the Speed list, select 1 seconds (Fast). On the SmartArt Animation tab, in the Group graphic list, select From center one by one. In the Custom Animation task pane, expand the contents of the list by clicking the double arrow under the zoom entrance effect, and then do the following:Select the first effect (zoom entrance effect), and under Modify: Zoom, in the Start list, select With Previous.Select the second effect (zoom entrance effect), click Change, point to Entrance, and then select More Effects. In the Change Entrance Effect dialog box, under Basic, select Wipe.Click the arrow to the right of the second effect (now wipe effect) and select Effect Options, and then in the Wipe dialog box do the following:On the Effect tab, in the Direction list, select From Bottom.On the Timing tab, in the Delay box, enter 0.5.On the Timing tab, in the Speed list, select 0.5 seconds (Very Fast).Select the fourth effect (zoom entrance effect), click Change, point to Entrance, and select More Effects. In the Change Entrance Effect dialog box, under Basic, select Wipe.Click the arrow to the right of the fourth effect (now wipe effect) and select Effect Options, and then in the Wipe dialog box, do the following:On the Effect tab, in the Direction list, select From Left.On the Timing tab, in the Delay box, enter 0.5.On the Timing tab, in the Speed list, select 0.5 seconds (Very Fast).Select the sixth effect (zoom entrance effect), click Change, point to Entrance, and select More Effects. In the Change Entrance Effect dialog box, under Basic, select Wipe.Click the arrow to the right of the sixth effect (now wipe effect) and select Effect Options, and then in the Wipe dialog box, do the following:On the Effect tab, in the Direction list, select From Left.On the Timing tab, in the Delay box, enter 0.5.On the Timing tab, in the Speed list, select 0.5 seconds (Very Fast).Select the eighth effect (zoom entrance effect), click Change, point to Entrance, and then select More Effects. In the Change Entrance Effect dialog box, under Basic, select Wipe.Click the arrow to the right of the eighth effect (now wipe effect) and select Effect Options, and then in the Wipe dialog box, do the following:On the Effect tab, in the Direction list, select From Right.On the Timing tab, in the Delay box, enter 0.5.On the Timing tab, in the Speed list, select 0.5 seconds (Very Fast).

To reproduce the background on this slide, do the following:Right-click the slide background area, and then click Format Background. In the Format Background dialog box, click Fill in the left pane, select Gradient fill in the Fill pane, and then do the following:In the Type list, select Radial.In the Direction, list click From Center (third option from the left).Under Gradient stops, click Add or Remove until two stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 0%.Click the button next to Color, and then under Theme Colors click Black, Text 1, Lighter 35% (third row, second option from the left). Select Stop 2 from the list, and then do the following: In the Stop position box, enter 100%.Click the button next to Color, and then under Theme Colors click Black, Text 1 (first row, second option from the left).

A summary of the different classes of nucleosome remodeling ATPases and reactions they catalyze.

A summary of the different classes of nucleosome remodeling ATPases and reactions they catalyze. (a) Each catalytic subunit is characterized by an ATPase domain (DExxspacerHELICc)flanked by unique domains characteristic of each family. Members of the SWI/SNF subfamily contain a bromodomain (red) that binds acetylated histones. ISWI contains a SANT-SLIDE (blue)module recognizing unmodified histones. The CHD subfamily contains a chromodomain (yellow) recognizingmethylated histones. The INO80 subfamily has a characteristic long spacer (gray)within the ATPase domain and like the SWI/SNF subfamily also contains an HSA (helicase-SANT) domain (green).8

main families: SWI/SNF: enzyme contains bromo-domain that binds to acetylated histone CHD: enzyme contains chromo-domain that binds to methylated histone

ATP-dependent chromatin remodeling complexes

Target location signals and translocation reaction scheme for chromatin remodelers.

DNA, RNA, posttranslationally modified histone tails, histone variants or otherchromatin-associated proteins represent chromatin signals that can target chromatin remodelers.10

Mechanisms of Chromatin Remodeling

SmartArt custom animation effects: vertical chevron list with dark colors(Basic)

To reproduce the SmartArt effects on this slide, do the following:On the Home tab, in the Slides group, click Layout, and then click Blank. On the Insert tab, in the Illustrations group, click SmartArt. In the Choose a SmartArt Graphic dialog box, in the left pane, click List. In the List pane, click Vertical Chevron List (fourth row, fourth option from the left), and then click OK to insert the graphic into the slide. To create a fourth chevron, select the third chevron at the bottom of the graphic, and then under SmartArt Tools, on the Design tab, in the Create Graphic group, click the arrow next to Add Shape, and select Add Shape After.To add bullets for the fourth chevron, select the fourth chevron, and then under SmartArt Tools, on the Design tab, in the Create Graphic group, click Add Bullet.To enter text, select the SmartArt graphic, and then click one of the arrows on the left border. In the Type your text here dialog box, enter text for each level. (Note: In the example slide, the first-level text boxes contain One, Two, Three, and Four. The second-level text is Supporting Text.)On the slide, select the SmartArt graphic and drag the right center sizing handle to the right edge of the slide.With the SmartArt graphic still selected, on the Design Tab, in the Themes group, click Colors, and then under Built-In select Median. (Note: If this action is taken in a PowerPoint presentation containing more than one slide, the theme will be applied to all of the slides.)With the SmartArt graphic still selected, under SmartArt Tools, on the Design tab, in the SmartArt Styles group, click More Styles, and then under 3-D select Inset (first row, second option from the left). Also under SmartArt Tools, on the Design tab, in the SmartArt Styles group, click Change Colors, and then under Colorful select Colorful -Accent Colors (first option from the left).

To reproduce the chevron effects on this slide, do the following:Press and hold CTRL, and select all four chevrons in the SmartArt graphic. On the Home tab, in the Font group, in the Font list select Franklin Gothic Medium Cond, and then in the Font Size box select 28.On the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Text Box in the left pane, and in the Text Box pane do the following:Under Text layout, in the Vertical alignment list select Bottom.Under Internal margin, do the following: In the Left box, enter 0. In the Right box, enter 0. In the Bottom box, enter 0. In the Top box, enter 0.6.

To reproduce the rectangle effects on this slide, do the following:Press and hold CTRL, and the four of the rectangles (with bulleted text). On the Home tab, in the Font group, do the following:In the Font list, select Franklin Gothic Book.In the Font Size box, enter 21.In the Font Color list, under Theme Colors select White, Background 1 (first row, first option from the left).On the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Fill in the left pane, select Gradient fill in the Fill pane, and then do the following:In the Type list, select Linear.Click the button next to Direction, and then click Linear Down (first row, second option from the left). Under Gradient stops, click Add or Remove until two stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops that you added as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 0%.Click the button next to Color, and then under Theme Colors select Black, Text 1 (first row, second option from the left).In the Transparency box, enter 100%. Select Stop 2 from the list, and then do the following: In the Stop position box, enter 100%.Click the button next to Color, and then under Theme Colors select Black, Text 1 (first row, second option from the left).In the Transparency box, enter 45%. Also in the Format Shape dialog box, click Shadow in the left pane, and in the Shadow pane, in the Presets list, select No Shadow.Also in the Format Shape dialog box, click 3-D Format in the left pane, and in the 3-D Format pane, under Bevel, in the Top list select No Bevel.Select the top rectangle with bulleted text.On the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Line Color in the left pane, select Gradient fill in the Line Color pane, and then do the following:In the Type list, select Linear.Click the button next to Direction, and then click Linear Down (first row, second option from the left). Under Gradient stops, click Add or Remove until two stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops that you added as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 0%.Click the button next to Color, and then under Theme Colors select Orange, Accent 2 (first row, sixth option from the left).In the Transparency box, enter 100%. Select Stop 2 from the list, and then do the following: In the Stop position box, enter 100%.Click the button next to Color, and then under Theme Colors select Orange, Accent 2 (first row, sixth option from the left).In the Transparency box, enter 0%. Select the second rectangle from the top with bulleted text.On the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Line Color in the left pane, select Gradient fill in the Line Color pane, and then do the following:In the Type list, select Linear.Click the button next to Direction, and then click Linear Down (first row, second option from the left). Under Gradient stops, click Add or Remove until two stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops that you added as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 0%.Click the button next to Color, and then under Theme Colors select Olive Green, Accent 3 (first row, seventh option from the left).In the Transparency box, enter 100%. Select Stop 2 from the list, and then do the following: In the Stop position box, enter 100%.Click the button next to Color, and then under Theme Colors select Olive Green, Accent 3 (first row, seventh option from the left).In the Transparency box, enter 0%. Select the third rectangle from the top with bulleted text.On the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Line Color in the left pane, select Gradient fill in the Line Color pane, and then do the following:In the Type list, select Linear.Click the button next to Direction, and then click Linear Down (first row, second option from the left). Under Gradient stops, click Add or Remove until two stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops that you added as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 0%.Click the button next to Color, and then under Theme Colors select Gold, Accent 4 (first row, eighth option from the left).In the Transparency box, enter 100%. Select Stop 2 from the list, and then do the following: In the Stop position box, enter 100%.Click the button next to Color, and then under Theme Colors select Gold, Accent 4 (first row, eighth option from the left).In the Transparency box, enter 0%. Select the fourth rectangle from the top with bulleted text.On the Home tab, in the bottom right corner of the Drawing group, click the Format Shape dialog box launcher. In the Format Shape dialog box, click Line Color in the left pane, select Gradient fill in the Line Color pane, and then do the following:In the Type list, select Linear.Click the button next to Direction, and then click Linear Down (first row, second option from the left). Under Gradient stops, click Add or Remove until two stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops that you added as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 0%.Click the button next to Color, and then under Theme Colors select Green, Accent 5 (first row, ninth option from the left).In the Transparency box, enter 100%. Select Stop 2 from the list, and then do the following: In the Stop position box, enter 100%.Click the button next to Color, and then under Theme Colors select Green, Accent 5 (first row, ninth option from the left).In the Transparency box, enter 0%.

To reproduce the animation effects on this slide, do the following: On the Animations tab, in the Animations group, click Custom Animation.Select the SmartArt graphic, and then in the Custom Animation task pane do the following:Click Add Effect, point to Entrance, and select More Effects. In the Add Entrance Effect dialog box, under Moderate select Grow & Turn.Click the arrow to the right of the animation effect (grow & turn effect for the graphic), select Effect Options, and then in the Grow & Turn dialog box, do the following:On the Timing tab, in the Speed list, select 0.5 seconds (Very Fast).On the SmartArt Animation tab, in the Group graphic list, select One by one.Click the double arrow to expand the contents of the list in the Custom Animation task pane.Press and hold CTRL, and select the second, fourth, sixth, and eighth effects (grow & turn entrance effects), and then do the following:Click Change, point to Entrance and select More Effects. In the Change Entrance Effect dialog box, under Moderate select Ease In.With the four ease-in entrance effects still selected, under Modify: Ease In do the following:In the Start list, select With Previous.In the Speed list, select Fast.Select the grow & turn entrance effect (first effect in the list), and under Modify: Grow & Turn, in the Start list, select With Previous.

To reproduce the background effects on this slide, do the following:Right-click the slide background area, and then click Format Background. In the Format Background dialog box, click Fill in the left pane, select Gradient fill in the Fill pane, and then do the following:In the Type list, select Radial.Click the button next to Direction, and then click From Center (third option from the left). Under Gradient stops, click Add or Remove until two stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops that you added as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 20%.Click the button next to Color, and then under Theme Colors select White, Background 1, Darker 25% (fourth row, first option from the left). Select Stop 2 from the list, and then do the following: In the Stop position box, enter 100%.Click the button next to Color, and then under Theme Colors select Black, Text 1 (first row, second option from the left).

Mechanisms of Chromatin Remodeling

1. Nucleosome Sliding

SmartArt custom animation effects: bending process(Intermediate)

To reproduce the SmartArt effects on this slide, do the following:On the Home tab, in the Slides group, click Layout, and then click Blank. On the Insert tab, in the Illustrations group, click SmartArt. In the Choose a SmartArt Graphic dialog box, in the left pane, click Process. In the Process pane, click Vertical Bending Process (fifth row, third option from the left), and then click OK to insert the graphic into the slide.Select the graphic, and then click one of the arrows on the left border. In the Type your text here dialog box, enter text. On the slide, select the graphic. Under SmartArt Tools, on the Design tab, in the SmartArt Styles group, do the following:Click Change Colors, and then under Accent 1 click Colored Fill Accent 1 (second option from the left).Click More, and then under 3-D click Polished (first option from the left).On the Home tab, in the Font group, select Gill Sans MT from the Font list, and then select 24 from the Font Size list. Select the top left shape (starting point) in the graphic, and then do the following: Under SmartArt Tools, on the Format tab, in the Shape Styles group, click the arrow next to Shape Fill, and then under Theme Colors click Olive Green, Accent 3, Darker 25% (fifth row, seventh option from the left).Under SmartArt Tools, on the Format tab, in the Shapes group, click Change Shape, and then under Flowchart click Off-page Connector (second row, second option from the left).Select the bottom right shape (ending point) in the graphic, and then do the following:Under SmartArt Tools, on the Format tab, in the Shape Styles group, click the arrow next to Shape Fill, and then under Theme Colors click Red, Accent 2, Darker 25% (fifth row, sixth option from the left).Under SmartArt Tools, on the Format tab, in the Shapes group, click Change Shape, and then under Basic Shapes click Hexagon (first row, eighth option from the left).

To reproduce the animation effects on this slide, do the following:On the Animations tab, in the Animations group, click Custom Animation.On the slide, select the graphic. In the Custom Animation task pane, do the following:Click Add Effect, point to Entrance, and then click More Effects. In the Add Entrance Effect dialog box, under Subtle, click Fade.Under Modify: Fade, in the Speed list, select Fast.Also in the Custom Animation task pane, select the fade effect. Click the arrow to the right of the fade effect, and then click Effect Options. In the Fade dialog box, on the SmartArt Animation tab, in the Group graphic list, select One by one, and then click OK.Also in the Custom Animation task pane, click the double arrow under the fade effect to expand the contents of the list of effects, and then do the following:Press and hold CTRL, select the first, third, fifth, seventh, ninth, 11th, 13th, 15th, and 17th animation effects (fade effects for the rectangles), and then do the following:Click Change, point to Entrance, and then click More Effects. In the Change Entrance Effect dialog box, under Moderate, click Stretch.Under Modify: Stretch, in the Start list, select With Previous. Under Modify: Stretch, in the Speed list, select Fast.Press and hold CTRL, and then select the first, third, fifth, 15th, and 17th animation effects (stretch effects for the first, second, third, eighth, and ninth rectangles in the path). Under Modify: Stretch, in the Direction list, select From Top.Press and hold CTRL, and then select the seventh and 13th animation effects (stretch effects for the fourth and seventh rectangles in the path). Under Modify: Stretch, in the Direction list, select From Left. Press and hold CTRL, and then select the ninth and 11th animation effects (stretch effects for the fifth and sixth rectangles in the path). Under Modify: Stretch, in the Direction list, select From Bottom.Press and hold CTRL, and then select the second, fourth, sixth, eighth, 10th, 12th, 14th, and 16th animation effects (fade effects for the connectors). Under Modify: Fade, in the Start list, select After Previous.Select the eighth animation effect (fade effect for the connector between the fourth and fifth rectangle). Click the arrow to the right of the eighth animation effect, and then click Timing. In the Fade dialog box, on the Timing tab, in the Delay box, enter 0.5, and then click OK.Select the 10th animation effect (fade effect for the connector between the fifth and sixth rectangle). Click the arrow to the right of the 10th animation effect, and then click Timing. In the Fade dialog box, on the Timing tab, in the Delay box, enter 0.5.

To reproduce the background effects on this slide, do the following:Right-click the slide background area, and then click Format Background. In the Format Background dialog box, click Fill in the left pane, select Gradient fill in the Fill pane, and then do the following:In the Type list, select Linear.In the Direction list, click Linear Down (first row, second option from the left). Under Gradient stops, click Add or Remove until two stops appear in the drop-down list.Also under Gradient stops, customize the gradient stops that you added as follows:Select Stop 1 from the list, and then do the following:In the Stop position box, enter 0%.Click the button next to Color, and then under Theme Colors click Blue, Accent 1, Darker 25% (fifth row, fifth option from the left). Select Stop 2 from the list, and then do the following: In the Stop position box, enter 71%.Click the button next to Color, and then under Theme Colors click Black, Text 1 (first row, second option from the left).

ATP-dependent chromatin remodeling.(a) change the locations of nucleosomes

Nucleosome Conformational ChangeSliding provides an efficient way to allow access to DNA which was once contained within a nucleosome.

The SWI/SNF complex create accessible DNA by generating stable DNA loops within the context of the nucleosome.

The average loop size on nucleosomal templates approximately 100 bp.

2. Nucleosome ejectionAll members of the SWI/SNF family and only a subset of ISWI remodelers are able to eject histone dimers.

DNA loops Remove dimers or the entire octamer

Tendency of the octamer to dissociate into H2AH2B dimers and the (H3H4)2 tetramer

Large loops may allow for other DNA molecules to invade the open histone-DNA contacts

DNA translocation release of the neighboring histone dimer or octamer

ATP-dependent chromatin remodeling.(b) remove histones from the DNA

Proposed Mechanism of SWI/SNF Nucleosome Eviction

Top of figure shows unperturbed chromatin with two nucleosomes. SWI/SNF is recruited by the transcriptionfactor (Gal4-VP16, yellow hexagon) and binds the proximal nucleosome. SWI/SNF remodels thenucleosome in its active site and translocates in one direction along the DNA. Upon encountering thedownstream nucleosome, an H2A dimer is first displaced, followed by eviction of the entire neighboringnucleosome from the DNA template.18

Histone ExchangeThe SWR1 complex catalyzes the exchange of nucleosomal H2A for the H2AZ variant.

relaxation of DNA

Release of H2AZ-H2Bfrom the SWR1 complex reassembly of a histone octamer containing one of each H2AZH2B and H2AH2B

ATP-dependent chromatin remodeling.(c) replace core histones with variant histones.

Role of histone tailsHistone tails have been found to be required for the nucleosome remodeling activity of some remodeler complexes and not for others.

Modification of histone tails can affect remodeler complex recruitment and stability.

Histone acetylation stabilizes SWI/SNF interaction with nucleosomes.

Histone modifications and their effects on nucleosome structure

Examples of histone modifications that mayoccur at the amino-terminal tail of the four core histone proteins. Theabbreviations are: p, phosphate; ac, acetyl group; and m, methyl group22

Histone modifications and their effects on nucleosome structure

Effect of acetylation. When the core histones are acetylated viahistone acetyltransferase, the DNA becomes less tightly bound to thehistones. Histone deacetylase removes the acetyl groups.23

Acetylated histones allow transcription to begin. Once acetyl groups are added to particular amino acids in the tails of certain histones, the TATA box becomes accessible to transcription factors.

Acetylated histones allow transcription tobegin. Once acetyl groups are added to particular amino acids inthe tails of certain histones, the TATA box becomes accessible totranscription factors. H3 and H4 are histone types.24

Reactions catalyzed by ATP-dependent chromatin remodeling factors

Schematic representation of divers reactions catalyzed by chromatin remodelingfactors. Remodelers (green) assist in chromatin assembly by moving already deposited histone octamers (A). Theremodeling activity on a nucleosome array results in various products that can be classified in two categories: (B) aDNA-binding protein (DBP) (red) becomes accessible by nucleosomal sliding (repositioning), or nucleosomaleviction (ejection), or local unwrapping, and (D) altered histone composition, in which the nucleosome content ismodified by dimer replacement [exchange of H2A-H2B dimer with a histone variant (blue)] or through dimerejection25

Disorders of Chromatin Remodeling

Nucleosomal arraysElectromobility gel shift assay (EMSA)Chromatin Immunoprecipitation (ChIP)

Chromatin immunoprecipitation (ChIP)

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Eukaryotic Genes Are Flanked by Nucleosome-Free Regions and Well-Positioned Nucleosomes

Transcriptional Activation Involves Changes in Nucleosome Locations, Composition, and Histone Modifications

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